- using R version 2.11.1 Patched (2010-07-29 r52657)
- using session charset: ISO8859-1
- checking for file 'RBrownie/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'RBrownie' version '0.0.5'
- checking package name space information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking whether package 'RBrownie' can be installed ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the name space can be loaded with stated dependencies ... OK
- checking whether the name space can be unloaded cleanly ... OK
- checking for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... OK
- checking Rd files ... WARNING
prepare_Rd: addCensored.Rd:61-63: Dropping empty section \note
prepare_Rd: addCensored.Rd:55-57: Dropping empty section \references
prepare_Rd: addCensored.Rd:72-74: Dropping empty section \examples
prepare_Rd: addChoose.Rd:46-48: Dropping empty section \note
prepare_Rd: addChoose.Rd:40-42: Dropping empty section \references
prepare_Rd: addChoose.Rd:52-54: Dropping empty section \seealso
prepare_Rd: addDiscrete.Rd:119-121: Dropping empty section \note
prepare_Rd: addDiscrete.Rd:116-118: Dropping empty section \author
prepare_Rd: addDiscrete.Rd:113-115: Dropping empty section \references
prepare_Rd: addDiscrete.Rd:125-127: Dropping empty section \seealso
prepare_Rd: addEndLog.Rd:23-29: Dropping empty section \value
prepare_Rd: addEndLog.Rd:36-38: Dropping empty section \note
prepare_Rd: addEndLog.Rd:42-44: Dropping empty section \seealso
prepare_Rd: addEndLog.Rd:45-47: Dropping empty section \examples
prepare_Rd: addHS.Rd:131-133: Dropping empty section \note
prepare_Rd: addHS.Rd:125-127: Dropping empty section \references
prepare_Rd: addHS.Rd:137-139: Dropping empty section \seealso
prepare_Rd: addLiteral.Rd:34-36: Dropping empty section \note
prepare_Rd: addLiteral.Rd:28-30: Dropping empty section \references
prepare_Rd: addLiteral.Rd:40-42: Dropping empty section \seealso
prepare_Rd: addModel.Rd:49-51: Dropping empty section \note
prepare_Rd: addModel.Rd:43-45: Dropping empty section \references
prepare_Rd: addModel.Rd:55-57: Dropping empty section \seealso
prepare_Rd: addModel.Rd:58-60: Dropping empty section \examples
prepare_Rd: addNonCensored.Rd:62-64: Dropping empty section \note
prepare_Rd: addNonCensored.Rd:68-70: Dropping empty section \seealso
prepare_Rd: addNumopt.Rd:63-65: Dropping empty section \note
prepare_Rd: addNumopt.Rd:57-59: Dropping empty section \references
prepare_Rd: addNumopt.Rd:69-71: Dropping empty section \seealso
prepare_Rd: addOpt.Rd:53-55: Dropping empty section \note
prepare_Rd: addOpt.Rd:59-61: Dropping empty section \seealso
prepare_Rd: addStartLog.Rd:51-53: Dropping empty section \note
prepare_Rd: addStartLog.Rd:45-47: Dropping empty section \references
prepare_Rd: addStartLog.Rd:57-59: Dropping empty section \seealso
prepare_Rd: addSubNode.Rd:31-33: Dropping empty section \details
prepare_Rd: addSubNode.Rd:43-45: Dropping empty section \note
prepare_Rd: addSubNode.Rd:40-42: Dropping empty section \author
prepare_Rd: addSubNode.Rd:37-39: Dropping empty section \references
prepare_Rd: addSubNode.Rd:52-55: Dropping empty section \examples
checkRd: (5) addSubNode.Rd:4-6: \title content must be plain text
prepare_Rd: addTipvariance.Rd:42-44: Dropping empty section \note
prepare_Rd: addTipvariance.Rd:36-38: Dropping empty section \references
prepare_Rd: addTipvariance.Rd:48-50: Dropping empty section \seealso
prepare_Rd: addcmd.binary.Rd:25-27: Dropping empty section \details
prepare_Rd: addcmd.binary.Rd:28-34: Dropping empty section \value
prepare_Rd: addcmd.binary.Rd:41-43: Dropping empty section \note
prepare_Rd: addcmd.binary.Rd:35-37: Dropping empty section \references
prepare_Rd: addcmd.binary.Rd:47-49: Dropping empty section \seealso
prepare_Rd: addcmd.binary.Rd:50-52: Dropping empty section \examples
prepare_Rd: addcmd.freq.Rd:28-30: Dropping empty section \details
prepare_Rd: addcmd.freq.Rd:31-37: Dropping empty section \value
prepare_Rd: addcmd.freq.Rd:44-46: Dropping empty section \note
prepare_Rd: addcmd.freq.Rd:38-40: Dropping empty section \references
prepare_Rd: addcmd.freq.Rd:50-52: Dropping empty section \seealso
prepare_Rd: addcmd.freq.Rd:53-55: Dropping empty section \examples
prepare_Rd: addcmd.literal.Rd:25-27: Dropping empty section \details
prepare_Rd: addcmd.literal.Rd:28-34: Dropping empty section \value
prepare_Rd: addcmd.literal.Rd:41-43: Dropping empty section \note
prepare_Rd: addcmd.literal.Rd:35-37: Dropping empty section \references
prepare_Rd: addcmd.literal.Rd:47-49: Dropping empty section \seealso
prepare_Rd: addcmd.literal.Rd:50-52: Dropping empty section \examples
prepare_Rd: addcmd.model.continuous.Rd:22-24: Dropping empty section \details
prepare_Rd: addcmd.model.continuous.Rd:25-31: Dropping empty section \value
prepare_Rd: addcmd.model.continuous.Rd:38-40: Dropping empty section \note
prepare_Rd: addcmd.model.continuous.Rd:32-34: Dropping empty section \references
prepare_Rd: addcmd.model.continuous.Rd:44-46: Dropping empty section \seealso
prepare_Rd: addcmd.model.continuous.Rd:47-49: Dropping empty section \examples
prepare_Rd: addcmd.model.discrete.Rd:28-30: Dropping empty section \details
prepare_Rd: addcmd.model.discrete.Rd:31-37: Dropping empty section \value
prepare_Rd: addcmd.model.discrete.Rd:44-46: Dropping empty section \note
prepare_Rd: addcmd.model.discrete.Rd:38-40: Dropping empty section \references
prepare_Rd: addcmd.model.discrete.Rd:50-52: Dropping empty section \seealso
prepare_Rd: addcmd.model.discrete.Rd:53-55: Dropping empty section \examples
prepare_Rd: addcmd.states.Rd:25-27: Dropping empty section \details
prepare_Rd: addcmd.states.Rd:28-34: Dropping empty section \value
prepare_Rd: addcmd.states.Rd:41-43: Dropping empty section \note
prepare_Rd: addcmd.states.Rd:35-37: Dropping empty section \references
prepare_Rd: addcmd.states.Rd:47-49: Dropping empty section \seealso
prepare_Rd: addcmd.states.Rd:50-52: Dropping empty section \examples
prepare_Rd: addcmd.taxaset.Rd:25-27: Dropping empty section \details
prepare_Rd: addcmd.taxaset.Rd:28-34: Dropping empty section \value
prepare_Rd: addcmd.taxaset.Rd:41-43: Dropping empty section \note
prepare_Rd: addcmd.taxaset.Rd:35-37: Dropping empty section \references
prepare_Rd: addcmd.taxaset.Rd:47-49: Dropping empty section \seealso
prepare_Rd: addcmd.taxaset.Rd:50-52: Dropping empty section \examples
prepare_Rd: addcmd.tvtype.Rd:22-24: Dropping empty section \details
prepare_Rd: addcmd.tvtype.Rd:25-31: Dropping empty section \value
prepare_Rd: addcmd.tvtype.Rd:38-40: Dropping empty section \note
prepare_Rd: addcmd.tvtype.Rd:32-34: Dropping empty section \references
prepare_Rd: addcmd.tvtype.Rd:44-46: Dropping empty section \seealso
prepare_Rd: addcmd.tvtype.Rd:47-49: Dropping empty section \examples
prepare_Rd: areTaxaMono.Rd:34-36: Dropping empty section \note
prepare_Rd: areTaxaMono.Rd:28-30: Dropping empty section \references
prepare_Rd: areTaxaMutex.Rd:34-36: Dropping empty section \note
prepare_Rd: areTaxaMutex.Rd:28-30: Dropping empty section \references
prepare_Rd: areTaxaMutex.Rd:40-42: Dropping empty section \seealso
prepare_Rd: areTaxaPara.Rd:37-39: Dropping empty section \note
prepare_Rd: areTaxaPara.Rd:31-33: Dropping empty section \references
prepare_Rd: areTaxaPara.Rd:43-45: Dropping empty section \seealso
prepare_Rd: as.contData.Rd:33-35: Dropping empty section \note
prepare_Rd: as.contData.Rd:30-32: Dropping empty section \author
prepare_Rd: as.contData.Rd:27-29: Dropping empty section \references
prepare_Rd: as.contData.Rd:39-41: Dropping empty section \seealso
prepare_Rd: as.discData.Rd:34-36: Dropping empty section \note
prepare_Rd: as.discData.Rd:28-30: Dropping empty section \references
prepare_Rd: as.discData.Rd:40-42: Dropping empty section \seealso
prepare_Rd: brownie-class.Rd:98: Dropping empty section \note
prepare_Rd: brownie-class.Rd:96: Dropping empty section \references
prepare_Rd: brownie-class.Rd:100-102: Dropping empty section \seealso
prepare_Rd: brownie.datatypes.Rd:14-16: Dropping empty section \details
prepare_Rd: brownie.datatypes.Rd:17-23: Dropping empty section \value
prepare_Rd: brownie.datatypes.Rd:30-32: Dropping empty section \note
prepare_Rd: brownie.datatypes.Rd:27-29: Dropping empty section \author
prepare_Rd: brownie.datatypes.Rd:24-26: Dropping empty section \references
prepare_Rd: brownie.datatypes.Rd:36-38: Dropping empty section \seealso
prepare_Rd: brownie.freqs.Rd:19-21: Dropping empty section \details
prepare_Rd: brownie.freqs.Rd:22-28: Dropping empty section \value
prepare_Rd: brownie.freqs.Rd:35-37: Dropping empty section \note
prepare_Rd: brownie.freqs.Rd:29-31: Dropping empty section \references
prepare_Rd: brownie.freqs.Rd:41-43: Dropping empty section \seealso
prepare_Rd: brownie.freqs.Rd:44-46: Dropping empty section \examples
prepare_Rd: brownie.models.continuous.Rd:19-21: Dropping empty section \details
prepare_Rd: brownie.models.continuous.Rd:22-28: Dropping empty section \value
prepare_Rd: brownie.models.continuous.Rd:35-37: Dropping empty section \note
prepare_Rd: brownie.models.continuous.Rd:29-31: Dropping empty section \references
prepare_Rd: brownie.models.continuous.Rd:41-43: Dropping empty section \seealso
prepare_Rd: brownie.models.continuous.Rd:44-46: Dropping empty section \examples
prepare_Rd: brownie.models.discrete.Rd:19-21: Dropping empty section \details
prepare_Rd: brownie.models.discrete.Rd:22-28: Dropping empty section \value
