Package suggested but not available for checking: ‘mvMORPH’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_jive.Rd: make.simmap, as.phylo
  plot_jive.Rd: vioplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: ‘mvMORPH’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_jive.Rd: make.simmap, as.phylo
  plot_jive.Rd: vioplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: ‘mvMORPH’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Running examples in ‘bite-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_jive
> ### Title: Create a list that can be used as an input to mcmc_bite
> ### Aliases: make_jive
> 
> ### ** Examples
> 
> 
> ## Load test data
> data(Anolis_traits)
> data(Anolis_tree)
> data(Anolis_map)
> 
> ## JIVE object to run jive with single regimes
> my.jive <- make_jive(phy = Anolis_tree, traits = Anolis_traits[,-3],
+  model.priors = list(mean = "BM", logvar= c("OU", "root")))
mean prior model: BM [1]
logvar prior model: OU + root [1]
> 
> ## JIVE object to run jive with