prepare_Rd: brownie.models.discrete.Rd:35-37: Dropping empty section \note
prepare_Rd: brownie.models.discrete.Rd:29-31: Dropping empty section \references
prepare_Rd: brownie.models.discrete.Rd:41-43: Dropping empty section \seealso
prepare_Rd: brownie.models.discrete.Rd:44-46: Dropping empty section \examples
prepare_Rd: brownie.tvtypes.Rd:19-21: Dropping empty section \details
prepare_Rd: brownie.tvtypes.Rd:22-24: Dropping empty section \value
prepare_Rd: brownie.tvtypes.Rd:31-33: Dropping empty section \note
prepare_Rd: brownie.tvtypes.Rd:25-27: Dropping empty section \references
prepare_Rd: brownie.tvtypes.Rd:37-39: Dropping empty section \seealso
prepare_Rd: brownie.tvtypes.Rd:40-42: Dropping empty section \examples
prepare_Rd: check.empty.Rd:31-33: Dropping empty section \note
prepare_Rd: check.empty.Rd:25-27: Dropping empty section \references
prepare_Rd: check.empty.Rd:37-39: Dropping empty section \seealso
prepare_Rd: check.freq.Rd:19-21: Dropping empty section \details
prepare_Rd: check.freq.Rd:22-28: Dropping empty section \value
prepare_Rd: check.freq.Rd:35-37: Dropping empty section \note
prepare_Rd: check.freq.Rd:29-31: Dropping empty section \references
prepare_Rd: check.freq.Rd:41-43: Dropping empty section \seealso
prepare_Rd: check.freq.Rd:44-46: Dropping empty section \examples
prepare_Rd: check.statevector.Rd:34-36: Dropping empty section \note
prepare_Rd: check.statevector.Rd:28-30: Dropping empty section \references
prepare_Rd: check.statevector.Rd:40-42: Dropping empty section \seealso
prepare_Rd: check.statevector.Rd:43-45: Dropping empty section \examples
prepare_Rd: checkBrownie.Rd:19-21: Dropping empty section \details
prepare_Rd: checkBrownie.Rd:22-28: Dropping empty section \value
prepare_Rd: checkBrownie.Rd:35-37: Dropping empty section \note
prepare_Rd: checkBrownie.Rd:29-31: Dropping empty section \references
prepare_Rd: checkBrownie.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkBrownie.Rd:44-46: Dropping empty section \examples
prepare_Rd: checkCommands.Rd:19-21: Dropping empty section \details
prepare_Rd: checkCommands.Rd:22-28: Dropping empty section \value
prepare_Rd: checkCommands.Rd:35-37: Dropping empty section \note
prepare_Rd: checkCommands.Rd:29-31: Dropping empty section \references
prepare_Rd: checkCommands.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkCommands.Rd:44-45: Dropping empty section \examples
prepare_Rd: checkDataTypes.Rd:19-21: Dropping empty section \details
prepare_Rd: checkDataTypes.Rd:22-28: Dropping empty section \value
prepare_Rd: checkDataTypes.Rd:35-37: Dropping empty section \note
prepare_Rd: checkDataTypes.Rd:29-31: Dropping empty section \references
prepare_Rd: checkDataTypes.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkDataTypes.Rd:44-46: Dropping empty section \examples
prepare_Rd: checkMono.Rd:37-39: Dropping empty section \note
prepare_Rd: checkMono.Rd:31-33: Dropping empty section \references
prepare_Rd: checkPara.Rd:37-39: Dropping empty section \note
prepare_Rd: checkPara.Rd:31-33: Dropping empty section \references
prepare_Rd: checkval.dummy.Rd:19-21: Dropping empty section \details
prepare_Rd: checkval.dummy.Rd:22-28: Dropping empty section \value
prepare_Rd: checkval.dummy.Rd:35-37: Dropping empty section \note
prepare_Rd: checkval.dummy.Rd:29-31: Dropping empty section \references
prepare_Rd: checkval.dummy.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkval.dummy.Rd:44-46: Dropping empty section \examples
prepare_Rd: checkval.integer.Rd:19-21: Dropping empty section \details
prepare_Rd: checkval.integer.Rd:22-28: Dropping empty section \value
prepare_Rd: checkval.integer.Rd:35-37: Dropping empty section \note
prepare_Rd: checkval.integer.Rd:29-31: Dropping empty section \references
prepare_Rd: checkval.integer.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkval.integer.Rd:44-46: Dropping empty section \examples
prepare_Rd: checkval.model.continuous.Rd:19-21: Dropping empty section \details
prepare_Rd: checkval.model.continuous.Rd:22-28: Dropping empty section \value
prepare_Rd: checkval.model.continuous.Rd:35-37: Dropping empty section \note
prepare_Rd: checkval.model.continuous.Rd:29-31: Dropping empty section \references
prepare_Rd: checkval.model.continuous.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkval.model.continuous.Rd:44-46: Dropping empty section \examples
prepare_Rd: checkval.model.discrete.Rd:19-21: Dropping empty section \details
prepare_Rd: checkval.model.discrete.Rd:22-28: Dropping empty section \value
prepare_Rd: checkval.model.discrete.Rd:35-37: Dropping empty section \note
prepare_Rd: checkval.model.discrete.Rd:29-31: Dropping empty section \references
prepare_Rd: checkval.model.discrete.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkval.model.discrete.Rd:44-46: Dropping empty section \examples
prepare_Rd: checkval.ratemat.Rd:22-24: Dropping empty section \details
prepare_Rd: checkval.ratemat.Rd:25-31: Dropping empty section \value
prepare_Rd: checkval.ratemat.Rd:38-40: Dropping empty section \note
prepare_Rd: checkval.ratemat.Rd:32-34: Dropping empty section \references
prepare_Rd: checkval.ratemat.Rd:44-46: Dropping empty section \seealso
prepare_Rd: checkval.ratemat.Rd:47-49: Dropping empty section \examples
prepare_Rd: checkval.yesno.Rd:19-21: Dropping empty section \details
prepare_Rd: checkval.yesno.Rd:22-28: Dropping empty section \value
prepare_Rd: checkval.yesno.Rd:35-37: Dropping empty section \note
prepare_Rd: checkval.yesno.Rd:29-31: Dropping empty section \references
prepare_Rd: checkval.yesno.Rd:41-43: Dropping empty section \seealso
prepare_Rd: checkval.yesno.Rd:44-46: Dropping empty section \examples
prepare_Rd: collapse.singletons.Rd:19-21: Dropping empty section \details
prepare_Rd: collapse.singletons.Rd:31-33: Dropping empty section \note
prepare_Rd: collapse.singletons.Rd:25-27: Dropping empty section \references
prepare_Rd: collapse.singletons.Rd:37-39: Dropping empty section \seealso
prepare_Rd: collapse.to.singles.Rd:34-36: Dropping empty section \note
prepare_Rd: collapse.to.singles.Rd:28-30: Dropping empty section \references
prepare_Rd: collapse.to.singles.Rd:40-42: Dropping empty section \seealso
prepare_Rd: contData.Rd:14-16: Dropping empty section \details
prepare_Rd: contData.Rd:17-23: Dropping empty section \value
prepare_Rd: contData.Rd:30-32: Dropping empty section \note
prepare_Rd: contData.Rd:24-26: Dropping empty section \references
prepare_Rd: contData.Rd:36-38: Dropping empty section \seealso
prepare_Rd: contData.Rd:39-41: Dropping empty section \examples
prepare_Rd: discData.Rd:14-16: Dropping empty section \details
prepare_Rd: discData.Rd:17-23: Dropping empty section \value
prepare_Rd: discData.Rd:30-32: Dropping empty section \note
prepare_Rd: discData.Rd:24-26: Dropping empty section \references
prepare_Rd: discData.Rd:36-38: Dropping empty section \seealso
prepare_Rd: discData.Rd:39-41: Dropping empty section \examples
prepare_Rd: execute.brownie.Rd:32-34: Dropping empty section \note
prepare_Rd: execute.brownie.Rd:26-28: Dropping empty section \references
prepare_Rd: execute.brownie.Rd:43-45: Dropping empty section \examples
prepare_Rd: expand.singles.Rd:31-33: Dropping empty section \note
prepare_Rd: expand.singles.Rd:25-27: Dropping empty section \references
prepare_Rd: expand.singles.Rd:37-39: Dropping empty section \seealso
prepare_Rd: genericData.Rd:14-16: Dropping empty section \details
prepare_Rd: genericData.Rd:17-23: Dropping empty section \value
prepare_Rd: genericData.Rd:30-32: Dropping empty section \note
prepare_Rd: genericData.Rd:24-26: Dropping empty section \references
prepare_Rd: genericData.Rd:39-41: Dropping empty section \examples
prepare_Rd: geospiza_ext.Rd:21-23: Dropping empty section \references
prepare_Rd: get.left.right.Rd:22-24: Dropping empty section \details
prepare_Rd: get.left.right.Rd:34-36: Dropping empty section \note
prepare_Rd: get.left.right.Rd:28-30: Dropping empty section \references
prepare_Rd: get.left.right.Rd:40-42: Dropping empty section \seealso
prepare_Rd: get.nexus.comments.Rd:22-24: Dropping empty section \details
prepare_Rd: get.nexus.comments.Rd:25-31: Dropping empty section \value
prepare_Rd: get.nexus.comments.Rd:38-40: Dropping empty section \note
prepare_Rd: get.nexus.comments.Rd:32-34: Dropping empty section \references
prepare_Rd: get.nexus.comments.Rd:44-46: Dropping empty section \seealso
prepare_Rd: get.nexus.comments.Rd:47-49: Dropping empty section \examples
prepare_Rd: get.nodenames.Rd:19-20: Dropping empty section \details
prepare_Rd: get.nodenames.Rd:30-32: Dropping empty section \note
prepare_Rd: get.nodenames.Rd:24-26: Dropping empty section \references
prepare_Rd: get.nodenames.Rd:36-38: Dropping empty section \seealso
prepare_Rd: get.nodenames.Rd:39-40: Dropping empty section \examples
prepare_Rd: get.tree.weights.Rd:31-33: Dropping empty section \details
prepare_Rd: get.tree.weights.Rd:43-45: Dropping empty section \note
prepare_Rd: get.tree.weights.Rd:37-39: Dropping empty section \references
prepare_Rd: get.tree.weights.Rd:49-51: Dropping empty section \seealso
prepare_Rd: get.tree.weights.Rd:52-54: Dropping empty section \examples
prepare_Rd: getEmptyDataFrame.Rd:31-33: Dropping empty section \note
prepare_Rd: getEmptyDataFrame.Rd:25-27: Dropping empty section \references
prepare_Rd: getEmptyDataFrame.Rd:37-39: Dropping empty section \seealso
prepare_Rd: getEmptyDataFrame.Rd:40-42: Dropping empty section \examples
prepare_Rd: getSubNodeData.Rd:22-24: Dropping empty section \details
prepare_Rd: getSubNodeData.Rd:34-36: Dropping empty section \note
prepare_Rd: getSubNodeData.Rd:28-30: Dropping empty section \references
prepare_Rd: getSubNodeData.Rd:40-42: Dropping empty section \seealso
prepare_Rd: getSubNodeEdgeInds.Rd:22-24: Dropping empty section \value
prepare_Rd: getSubNodeEdgeInds.Rd:31-33: Dropping empty section \note
prepare_Rd: getSubNodeEdgeInds.Rd:25-27: Dropping empty section \references
prepare_Rd: getSubNodeEdgeInds.Rd:37-39: Dropping empty section \seealso
prepare_Rd: getSubNodePosish.Rd:19-21: Dropping empty section \details
prepare_Rd: getSubNodePosish.Rd:31-33: Dropping empty section \note
prepare_Rd: getSubNodePosish.Rd:25-27: Dropping empty section \references
prepare_Rd: getSubNodePosish.Rd:37-39: Dropping empty section \seealso
prepare_Rd: has.block.Rd:25-27: Dropping empty section \details
prepare_Rd: has.block.Rd:37-39: Dropping empty section \note
prepare_Rd: has.block.Rd:31-33: Dropping empty section \references
prepare_Rd: has.block.Rd:43-45: Dropping empty section \seealso
prepare_Rd: has.block.Rd:46-48: Dropping empty section \examples
prepare_Rd: has.characters2.Rd:34-36: Dropping empty section \note
prepare_Rd: has.characters2.Rd:28-30: Dropping empty section \references
prepare_Rd: has.characters2.Rd:40-42: Dropping empty section \seealso
prepare_Rd: has.characters2.Rd:43-45: Dropping empty section \examples
prepare_Rd: has.weights.Rd:22-24: Dropping empty section \details
prepare_Rd: has.weights.Rd:34-36: Dropping empty section \note
prepare_Rd: has.weights.Rd:28-30: Dropping empty section \references
prepare_Rd: has.weights.Rd:40-42: Dropping empty section \seealso
prepare_Rd: has.weights.Rd:43-45: Dropping empty section \examples
prepare_Rd: hasCommands.Rd:31-33: Dropping empty section \note
prepare_Rd: hasCommands.Rd:25-27: Dropping empty section \references
prepare_Rd: hasCommands.Rd:37-39: Dropping empty section \seealso
prepare_Rd: haschar.Rd:22-24: Dropping empty section \details
prepare_Rd: haschar.Rd:25-27: Dropping empty section \value
prepare_Rd: haschar.Rd:34-36: Dropping empty section \note
prepare_Rd: haschar.Rd:28-30: Dropping empty section \references
prepare_Rd: haschar.Rd:40-42: Dropping empty section \seealso
prepare_Rd: haschar.Rd:43-45: Dropping empty section \examples
prepare_Rd: is.binary.Rd:19-21: Dropping empty section \details
prepare_Rd: is.binary.Rd:22-24: Dropping empty section \value
prepare_Rd: is.binary.Rd:31-33: Dropping empty section \note
prepare_Rd: is.binary.Rd:25-27: Dropping empty section \references
prepare_Rd: is.binary.Rd:37-39: Dropping empty section \seealso
prepare_Rd: is.binary.Rd:40-41: Dropping empty section \examples
prepare_Rd: is.contData.Rd:19-21: Dropping empty section \details
prepare_Rd: is.contData.Rd:22-24: Dropping empty section \value
prepare_Rd: is.contData.Rd:31-33: Dropping empty section \note
prepare_Rd: is.contData.Rd:25-27: Dropping empty section \references
prepare_Rd: is.contData.Rd:37-39: Dropping empty section \seealso
prepare_Rd: is.contData.Rd:40-41: Dropping empty section \examples
prepare_Rd: is.discData.Rd:19-21: Dropping empty section \details
prepare_Rd: is.discData.Rd:22-28: Dropping empty section \value
prepare_Rd: is.discData.Rd:35-37: Dropping empty section \note
prepare_Rd: is.discData.Rd:29-31: Dropping empty section \references
prepare_Rd: is.discData.Rd:41-43: Dropping empty section \seealso
prepare_Rd: is.discData.Rd:44-46: Dropping empty section \examples
prepare_Rd: is.simmap.Rd:34-36: Dropping empty section \note
prepare_Rd: is.simmap.Rd:28-30: Dropping empty section \references
prepare_Rd: is.simmap.Rd:40-42: Dropping empty section \seealso
prepare_Rd: is.taxaname.internal.Rd:19-21: Dropping empty section \details
prepare_Rd: is.taxaname.internal.Rd:22-28: Dropping empty section \value
prepare_Rd: is.taxaname.internal.Rd:35-37: Dropping empty section \note
prepare_Rd: is.taxaname.internal.Rd:29-31: Dropping empty section \references
prepare_Rd: is.taxaname.internal.Rd:41-43: Dropping empty section \seealso
prepare_Rd: is.taxaname.internal.Rd:44-46: Dropping empty section \examples
prepare_Rd: is_valid_datatype.Rd:19-21: Dropping empty section \details
prepare_Rd: is_valid_datatype.Rd:22-28: Dropping empty section \value
prepare_Rd: is_valid_datatype.Rd:35-37: Dropping empty section \note
prepare_Rd: is_valid_datatype.Rd:32-34: Dropping empty section \author
prepare_Rd: is_valid_datatype.Rd:29-31: Dropping empty section \references
prepare_Rd: is_valid_datatype.Rd:41-43: Dropping empty section \seealso
prepare_Rd: is_valid_datatype.Rd:44-45: Dropping empty section \examples
prepare_Rd: is_valid_datatype_bound.Rd:19-21: Dropping empty section \details
prepare_Rd: is_valid_datatype_bound.Rd:22-28: Dropping empty section \value
prepare_Rd: is_valid_datatype_bound.Rd:35-37: Dropping empty section \note
prepare_Rd: is_valid_datatype_bound.Rd:32-34: Dropping empty section \author
prepare_Rd: is_valid_datatype_bound.Rd:29-31: Dropping empty section \references
prepare_Rd: is_valid_datatype_bound.Rd:41-43: Dropping empty section \seealso
prepare_Rd: is_valid_datatype_bound.Rd:44-45: Dropping empty section \examples
prepare_Rd: is_valid_datatype_prob.Rd:19-21: Dropping empty section \details
prepare_Rd: is_valid_datatype_prob.Rd:22-28: Dropping empty section \value
prepare_Rd: is_valid_datatype_prob.Rd:35-37: Dropping empty section \note
prepare_Rd: is_valid_datatype_prob.Rd:32-34: Dropping empty section \author
prepare_Rd: is_valid_datatype_prob.Rd:29-31: Dropping empty section \references
prepare_Rd: is_valid_datatype_prob.Rd:41-43: Dropping empty section \seealso
prepare_Rd: is_valid_datatype_prob.Rd:44-46: Dropping empty section \examples
prepare_Rd: isback.Rd:22-24: Dropping empty section \details
prepare_Rd: isback.Rd:25-31: Dropping empty section \value
prepare_Rd: isback.Rd:38-40: Dropping empty section \note
prepare_Rd: isback.Rd:32-34: Dropping empty section \references
prepare_Rd: isback.Rd:44-46: Dropping empty section \seealso
prepare_Rd: isback.Rd:47-49: Dropping empty section \examples
prepare_Rd: nSubNodes.Rd:19-20: Dropping empty section \details
prepare_Rd: nSubNodes.Rd:30-32: Dropping empty section \note
prepare_Rd: nSubNodes.Rd:24-26: Dropping empty section \references
prepare_Rd: nSubNodes.Rd:36-38: Dropping empty section \seealso
prepare_Rd: parrot.Rd:20-21: Dropping empty section \references
prepare_Rd: phyextPlot.Rd:62-63: Dropping empty section \value
prepare_Rd: phyextPlot.Rd:69-70: Dropping empty section \note
prepare_Rd: phyextPlot.Rd:64-65: Dropping empty section \references
prepare_Rd: phyextPlot.Rd:74-76: Dropping empty section \seealso
prepare_Rd: plot.censored.Rd:43-49: Dropping empty section \value
prepare_Rd: plot.censored.Rd:56-58: Dropping empty section \note
prepare_Rd: plot.censored.Rd:50-52: Dropping empty section \references
prepare_Rd: plot.censored.Rd:62-64: Dropping empty section \seealso
prepare_Rd: plot.taxaset.Rd:40-42: Dropping empty section \details
prepare_Rd: plot.taxaset.Rd:43-49: Dropping empty section \value
prepare_Rd: plot.taxaset.Rd:56-58: Dropping empty section \note
prepare_Rd: plot.taxaset.Rd:50-52: Dropping empty section \references
prepare_Rd: plot.taxaset.Rd:62-64: Dropping empty section \seealso
prepare_Rd: rcpp_hello_world.Rd:14-16: Dropping empty section \details
prepare_Rd: rcpp_hello_world.Rd:17-23: Dropping empty section \value
prepare_Rd: rcpp_hello_world.Rd:30-32: Dropping empty section \note
prepare_Rd: rcpp_hello_world.Rd:24-26: Dropping empty section \references
prepare_Rd: rcpp_hello_world.Rd:36-38: Dropping empty section \seealso
prepare_Rd: rcpp_hello_world.Rd:39-41: Dropping empty section \examples
prepare_Rd: read.analysis.output.Rd:42-44: Dropping empty section \note
prepare_Rd: read.analysis.output.Rd:36-38: Dropping empty section \references
prepare_Rd: read.analysis.output.Rd:48-50: Dropping empty section \seealso
prepare_Rd: read.analysis.output.Rd:51-53: Dropping empty section \examples
prepare_Rd: read.brownie.string.Rd:22-24: Dropping empty section \details
prepare_Rd: read.brownie.string.Rd:25-29: Dropping empty section \value
prepare_Rd: read.brownie.string.Rd:36-38: Dropping empty section \note
prepare_Rd: read.brownie.string.Rd:30-32: Dropping empty section \references
prepare_Rd: read.brownie.string.Rd:42-44: Dropping empty section \seealso
prepare_Rd: read.characters2.Rd:34-36: Dropping empty section \note
prepare_Rd: read.characters2.Rd:28-30: Dropping empty section \references
prepare_Rd: read.characters2.Rd:43-45: Dropping empty section \examples
prepare_Rd: read.continuous.output.Rd:37-39: Dropping empty section \note
prepare_Rd: read.continuous.output.Rd:31-33: Dropping empty section \references
prepare_Rd: read.continuous.output.Rd:46-48: Dropping empty section \examples
prepare_Rd: read.discrete.output.Rd:42-44: Dropping empty section \note
prepare_Rd: read.discrete.output.Rd:36-38: Dropping empty section \references
prepare_Rd: read.discrete.output.Rd:52-54: Dropping empty section \examples
prepare_Rd: read.nexus.block.Rd:43-45: Dropping empty section \note
prepare_Rd: read.nexus.block.Rd:37-39: Dropping empty section \references
prepare_Rd: read.nexus.block.Rd:49-51: Dropping empty section \seealso
prepare_Rd: read.nexus.block.Rd:52-54: Dropping empty section \examples
prepare_Rd: read.nexus.simmap.Rd:34-36: Dropping empty section \note
prepare_Rd: read.nexus.simmap.Rd:28-30: Dropping empty section \references
prepare_Rd: read.nexus.simmap.Rd:40-42: Dropping empty section \seealso
prepare_Rd: read.nexus.simmap.Rd:43-45: Dropping empty section \examples
prepare_Rd: read.ratetest.output.Rd:37-39: Dropping empty section \note
prepare_Rd: read.ratetest.output.Rd:31-33: Dropping empty section \references
prepare_Rd: read.ratetest.output.Rd:46-48: Dropping empty section \examples
prepare_Rd: read.simmap.Rd:28-30: Dropping empty section \details
prepare_Rd: read.simmap.Rd:40-42: Dropping empty section \note
prepare_Rd: read.simmap.Rd:34-36: Dropping empty section \references
prepare_Rd: read.simmap.Rd:46-48: Dropping empty section \seealso
prepare_Rd: readBrownie.Rd:33-35: Dropping empty section \note
prepare_Rd: readBrownie.Rd:27-29: Dropping empty section \references
prepare_Rd: readBrownie.Rd:39-41: Dropping empty section \seealso
prepare_Rd: rm.ending.Rd:19-21: Dropping empty section \details
prepare_Rd: rm.ending.Rd:22-28: Dropping empty section \value
prepare_Rd: rm.ending.Rd:35-37: Dropping empty section \note
prepare_Rd: rm.ending.Rd:29-31: Dropping empty section \references
prepare_Rd: rm.ending.Rd:41-43: Dropping empty section \seealso
prepare_Rd: rm.ending.Rd:44-46: Dropping empty section \examples
prepare_Rd: run.analysis.Rd:34-36: Dropping empty section \note
prepare_Rd: run.analysis.Rd:28-30: Dropping empty section \references
prepare_Rd: run.asis.Rd:41-43: Dropping empty section \note
prepare_Rd: run.asis.Rd:35-37: Dropping empty section \references
prepare_Rd: runCensored.Rd:42-44: Dropping empty section \note
prepare_Rd: runCensored.Rd:36-38: Dropping empty section \references
prepare_Rd: runDiscrete.Rd:57-59: Dropping empty section \note
prepare_Rd: runDiscrete.Rd:51-53: Dropping empty section \references
prepare_Rd: runNonCensored.Rd:61-63: Dropping empty section \note
prepare_Rd: runNonCensored.Rd:55-57: Dropping empty section \references
prepare_Rd: scan.textout.Rd:35-37: Dropping empty section \note
prepare_Rd: scan.textout.Rd:29-31: Dropping empty section \references
prepare_Rd: scan.textout.Rd:41-43: Dropping empty section \seealso
prepare_Rd: scan.treesout.Rd:31-33: Dropping empty section \note
prepare_Rd: scan.treesout.Rd:25-27: Dropping empty section \references
prepare_Rd: scan.treesout.Rd:37-39: Dropping empty section \seealso
prepare_Rd: showBrownie.Rd:14-16: Dropping empty section \details
prepare_Rd: showBrownie.Rd:26-28: Dropping empty section \note
prepare_Rd: showBrownie.Rd:20-22: Dropping empty section \references
prepare_Rd: showBrownie.Rd:32-34: Dropping empty section \seealso
prepare_Rd: showBrownie.Rd:35-37: Dropping empty section \examples
prepare_Rd: showSubNodes.Rd:31-33: Dropping empty section \note
prepare_Rd: showSubNodes.Rd:25-27: Dropping empty section \references
prepare_Rd: showSubNodes.Rd:37-39: Dropping empty section \seealso
prepare_Rd: summaryCont.Rd:37-39: Dropping empty section \note
prepare_Rd: summaryCont.Rd:31-33: Dropping empty section \references
prepare_Rd: summaryCont.Rd:43-45: Dropping empty section \seealso
prepare_Rd: summaryDiscrete.Rd:14-16: Dropping empty section \details
prepare_Rd: summaryDiscrete.Rd:17-23: Dropping empty section \value
prepare_Rd: summaryDiscrete.Rd:30-32: Dropping empty section \note
prepare_Rd: summaryDiscrete.Rd:24-26: Dropping empty section \references
prepare_Rd: summaryDiscrete.Rd:36-38: Dropping empty section \seealso
prepare_Rd: summaryDiscrete.Rd:39-41: Dropping empty section \examples
prepare_Rd: summaryRatetest.Rd:37-39: Dropping empty section \note
prepare_Rd: summaryRatetest.Rd:31-33: Dropping empty section \references
prepare_Rd: summaryRatetest.Rd:43-45: Dropping empty section \seealso
prepare_Rd: taxData.Rd:14-16: Dropping empty section \details
prepare_Rd: taxData.Rd:17-23: Dropping empty section \value
prepare_Rd: taxData.Rd:30-32: Dropping empty section \note
prepare_Rd: taxData.Rd:24-26: Dropping empty section \references
prepare_Rd: taxData.Rd:36-38: Dropping empty section \seealso
prepare_Rd: taxData.Rd:39-41: Dropping empty section \examples
prepare_Rd: taxa.charvect.Rd:37-39: Dropping empty section \note
prepare_Rd: taxa.charvect.Rd:31-33: Dropping empty section \references
prepare_Rd: taxa.charvect.Rd:43-45: Dropping empty section \seealso
prepare_Rd: taxa.mono.Rd:22-24: Dropping empty section \details
prepare_Rd: taxa.mono.Rd:25-31: Dropping empty section \value
prepare_Rd: taxa.mono.Rd:38-40: Dropping empty section \note
prepare_Rd: taxa.mono.Rd:32-34: Dropping empty section \references
prepare_Rd: taxa.mono.Rd:44-46: Dropping empty section \seealso
prepare_Rd: taxa.mono.Rd:47-49: Dropping empty section \examples
prepare_Rd: taxaname.to.taxind.Rd:22-24: Dropping empty section \details
prepare_Rd: taxaname.to.taxind.Rd:25-31: Dropping empty section \value
prepare_Rd: taxaname.to.taxind.Rd:38-40: Dropping empty section \note
prepare_Rd: taxaname.to.taxind.Rd:32-34: Dropping empty section \references
prepare_Rd: taxaname.to.taxind.Rd:44-46: Dropping empty section \seealso
prepare_Rd: taxaname.to.taxind.Rd:47-49: Dropping empty section \examples
prepare_Rd: taxaset.names.Rd:19-21: Dropping empty section \details
prepare_Rd: taxaset.names.Rd:31-33: Dropping empty section \note
prepare_Rd: taxaset.names.Rd:25-27: Dropping empty section \references
prepare_Rd: taxaset.names.Rd:37-39: Dropping empty section \seealso
prepare_Rd: taxaset.rename.Rd:19-21: Dropping empty section \details
prepare_Rd: taxaset.rename.Rd:22-28: Dropping empty section \value
prepare_Rd: taxaset.rename.Rd:35-37: Dropping empty section \note
prepare_Rd: taxaset.rename.Rd:29-31: Dropping empty section \references
prepare_Rd: taxaset.rename.Rd:41-43: Dropping empty section \seealso
prepare_Rd: taxaset.rename.Rd:44-46: Dropping empty section \examples
prepare_Rd: taxind.to.dataind.Rd:22-24: Dropping empty section \details
prepare_Rd: taxind.to.dataind.Rd:34-36: Dropping empty section \note
prepare_Rd: taxind.to.dataind.Rd:28-30: Dropping empty section \references
prepare_Rd: taxind.to.dataind.Rd:40-42: Dropping empty section \seealso
prepare_Rd: taxind.to.dataind.Rd:43-45: Dropping empty section \examples
prepare_Rd: validPhylo4d_ext.Rd:19-21: Dropping empty section \details
prepare_Rd: validPhylo4d_ext.Rd:31-33: Dropping empty section \note
prepare_Rd: validPhylo4d_ext.Rd:25-27: Dropping empty section \references
prepare_Rd: validPhylo4d_ext.Rd:37-39: Dropping empty section \seealso
prepare_Rd: validPhylo4d_ext.Rd:40-42: Dropping empty section \examples
prepare_Rd: which.mono.Rd:34-36: Dropping empty section \note
prepare_Rd: which.mono.Rd:28-30: Dropping empty section \references
prepare_Rd: which.para.Rd:34-36: Dropping empty section \note
prepare_Rd: which.para.Rd:28-30: Dropping empty section \references
prepare_Rd: write.brownie.matrix.Rd:19-21: Dropping empty section \details
prepare_Rd: write.brownie.matrix.Rd:22-28: Dropping empty section \value
prepare_Rd: write.brownie.matrix.Rd:35-37: Dropping empty section \note
prepare_Rd: write.brownie.matrix.Rd:29-31: Dropping empty section \references
prepare_Rd: write.brownie.string.Rd:22-24: Dropping empty section \details
prepare_Rd: write.brownie.string.Rd:25-31: Dropping empty section \value
prepare_Rd: write.brownie.string.Rd:38-40: Dropping empty section \note
prepare_Rd: write.brownie.string.Rd:32-34: Dropping empty section \references
prepare_Rd: write.brownie.string.Rd:44-46: Dropping empty section \seealso
prepare_Rd: write.brownie.string.Rd:47-48: Dropping empty section \examples
prepare_Rd: write.brownie.vector.Rd:22-24: Dropping empty section \details
prepare_Rd: write.brownie.vector.Rd:34-36: Dropping empty section \note
prepare_Rd: write.brownie.vector.Rd:28-30: Dropping empty section \references
prepare_Rd: write.nexus.simmap.Rd:39-41: Dropping empty section \note
prepare_Rd: write.nexus.simmap.Rd:33-35: Dropping empty section \references
prepare_Rd: write.simmap.Rd:31-33: Dropping empty section \details
prepare_Rd: write.simmap.Rd:43-45: Dropping empty section \note
prepare_Rd: write.simmap.Rd:37-39: Dropping empty section \references
prepare_Rd: write.simmap.Rd:49-51: Dropping empty section \seealso
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking data for non-ASCII characters ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable compilation flags in Makevars ... OK
- checking for portable use of $BLAS_LIBS ... OK
- checking examples ... OK
- checking package vignettes in 'inst/doc' ... NOTE
LIB: Generator type: mt19937
LIB: Seed = 1287164843
LIB: First value = 1361101496
RCPP: 'd:/temp/RtmpKu0z9n/file88338f5'
Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpKu0z9n/file88338f5'
.. conditioned command is: ;execute 'd:/temp/RtmpKu0z9n/file88338f5';end;
LIB: handle cmd ';execute 'd:/temp/RtmpKu0z9n/file88338f5';end;'
Opening d:/temp/RtmpKu0z9n/file88338f5...
Starting to execute NEXUS file
Entering TAXA block...done
Entering TREES block...done
Entering CHARACTERS block...done
(Skipping assumptions block)
(Skipping brownie block)
Finished executing NEXUS file
TREES block contains 10 trees
1 UNTITLED (rooted, weight = 1)
2 UNTITLED (rooted, weight = 1)
3 UNTITLED (rooted, weight = 1)
4 UNTITLED (rooted, weight = 1)
5 UNTITLED (rooted, weight = 1)
6 UNTITLED (rooted, weight = 1)
7 UNTITLED (rooted, weight = 1)
8 UNTITLED (rooted, weight = 1)
9 UNTITLED (rooted, weight = 1)
10 UNTITLED (rooted, weight = 1,default tree)
Reading TAXA block...
Reading TREES block...
Reading CHARACTERS block...
Reading ASSUMPTIONS block...
Reading BROWNIE block...
You have chosen a single rate Brownian motion model
Now optimizing with taxset ALL
LIB: Generator type: mt19937
LIB: Seed = 1287164843
LIB: First value = 1361101496
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164844
LIB: First value = 3078496947
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164845
LIB: First value = 3790483801
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164846
LIB: First value = 2620151362
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164847
LIB: First value = 955779633
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164848
LIB: First value = 2512847007
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164849
LIB: First value = 2067785931
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164849
LIB: First value = 2067785931
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164851
LIB: First value = 62949120
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164851
LIB: First value = 62949120
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164853
LIB: First value = 1500573360
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164853
LIB: First value = 1500573360
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164856
LIB: First value = 222393658
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164857
LIB: First value = 1079207073
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164857
LIB: First value = 1079207073
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666896 +/- 0.000032
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164858
LIB: First value = 3651592045
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666896 +/- 0.000032
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004729 +/- 0.000012
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164861
LIB: First value = 2765398437
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666896 +/- 0.000032
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004729 +/- 0.000012
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373263 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164862
LIB: First value = 544812055
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666896 +/- 0.000032
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004729 +/- 0.000012
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373263 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489956 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164863
LIB: First value = 4288188269
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666896 +/- 0.000032
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004729 +/- 0.000012
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373263 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489956 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582569
AIC = 209.165138
AICc = 209.552235
Ancestral state = -0.0
Optimal rate = 1120.318912 +/- 0.000061
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164863
LIB: First value = 4288188269
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175451 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.07772 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442963 +/- 0.000024
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373263 +/- 0.000034
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646944 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471372 +/- 0.000056
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.47565 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.942997 +/- 0.00002
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156413 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401495 +/- 0.000058
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533325 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.17557 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713838 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666896 +/- 0.000032
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004729 +/- 0.000012
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373263 +/- 0.000018
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489956 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582569
AIC = 209.165138
AICc = 209.552235
Ancestral state = -0.0
Optimal rate = 1120.318912 +/- 0.000061
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.819721
AICc = 189.206817
Ancestral state = -0.0
Optimal rate = 615.831891 +/- 0.000013
Note that +/- reflects imprecision due to numerical optimization
You have chosen Brownian motion with one rate parameter per state
Now optimizing with taxset ALL
LIB: Generator type: mt19937
LIB: Seed = 1287164865
LIB: First value = 2522069476
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 101.358522
AIC = 208.717044
AICc = 209.517044
Ancestral state = -0.568339 +/- 0.0
Rate in state 0 = 91.263036 +/- 0.000014
Rate in state 1 = 752.717403 +/- 0.000033
LIB: Generator type: mt19937
LIB: Seed = 1287164868
LIB: First value = 3960182888
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.179842
AIC = 188.359685
AICc = 189.159685
Ancestral state = 2.750468 +/- 0.0
Rate in state 0 = 48.767965 +/- 0.000004
Rate in state 1 = 415.385136 +/- 0.000007
LIB: Generator type: mt19937
LIB: Seed = 1287164871
LIB: First value = 3321046834
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.241775
AIC = 204.483549
AICc = 205.283549
Ancestral state = -0.710483 +/- 0.0
Rate in state 0 = 21.346395 +/- 0.000001
Rate in state 1 = 671.657926 +/- 0.000022
LIB: Generator type: mt19937
LIB: Seed = 1287164874
LIB: First value = 1144809923
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.983502
AIC = 187.967004
AICc = 188.767004
Ancestral state = 3.054602 +/- 0.0
Rate in state 0 = 41.680786 +/- 0.000005
Rate in state 1 = 325.951769 +/- 0.000011
LIB: Generator type: mt19937
LIB: Seed = 1287164878
LIB: First value = 46283188
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 98.403443
AIC = 202.806887
AICc = 203.606887
Ancestral state = -0.712707 +/- 0.010024
Rate in state 0 = 24.872614 +/- 0.893549
Rate in state 1 = 859.919452 +/- 122.339556
LIB: Generator type: mt19937
LIB: Seed = 1287164881
LIB: First value = 948698112
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.568177
AIC = 187.136354
AICc = 187.936354
Ancestral state = 3.330917 +/- 0.0
Rate in state 0 = 47.885894 +/- 0.000003
Rate in state 1 = 424.639151 +/- 0.00001
LIB: Generator type: mt19937
LIB: Seed = 1287164885
LIB: First value = 56149649
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.25393
AIC = 204.507859
AICc = 205.307859
Ancestral state = -0.720946 +/- 0.0
Rate in state 0 = 89.787497 +/- 0.000008
Rate in state 1 = 2852.305362 +/- 0.000075
LIB: Generator type: mt19937
LIB: Seed = 1287164888
LIB: First value = 3651989586
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.870567
AIC = 187.741134
AICc = 188.541134
Ancestral state = 3.365235 +/- 0.0
Rate in state 0 = 155.289326 +/- 0.000016
Rate in state 1 = 1406.590721 +/- 0.000038
LIB: Generator type: mt19937
LIB: Seed = 1287164892
LIB: First value = 4122565267
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 101.678334
AIC = 209.356668
AICc = 210.156668
Ancestral state = -0.438847 +/- 0.0
Rate in state 0 = 94.16415 +/- 0.000014
Rate in state 1 = 462.96564 +/- 0.000018
LIB: Generator type: mt19937
LIB: Seed = 1287164894
LIB: First value = 2555581001
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.255611
AIC = 188.511222
AICc = 189.311222
Ancestral state = 1.827769 +/- 0.0
Rate in state 0 = 42.895599 +/- 0.000004
Rate in state 1 = 257.636693 +/- 0.000006
LIB: Generator type: mt19937
LIB: Seed = 1287164898
LIB: First value = 3381652477
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 97.672424
AIC = 201.344848
AICc = 202.144848
Ancestral state = -0.718767 +/- 0.0
Rate in state 0 = 52.492217 +/- 0.000002
Rate in state 1 = 2218.494662 +/- 0.000052
LIB: Generator type: mt19937
LIB: Seed = 1287164901
LIB: First value = 2426234493
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.78148
AIC = 187.56296
AICc = 188.36296
Ancestral state = 2.47375 +/- 0.0
Rate in state 0 = 174.301704 +/- 0.000014
Rate in state 1 = 991.120329 +/- 0.000022
LIB: Generator type: mt19937
LIB: Seed = 1287164905
LIB: First value = 2452911357
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.045956
AIC = 204.091912
AICc = 204.891912
Ancestral state = -0.73727 +/- 0.0
Rate in state 0 = 31.188348 +/- 0.000003
Rate in state 1 = 983.465003 +/- 0.000023
LIB: Generator type: mt19937
LIB: Seed = 1287164907
LIB: First value = 115664565
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.061771
AIC = 188.123541
AICc = 188.923541
Ancestral state = 2.421296 +/- 0.0
Rate in state 0 = 77.340206 +/- 0.000005
Rate in state 1 = 459.763735 +/- 0.000017
LIB: Generator type: mt19937
LIB: Seed = 1287164911
LIB: First value = 700022333
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 100.073359
AIC = 206.146717
AICc = 206.946717
Ancestral state = -0.664456 +/- 0.0
Rate in state 0 = 64.535106 +/- 0.000007
Rate in state 1 = 1320.170024 +/- 0.00004
LIB: Generator type: mt19937
LIB: Seed = 1287164914
LIB: First value = 3802288652
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.132001
AIC = 188.264002
AICc = 189.064002
Ancestral state = 2.905147 +/- 0.0
Rate in state 0 = 103.759454 +/- 0.000008
Rate in state 1 = 650.004129 +/- 0.000013
LIB: Generator type: mt19937
LIB: Seed = 1287164918
LIB: First value = 820403939
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.299029
AIC = 204.598057
AICc = 205.398057
Ancestral state = -0.68127 +/- 0.0
Rate in state 0 = 28.801419 +/- 0.000002
Rate in state 1 = 884.378941 +/- 0.000026
LIB: Generator type: mt19937
LIB: Seed = 1287164921
LIB: First value = 966901172
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.987651
AIC = 187.975303
AICc = 188.775303
Ancestral state = 3.017591 +/- 0.0
Rate in state 0 = 56.273543 +/- 0.000005
Rate in state 1 = 429.108616 +/- 0.000013
LIB: Generator type: mt19937
LIB: Seed = 1287164925
LIB: First value = 407736370
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.397679
AIC = 204.795357
AICc = 205.595357
Ancestral state = -0.684373 +/- 0.0
Rate in state 0 = 59.01483 +/- 0.000006
Rate in state 1 = 1843.943322 +/- 0.000048
LIB: Generator type: mt19937
LIB: Seed = 1287164928
LIB: First value = 1645434161
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.660259
AIC = 187.320518
AICc = 188.120518
Ancestral state = 3.750794 +/- 0.0
Rate in state 0 = 87.830935 +/- 0.000006
Rate in state 1 = 918.875032 +/- 0.000022
LIB: Generator type: mt19937
LIB: Seed = 1287164933
LIB: First value = 3663110643
RCPP: 'd:/temp/RtmpKu0z9n/file4a0f52b4'
Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpKu0z9n/file4a0f52b4'
.. conditioned command is: ;execute 'd:/temp/RtmpKu0z9n/file4a0f52b4';end;
LIB: handle cmd ';execute 'd:/temp/RtmpKu0z9n/file4a0f52b4';end;'
Opening d:/temp/RtmpKu0z9n/file4a0f52b4...
Starting to execute NEXUS file
Entering TAXA block...done
Entering TREES block...done
Entering CHARACTERS block...done
(Skipping assumptions block)
(Skipping brownie block)
Finished executing NEXUS file
TREES block contains 10 trees
1 UNTITLED (rooted, weight = 1)
2 UNTITLED (rooted, weight = 1)
3 UNTITLED (rooted, weight = 1)
4 UNTITLED (rooted, weight = 1)
5 UNTITLED (rooted, weight = 1)
6 UNTITLED (rooted, weight = 1)
7 UNTITLED (rooted, weight = 1)
8 UNTITLED (rooted, weight = 1)
9 UNTITLED (rooted, weight = 1)
10 UNTITLED (rooted, weight = 1,default tree)
Reading TAXA block...
Reading TREES block...
Reading CHARACTERS block...
Reading ASSUMPTIONS block...
Reading BROWNIE block...
You have chosen a single rate Brownian motion model
Now optimizing with taxset ALL
LIB: Generator type: mt19937
LIB: Seed = 1287164933
LIB: First value = 3663110643
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164933
LIB: First value = 3663110643
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164935
LIB: First value = 4226970732
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164935
LIB: First value = 4226970732
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164936
LIB: First value = 2347873852
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164937
LIB: First value = 2507914602
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164938
LIB: First value = 1158278135
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164938
LIB: First value = 1158278135
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164939
LIB: First value = 1249537852
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164940
LIB: First value = 1866540674
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164941
LIB: First value = 411732224
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164942
LIB: First value = 3305231241
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164944
LIB: First value = 3653932545
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164944
LIB: First value = 3653932545
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164946
LIB: First value = 1239853962
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666917 +/- 0.000037
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164946
LIB: First value = 1239853962
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666917 +/- 0.000037
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004735 +/- 0.000011
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164949
LIB: First value = 1037581735
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666917 +/- 0.000037
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004735 +/- 0.000011
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373284 +/- 0.000033
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164949
LIB: First value = 1037581735
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666917 +/- 0.000037
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004735 +/- 0.000011
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373284 +/- 0.000033
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489961 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164950
LIB: First value = 2502713901
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666917 +/- 0.000037
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004735 +/- 0.000011
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373284 +/- 0.000033
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489961 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582569
AIC = 209.165138
AICc = 209.552235
Ancestral state = -0.0
Optimal rate = 1120.318913 +/- 0.00006
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287164951
LIB: First value = 3320299560
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175444 +/- 0.000039
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077718 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442929 +/- 0.000029
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968399 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373233 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646943 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471291 +/- 0.000091
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475631 +/- 0.000019
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943014 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.156418 +/- 0.000004
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401484 +/- 0.000088
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533307 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175579 +/- 0.000026
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713839 +/- 0.000006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.666917 +/- 0.000037
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004735 +/- 0.000011
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373284 +/- 0.000033
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489961 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582569
AIC = 209.165138
AICc = 209.552235
Ancestral state = -0.0
Optimal rate = 1120.318913 +/- 0.00006
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.819721
AICc = 189.206817
Ancestral state = -0.0
Optimal rate = 615.831883 +/- 0.000016
Note that +/- reflects imprecision due to numerical optimization
You have chosen Brownian motion with one rate parameter per state
Now optimizing with taxset ALL
LIB: Generator type: mt19937
LIB: Seed = 1287164953
LIB: First value = 1442438115
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 101.358522
AIC = 208.717044
AICc = 209.517044
Ancestral state = -0.568338 +/- 0.0
Rate in state 0 = 91.263031 +/- 0.000018
Rate in state 1 = 752.71741 +/- 0.00002
LIB: Generator type: mt19937
LIB: Seed = 1287164955
LIB: First value = 1500231319
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.179842
AIC = 188.359685
AICc = 189.159685
Ancestral state = 2.750468 +/- 0.0
Rate in state 0 = 48.767964 +/- 0.000006
Rate in state 1 = 415.385142 +/- 0.000016
LIB: Generator type: mt19937
LIB: Seed = 1287164958
LIB: First value = 1087799423
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 99.241775
AIC = 204.483549
AICc = 205.283549
Ancestral state = -0.710483 +/- 0.0
Rate in state 0 = 21.346394 +/- 0.000002
Rate in state 1 = 671.657923 +/- 0.000019
LIB: Generator type: mt19937
LIB: Seed = 1287164962
LIB: First value = 2863016803
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.983502
AIC = 187.967004
AICc = 188.767004
Ancestral state = 3.054602 +/- 0.0
Rate in state 0 = 41.680784 +/- 0.000004
Rate in state 1 = 325.95176 +/- 0.000009
LIB: Generator type: mt19937
LIB: Seed = 1287164966
LIB: First value = 36721648
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 98.403443
AIC = 202.806887
AICc = 203.606887
Ancestral state = -0.712707 +/- 0.0
Rate in state 0 = 24.872616 +/- 0.000002
Rate in state 1 = 859.91948 +/- 0.000021
LIB: Generator type: mt19937
LIB: Seed = 1287164969
LIB: First value = 1441507420
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.568177
AIC = 187.136354
AICc = 187.936354
Ancestral state = 3.330917 +/- 0.0
Rate in state 0 = 47.885895 +/- 0.000003
Rate in state 1 = 424.63914 +/- 0.000009
LIB: Generator type: mt19937
LIB: Seed = 1287164972
LIB: First value = 1176614749
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.25393
AIC = 204.507859
AICc = 205.307859
Ancestral state = -0.720946 +/- 0.0
Rate in state 0 = 89.7875 +/- 0.000006
Rate in state 1 = 2852.305362 +/- 0.000091
LIB: Generator type: mt19937
LIB: Seed = 1287164976
LIB: First value = 1315584009
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.870567
AIC = 187.741134
AICc = 188.541134
Ancestral state = 3.365235 +/- 0.0
Rate in state 0 = 155.289333 +/- 0.000017
Rate in state 1 = 1406.590718 +/- 0.000039
LIB: Generator type: mt19937
LIB: Seed = 1287164980
LIB: First value = 1456094903
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 101.678334
AIC = 209.356668
AICc = 210.156668
Ancestral state = -0.438846 +/- 0.0
Rate in state 0 = 94.164138 +/- 0.000012
Rate in state 1 = 462.965631 +/- 0.000016
LIB: Generator type: mt19937
LIB: Seed = 1287164982
LIB: First value = 4227473696
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.255611
AIC = 188.511222
AICc = 189.311222
Ancestral state = 1.82777 +/- 0.0
Rate in state 0 = 42.895601 +/- 0.000004
Rate in state 1 = 257.636691 +/- 0.000006
LIB: Generator type: mt19937
LIB: Seed = 1287164986
LIB: First value = 598977948
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 97.672424
AIC = 201.344848
AICc = 202.144848
Ancestral state = -0.718767 +/- 0.0
Rate in state 0 = 52.492216 +/- 0.000003
Rate in state 1 = 2218.494586 +/- 0.000055
LIB: Generator type: mt19937
LIB: Seed = 1287164989
LIB: First value = 2995518866
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.78148
AIC = 187.56296
AICc = 188.36296
Ancestral state = 2.473751 +/- 0.0
Rate in state 0 = 174.301687 +/- 0.000011
Rate in state 1 = 991.12034 +/- 0.000019
LIB: Generator type: mt19937
LIB: Seed = 1287164993
LIB: First value = 706110851
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.045956
AIC = 204.091912
AICc = 204.891912
Ancestral state = -0.73727 +/- 0.0
Rate in state 0 = 31.188344 +/- 0.000003
Rate in state 1 = 983.46501 +/- 0.000025
LIB: Generator type: mt19937
LIB: Seed = 1287164996
LIB: First value = 3775438853
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.061771
AIC = 188.123541
AICc = 188.923541
Ancestral state = 2.421296 +/- 0.0
Rate in state 0 = 77.340199 +/- 0.000005
Rate in state 1 = 459.763736 +/- 0.000013
LIB: Generator type: mt19937
LIB: Seed = 1287165000
LIB: First value = 3559151613
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 100.073359
AIC = 206.146717
AICc = 206.946717
Ancestral state = -0.664456 +/- 0.0
Rate in state 0 = 64.535101 +/- 0.000006
Rate in state 1 = 1320.17006 +/- 0.000038
LIB: Generator type: mt19937
LIB: Seed = 1287165003
LIB: First value = 2624849968
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.132001
AIC = 188.264002
AICc = 189.064002
Ancestral state = 2.905147 +/- 0.0
Rate in state 0 = 103.759449 +/- 0.000007
Rate in state 1 = 650.004159 +/- 0.000018
LIB: Generator type: mt19937
LIB: Seed = 1287165006
LIB: First value = 1460111326
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.299029
AIC = 204.598057
AICc = 205.398057
Ancestral state = -0.68127 +/- 0.0
Rate in state 0 = 28.801418 +/- 0.000002
Rate in state 1 = 884.378963 +/- 0.000025
LIB: Generator type: mt19937
LIB: Seed = 1287165010
LIB: First value = 2331656303
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.987651
AIC = 187.975303
AICc = 188.775303
Ancestral state = 3.017591 +/- 0.0
Rate in state 0 = 56.273545 +/- 0.000004
Rate in state 1 = 429.10861 +/- 0.000014
LIB: Generator type: mt19937
LIB: Seed = 1287165013
LIB: First value = 523565074
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.397679
AIC = 204.795357
AICc = 205.595357
Ancestral state = -0.684374 +/- 0.0
Rate in state 0 = 59.014817 +/- 0.000004
Rate in state 1 = 1843.943357 +/- 0.000072
LIB: Generator type: mt19937
LIB: Seed = 1287165017
LIB: First value = 3772964352
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.660259
AIC = 187.320518
AICc = 188.120518
Ancestral state = 3.750794 +/- 0.0
Rate in state 0 = 87.830935 +/- 0.000007
Rate in state 1 = 918.874998 +/- 0.000014
LIB: Generator type: mt19937
LIB: Seed = 1287165021
LIB: First value = 1033560058
RCPP: 'd:/temp/RtmpKu0z9n/file25e83f86'
Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpKu0z9n/file25e83f86'
.. conditioned command is: ;execute 'd:/temp/RtmpKu0z9n/file25e83f86';end;
LIB: handle cmd ';execute 'd:/temp/RtmpKu0z9n/file25e83f86';end;'
Opening d:/temp/RtmpKu0z9n/file25e83f86...
Starting to execute NEXUS file
Entering TAXA block...done
Entering TREES block...done
Entering CHARACTERS block...done
(Skipping assumptions block)
(Skipping brownie block)
Finished executing NEXUS file
TREES block contains 10 trees
1 UNTITLED (rooted, weight = 1)
2 UNTITLED (rooted, weight = 1)
3 UNTITLED (rooted, weight = 1)
4 UNTITLED (rooted, weight = 1)
5 UNTITLED (rooted, weight = 1)
6 UNTITLED (rooted, weight = 1)
7 UNTITLED (rooted, weight = 1)
8 UNTITLED (rooted, weight = 1)
9 UNTITLED (rooted, weight = 1)
10 UNTITLED (rooted, weight = 1,default tree)
Reading TAXA block...
Reading TREES block...
Reading CHARACTERS block...
Reading ASSUMPTIONS block...
Reading BROWNIE block...
You have chosen a single rate Brownian motion model
Now optimizing with taxset ALL
LIB: Generator type: mt19937
LIB: Seed = 1287165022
LIB: First value = 1507629618
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165022
LIB: First value = 1507629618
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165024
LIB: First value = 1367952168
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165024
LIB: First value = 1367952168
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165025
LIB: First value = 432524386
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165026
LIB: First value = 19126802
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165027
LIB: First value = 3532678837
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165028
LIB: First value = 1077080909
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165028
LIB: First value = 1077080909
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165029
LIB: First value = 3208274922
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165030
LIB: First value = 3112872362
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165031
LIB: First value = 616141334
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165032
LIB: First value = 2975782285
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165033
LIB: First value = 2475890960
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165034
LIB: First value = 4196742615
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.6669 +/- 0.00005
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165035
LIB: First value = 1119473622
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.6669 +/- 0.00005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004728 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165037
LIB: First value = 3579538526
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.6669 +/- 0.00005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004728 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373258 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165037
LIB: First value = 3579538526
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.6669 +/- 0.00005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004728 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373258 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489954 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165038
LIB: First value = 755163173
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.6669 +/- 0.00005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004728 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373258 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489954 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582569
AIC = 209.165138
AICc = 209.552235
Ancestral state = -0.0
Optimal rate = 1120.318819 +/- 0.000067
Note that +/- reflects imprecision due to numerical optimization
LIB: Generator type: mt19937
LIB: Seed = 1287165038
LIB: First value = 755163173
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Now optimizing with taxset ALL
-lnL = 102.58253
AIC = 209.165059
AICc = 209.552156
Ancestral state = 0.0
Optimal rate = 553.175414 +/- 0.00003
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409867
AIC = 188.819734
AICc = 189.206831
Ancestral state = 0.0
Optimal rate = 304.077715 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.58259
AIC = 209.165181
AICc = 209.552277
Ancestral state = -0.0
Optimal rate = 407.442971 +/- 0.000021
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.81972
AICc = 189.206817
Ancestral state = 0.0
Optimal rate = 223.968406 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582641
AIC = 209.165282
AICc = 209.552379
Ancestral state = -0.0
Optimal rate = 512.373257 +/- 0.000031
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409857
AIC = 188.819714
AICc = 189.206811
Ancestral state = 0.0
Optimal rate = 281.646937 +/- 0.000007
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582653
AIC = 209.165305
AICc = 209.552402
Ancestral state = -0.0
Optimal rate = 1725.471303 +/- 0.000078
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409862
AIC = 188.819725
AICc = 189.206822
Ancestral state = 0.0
Optimal rate = 948.475648 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582565
AIC = 209.16513
AICc = 209.552227
Ancestral state = -0.0
Optimal rate = 365.943016 +/- 0.000022
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409854
AIC = 188.819707
AICc = 189.206804
Ancestral state = -0.0
Optimal rate = 201.15642 +/- 0.000005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582495
AIC = 209.164991
AICc = 209.552087
Ancestral state = 0.0
Optimal rate = 1274.401609 +/- 0.000098
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409865
AIC = 188.819729
AICc = 189.206826
Ancestral state = 0.0
Optimal rate = 700.533316 +/- 0.00001
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582564
AIC = 209.165128
AICc = 209.552224
Ancestral state = -0.0
Optimal rate = 596.175545 +/- 0.000038
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409859
AIC = 188.819718
AICc = 189.206814
Ancestral state = 0.0
Optimal rate = 327.713835 +/- 0.000009
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582526
AIC = 209.165052
AICc = 209.552149
Ancestral state = -0.0
Optimal rate = 858.6669 +/- 0.00005
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409861
AIC = 188.819722
AICc = 189.206819
Ancestral state = 0.0
Optimal rate = 472.004728 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582562
AIC = 209.165124
AICc = 209.552221
Ancestral state = 0.0
Optimal rate = 539.373258 +/- 0.000027
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.409855
AIC = 188.81971
AICc = 189.206807
Ancestral state = 0.0
Optimal rate = 296.489954 +/- 0.000008
Note that +/- reflects imprecision due to numerical optimization
-lnL = 102.582569
AIC = 209.165138
AICc = 209.552235
Ancestral state = -0.0
Optimal rate = 1120.318819 +/- 0.000067
Note that +/- reflects imprecision due to numerical optimization
-lnL = 92.40986
AIC = 188.819721
AICc = 189.206817
Ancestral state = -0.0
Optimal rate = 615.831891 +/- 0.000015
Note that +/- reflects imprecision due to numerical optimization
You have chosen Brownian motion with one rate parameter per state
Now optimizing with taxset ALL
LIB: Generator type: mt19937
LIB: Seed = 1287165040
LIB: First value = 2109283670
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 101.358522
AIC = 208.717044
AICc = 209.517044
Ancestral state = -0.568339 +/- 0.0
Rate in state 0 = 91.263057 +/- 0.000017
Rate in state 1 = 752.717401 +/- 0.000037
LIB: Generator type: mt19937
LIB: Seed = 1287165043
LIB: First value = 1053161102
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 91.179842
AIC = 188.359685
AICc = 189.159685
Ancestral state = 2.750468 +/- 0.0
Rate in state 0 = 48.767966 +/- 0.000005
Rate in state 1 = 415.385118 +/- 0.000012
LIB: Generator type: mt19937
LIB: Seed = 1287165047
LIB: First value = 704611791
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.241775
AIC = 204.483549
AICc = 205.283549
Ancestral state = -0.710483 +/- 0.0
Rate in state 0 = 21.346394 +/- 0.000002
Rate in state 1 = 671.657928 +/- 0.000014
LIB: Generator type: mt19937
LIB: Seed = 1287165050
LIB: First value = 1220213452
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.983502
AIC = 187.967004
AICc = 188.767004
Ancestral state = 3.054602 +/- 0.0
Rate in state 0 = 41.680782 +/- 0.000003
Rate in state 1 = 325.951763 +/- 0.000007
LIB: Generator type: mt19937
LIB: Seed = 1287165053
LIB: First value = 3252527206
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 98.403443
AIC = 202.806887
AICc = 203.606887
Ancestral state = -0.712707 +/- 0.0
Rate in state 0 = 24.872617 +/- 0.000001
Rate in state 1 = 859.919455 +/- 0.000026
LIB: Generator type: mt19937
LIB: Seed = 1287165057
LIB: First value = 601045896
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.568177
AIC = 187.136354
AICc = 187.936354
Ancestral state = 3.330917 +/- 0.0
Rate in state 0 = 47.885895 +/- 0.000003
Rate in state 1 = 424.639141 +/- 0.00001
LIB: Generator type: mt19937
LIB: Seed = 1287165061
LIB: First value = 3190167957
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.25393
AIC = 204.507859
AICc = 205.307859
Ancestral state = -0.720946 +/- 0.0
Rate in state 0 = 89.787507 +/- 0.000008
Rate in state 1 = 2852.305245 +/- 0.000084
LIB: Generator type: mt19937
LIB: Seed = 1287165064
LIB: First value = 309888716
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.870567
AIC = 187.741134
AICc = 188.541134
Ancestral state = 3.365235 +/- 0.0
Rate in state 0 = 155.289337 +/- 0.00001
Rate in state 1 = 1406.590711 +/- 0.000038
LIB: Generator type: mt19937
LIB: Seed = 1287165068
LIB: First value = 1241825432
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 101.678334
AIC = 209.356668
AICc = 210.156668
Ancestral state = -0.438846 +/- 0.000001
Rate in state 0 = 94.164137 +/- 0.000011
Rate in state 1 = 462.965638 +/- 0.000017
LIB: Generator type: mt19937
LIB: Seed = 1287165070
LIB: First value = 2424370302
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.255611
AIC = 188.511222
AICc = 189.311222
Ancestral state = 1.82777 +/- 0.0
Rate in state 0 = 42.895602 +/- 0.000003
Rate in state 1 = 257.636688 +/- 0.000004
LIB: Generator type: mt19937
LIB: Seed = 1287165074
LIB: First value = 692967042
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 97.672424
AIC = 201.344848
AICc = 202.144848
Ancestral state = -0.718767 +/- 0.0
Rate in state 0 = 52.492222 +/- 0.000003
Rate in state 1 = 2218.494753 +/- 0.000055
LIB: Generator type: mt19937
LIB: Seed = 1287165077
LIB: First value = 1205521882
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.78148
AIC = 187.56296
AICc = 188.36296
Ancestral state = 2.473751 +/- 0.0
Rate in state 0 = 174.301709 +/- 0.000011
Rate in state 1 = 991.120288 +/- 0.000026
LIB: Generator type: mt19937
LIB: Seed = 1287165081
LIB: First value = 2732861917
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.045956
AIC = 204.091912
AICc = 204.891912
Ancestral state = -0.73727 +/- 0.0
Rate in state 0 = 31.188343 +/- 0.000002
Rate in state 1 = 983.464991 +/- 0.000032
LIB: Generator type: mt19937
LIB: Seed = 1287165084
LIB: First value = 978500404
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 91.061771
AIC = 188.123541
AICc = 188.923541
Ancestral state = 2.421296 +/- 0.0
Rate in state 0 = 77.340201 +/- 0.000007
Rate in state 1 = 459.763726 +/- 0.000012
LIB: Generator type: mt19937
LIB: Seed = 1287165088
LIB: First value = 777524463
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 100.073359
AIC = 206.146717
AICc = 206.946717
Ancestral state = -0.664456 +/- 0.0
Rate in state 0 = 64.535099 +/- 0.000007
Rate in state 1 = 1320.170047 +/- 0.000026
LIB: Generator type: mt19937
LIB: Seed = 1287165091
LIB: First value = 1620829471
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 91.132001
AIC = 188.264002
AICc = 189.064002
Ancestral state = 2.905147 +/- 0.0
Rate in state 0 = 103.759438 +/- 0.000008
Rate in state 1 = 650.00418 +/- 0.000017
LIB: Generator type: mt19937
LIB: Seed = 1287165095
LIB: First value = 2940709122
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.299029
AIC = 204.598057
AICc = 205.398057
Ancestral state = -0.68127 +/- 0.0
Rate in state 0 = 28.801418 +/- 0.000003
Rate in state 1 = 884.378989 +/- 0.00002
LIB: Generator type: mt19937
LIB: Seed = 1287165098
LIB: First value = 96648825
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.987651
AIC = 187.975303
AICc = 188.775303
Ancestral state = 3.017591 +/- 0.0
Rate in state 0 = 56.273553 +/- 0.000006
Rate in state 1 = 429.108611 +/- 0.000011
LIB: Generator type: mt19937
LIB: Seed = 1287165101
LIB: First value = 1625427109
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
-lnL = 99.397679
AIC = 204.795357
AICc = 205.595357
Ancestral state = -0.684374 +/- 0.0
Rate in state 0 = 59.014829 +/- 0.000004
Rate in state 1 = 1843.943293 +/- 0.000042
LIB: Generator type: mt19937
LIB: Seed = 1287165104
LIB: First value = 153148034
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
----------------------------------------------------------------------------
WARNING: Out of 15 optimization starts, 15 were stopped by hitting
the maximum # of iterations. This means that those replicates
may not even have hit the local maximum.
You can increase the maximum number of iterations or decrease the
precision with the NumOpt command. You could also consider
increasing the number of random starts using that same command.
If this happened on a small proportion of replicates, though,
or if the precision (below) is good enough, don't worry about it.
----------------------------------------------------------------------------
-lnL = 90.660259
AIC = 187.320518
AICc = 188.120518
Ancestral state = 3.750794 +/- 0.0
Rate in state 0 = 87.830933 +/- 0.000004
Rate in state 1 = 918.874982 +/- 0.00005
LIB: Generator type: mt19937
LIB: Seed = 1287165108
LIB: First value = 2547224846
RCPP: 'd:/temp/RtmpKu0z9n/file7ec141e5'
Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpKu0z9n/file7ec141e5'
.. conditioned command is: ;execute 'd:/temp/RtmpKu0z9n/file7ec141e5';end;
LIB: handle cmd ';execute 'd:/temp/RtmpKu0z9n/file7ec141e5';end;'
Opening d:/temp/RtmpKu0z9n/file7ec141e5...
Starting to execute NEXUS file
Entering TAXA block...done
Entering TREES block...done
Entering CHARACTERS block...done
(Skipping brownie block)
Finished executing NEXUS file
TREES block contains one tree
1 UNTITLED (rooted, weight = 1,default tree)
Reading TAXA block...
Reading TREES block...
Reading CHARACTERS block...
Reading BROWNIE block...
You have chosen a non-time-reversible model: rates are free to vary
You have chosen equal frequencies for all states
WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars
-------------------------------------------------------------------------------
WARNING: You are trying to estimate 2 parameters, but only have 13 taxa.
Make sure to try some simpler models, and expect quite imprecise estimates.
-------------------------------------------------------------------------------
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Tree = 1: UNTITLED
-lnL = 6.043574
AIC = 16.087148
AICc = 17.287148
Rates: nonreversible
q_0_1 = 1.652106 +/- 0.0
q_1_0 = 6.252674 +/- 0.0
Statefreqs: uniform
P(0) = 0.5
P(1) = 0.5
tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333);
tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333});
<da><c4> fuliginosa:{1,0.055}
ڴ:{0,0.0275:1,0.0275}
<b3><c0><c4> fortis:{1,0.055}
ڴ:{0,0.07333}
<b3><c0><c4><c4> magnirostris:{0,0.11}
ڴ:{0,0.00917}
<b3><c0><c4><c4><c4> conirostris:{0,0.18333}
ڴ:{0,0.0355}
<b3><c0><c4><c4><c4><c4> scandens:{0,0.1925}
<da><c4><c4>Ĵ:{0,0.10346}
<b3> <c0><c4><c4><c4><c4><c4> difficilis:{0,0.114:1,0.114}
ڴ:{0,0.13404}
<b3><b3> <da><c4><c4><c4> pallida:{0,0.08667}
<b3><c0><c4><c4><c4><c4>Ĵ:{0,0.24479}
<b3> <b3> <da><c4> parvulus:{0,0.02}
<b3> <b3>ڴ:{0,0.015}
<b3> <b3><b3><c0><c4> psittacula:{0,0.02}
<b3> <c0><b4>:{0,0.05167}
<b3> <c0><c4><c4> pauper:{0,0.035}
ڴ:{0,0.06859}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Platyspiza:{0,0.4655}
ڴ:{0,0.04924}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> fusca:{0,0.53409}
<b4>
<c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Pinaroloxias:{0,0.58333}
You have chosen a non-time-reversible model: rates are free to vary
You have chosen to use equilibrium state frequencies
WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars
-------------------------------------------------------------------------------
WARNING: You are trying to estimate 2 parameters, but only have 13 taxa.
Make sure to try some simpler models, and expect quite imprecise estimates.
-------------------------------------------------------------------------------
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Tree = 1: UNTITLED
-lnL = 6.042915
AIC = 16.085830
AICc = 17.285830
Rates: nonreversible
q_0_1 = 1.661837 +/- 0.000001
q_1_0 = 6.181368 +/- 0.000002
Statefreqs: equilibrium
P(0) = 0.788118
P(1) = 0.211882
tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333);
tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333});
<da><c4> fuliginosa:{1,0.055}
ڴ:{0,0.0275:1,0.0275}
<b3><c0><c4> fortis:{1,0.055}
ڴ:{0,0.07333}
<b3><c0><c4><c4> magnirostris:{0,0.11}
ڴ:{0,0.00917}
<b3><c0><c4><c4><c4> conirostris:{0,0.18333}
ڴ:{0,0.0355}
<b3><c0><c4><c4><c4><c4> scandens:{0,0.1925}
<da><c4><c4>Ĵ:{0,0.10346}
<b3> <c0><c4><c4><c4><c4><c4> difficilis:{0,0.114:1,0.114}
ڴ:{0,0.13404}
<b3><b3> <da><c4><c4><c4> pallida:{0,0.08667}
<b3><c0><c4><c4><c4><c4>Ĵ:{0,0.24479}
<b3> <b3> <da><c4> parvulus:{0,0.02}
<b3> <b3>ڴ:{0,0.015}
<b3> <b3><b3><c0><c4> psittacula:{0,0.02}
<b3> <c0><b4>:{0,0.05167}
<b3> <c0><c4><c4> pauper:{0,0.035}
ڴ:{0,0.06859}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Platyspiza:{0,0.4655}
ڴ:{0,0.04924}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> fusca:{0,0.53409}
<b4>
<c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Pinaroloxias:{0,0.58333}
LIB: Generator type: mt19937
LIB: Seed = 1287165112
LIB: First value = 2336286128
RCPP: 'd:/temp/RtmpKu0z9n/file2ccf1d83'
Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpKu0z9n/file2ccf1d83'
.. conditioned command is: ;execute 'd:/temp/RtmpKu0z9n/file2ccf1d83';end;
LIB: handle cmd ';execute 'd:/temp/RtmpKu0z9n/file2ccf1d83';end;'
Opening d:/temp/RtmpKu0z9n/file2ccf1d83...
Starting to execute NEXUS file
Entering TAXA block...done
Entering TREES block...done
Entering CHARACTERS block...done
(Skipping brownie block)
Finished executing NEXUS file
TREES block contains one tree
1 UNTITLED (rooted, weight = 1,default tree)
Reading TAXA block...
Reading TREES block...
Reading CHARACTERS block...
Reading BROWNIE block...
You have chosen a non-time-reversible model: rates are free to vary
You have chosen equal frequencies for all states
WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars
-------------------------------------------------------------------------------
WARNING: You are trying to estimate 2 parameters, but only have 13 taxa.
Make sure to try some simpler models, and expect quite imprecise estimates.
-------------------------------------------------------------------------------
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Tree = 1: UNTITLED
-lnL = 6.043574
AIC = 16.087148
AICc = 17.287148
Rates: nonreversible
q_0_1 = 1.652106 +/- 0.0
q_1_0 = 6.252674 +/- 0.0
Statefreqs: uniform
P(0) = 0.5
P(1) = 0.5
tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333);
tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333});
<da><c4> fuliginosa:{1,0.055}
ڴ:{0,0.0275:1,0.0275}
<b3><c0><c4> fortis:{1,0.055}
ڴ:{0,0.07333}
<b3><c0><c4><c4> magnirostris:{0,0.11}
ڴ:{0,0.00917}
<b3><c0><c4><c4><c4> conirostris:{0,0.18333}
ڴ:{0,0.0355}
<b3><c0><c4><c4><c4><c4> scandens:{0,0.1925}
<da><c4><c4>Ĵ:{0,0.10346}
<b3> <c0><c4><c4><c4><c4><c4> difficilis:{0,0.114:1,0.114}
ڴ:{0,0.13404}
<b3><b3> <da><c4><c4><c4> pallida:{0,0.08667}
<b3><c0><c4><c4><c4><c4>Ĵ:{0,0.24479}
<b3> <b3> <da><c4> parvulus:{0,0.02}
<b3> <b3>ڴ:{0,0.015}
<b3> <b3><b3><c0><c4> psittacula:{0,0.02}
<b3> <c0><b4>:{0,0.05167}
<b3> <c0><c4><c4> pauper:{0,0.035}
ڴ:{0,0.06859}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Platyspiza:{0,0.4655}
ڴ:{0,0.04924}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> fusca:{0,0.53409}
<b4>
<c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Pinaroloxias:{0,0.58333}
You have chosen a non-time-reversible model: rates are free to vary
You have chosen to use equilibrium state frequencies
WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars
-------------------------------------------------------------------------------
WARNING: You are trying to estimate 2 parameters, but only have 13 taxa.
Make sure to try some simpler models, and expect quite imprecise estimates.
-------------------------------------------------------------------------------
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Tree = 1: UNTITLED
-lnL = 6.042915
AIC = 16.085830
AICc = 17.285830
Rates: nonreversible
q_0_1 = 1.661837 +/- 0.000001
q_1_0 = 6.181369 +/- 0.000002
Statefreqs: equilibrium
P(0) = 0.788118
P(1) = 0.211882
tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333);
tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333});
<da><c4> fuliginosa:{1,0.055}
ڴ:{0,0.0275:1,0.0275}
<b3><c0><c4> fortis:{1,0.055}
ڴ:{0,0.07333}
<b3><c0><c4><c4> magnirostris:{0,0.11}
ڴ:{0,0.00917}
<b3><c0><c4><c4><c4> conirostris:{0,0.18333}
ڴ:{0,0.0355}
<b3><c0><c4><c4><c4><c4> scandens:{0,0.1925}
<da><c4><c4>Ĵ:{0,0.10346}
<b3> <c0><c4><c4><c4><c4><c4> difficilis:{0,0.114:1,0.114}
ڴ:{0,0.13404}
<b3><b3> <da><c4><c4><c4> pallida:{0,0.08667}
<b3><c0><c4><c4><c4><c4>Ĵ:{0,0.24479}
<b3> <b3> <da><c4> parvulus:{0,0.02}
<b3> <b3>ڴ:{0,0.015}
<b3> <b3><b3><c0><c4> psittacula:{0,0.02}
<b3> <c0><b4>:{0,0.05167}
<b3> <c0><c4><c4> pauper:{0,0.035}
ڴ:{0,0.06859}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Platyspiza:{0,0.4655}
ڴ:{0,0.04924}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> fusca:{0,0.53409}
<b4>
<c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Pinaroloxias:{0,0.58333}
LIB: Generator type: mt19937
LIB: Seed = 1287165115
LIB: First value = 3978841195
RCPP: 'd:/temp/RtmpKu0z9n/file6a995179'
Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpKu0z9n/file6a995179'
.. conditioned command is: ;execute 'd:/temp/RtmpKu0z9n/file6a995179';end;
LIB: handle cmd ';execute 'd:/temp/RtmpKu0z9n/file6a995179';end;'
Opening d:/temp/RtmpKu0z9n/file6a995179...
Starting to execute NEXUS file
Entering TAXA block...done
Entering TREES block...done
Entering CHARACTERS block...done
(Skipping brownie block)
Finished executing NEXUS file
TREES block contains one tree
1 UNTITLED (rooted, weight = 1,default tree)
Reading TAXA block...
Reading TREES block...
Reading CHARACTERS block...
Reading BROWNIE block...
You have chosen a non-time-reversible model: rates are free to vary
You have chosen equal frequencies for all states
WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars
-------------------------------------------------------------------------------
WARNING: You are trying to estimate 2 parameters, but only have 13 taxa.
Make sure to try some simpler models, and expect quite imprecise estimates.
-------------------------------------------------------------------------------
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Tree = 1: UNTITLED
-lnL = 6.043574
AIC = 16.087148
AICc = 17.287148
Rates: nonreversible
q_0_1 = 1.652106 +/- 0.0
q_1_0 = 6.252674 +/- 0.0
Statefreqs: uniform
P(0) = 0.5
P(1) = 0.5
tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333);
tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333});
<da><c4> fuliginosa:{1,0.055}
ڴ:{0,0.0275:1,0.0275}
<b3><c0><c4> fortis:{1,0.055}
ڴ:{0,0.07333}
<b3><c0><c4><c4> magnirostris:{0,0.11}
ڴ:{0,0.00917}
<b3><c0><c4><c4><c4> conirostris:{0,0.18333}
ڴ:{0,0.0355}
<b3><c0><c4><c4><c4><c4> scandens:{0,0.1925}
<da><c4><c4>Ĵ:{0,0.10346}
<b3> <c0><c4><c4><c4><c4><c4> difficilis:{0,0.114:1,0.114}
ڴ:{0,0.13404}
<b3><b3> <da><c4><c4><c4> pallida:{0,0.08667}
<b3><c0><c4><c4><c4><c4>Ĵ:{0,0.24479}
<b3> <b3> <da><c4> parvulus:{0,0.02}
<b3> <b3>ڴ:{0,0.015}
<b3> <b3><b3><c0><c4> psittacula:{0,0.02}
<b3> <c0><b4>:{0,0.05167}
<b3> <c0><c4><c4> pauper:{0,0.035}
ڴ:{0,0.06859}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Platyspiza:{0,0.4655}
ڴ:{0,0.04924}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> fusca:{0,0.53409}
<b4>
<c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Pinaroloxias:{0,0.58333}
You have chosen a non-time-reversible model: rates are free to vary
You have chosen to use equilibrium state frequencies
WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars
-------------------------------------------------------------------------------
WARNING: You are trying to estimate 2 parameters, but only have 13 taxa.
Make sure to try some simpler models, and expect quite imprecise estimates.
-------------------------------------------------------------------------------
Progress:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|********************************************************************************|
Tree = 1: UNTITLED
-lnL = 6.042915
AIC = 16.085830
AICc = 17.285830
Rates: nonreversible
q_0_1 = 1.661837 +/- 0.000001
q_1_0 = 6.181368 +/- 0.000002
Statefreqs: equilibrium
P(0) = 0.788118
P(1) = 0.211882
tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333);
tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333});
<da><c4> fuliginosa:{1,0.055}
ڴ:{0,0.0275:1,0.0275}
<b3><c0><c4> fortis:{1,0.055}
ڴ:{0,0.07333}
<b3><c0><c4><c4> magnirostris:{0,0.11}
ڴ:{0,0.00917}
<b3><c0><c4><c4><c4> conirostris:{0,0.18333}
ڴ:{0,0.0355}
<b3><c0><c4><c4><c4><c4> scandens:{0,0.1925}
<da><c4><c4>Ĵ:{0,0.10346}
<b3> <c0><c4><c4><c4><c4><c4> difficilis:{0,0.114:1,0.114}
ڴ:{0,0.13404}
<b3><b3> <da><c4><c4><c4> pallida:{0,0.08667}
<b3><c0><c4><c4><c4><c4>Ĵ:{0,0.24479}
<b3> <b3> <da><c4> parvulus:{0,0.02}
<b3> <b3>ڴ:{0,0.015}
<b3> <b3><b3><c0><c4> psittacula:{0,0.02}
<b3> <c0><b4>:{0,0.05167}
<b3> <c0><c4><c4> pauper:{0,0.035}
ڴ:{0,0.06859}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Platyspiza:{0,0.4655}
ڴ:{0,0.04924}
<b3><c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> fusca:{0,0.53409}
<b4>
<c0><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4><c4> Pinaroloxias:{0,0.58333}
- checking PDF version of manual ... OK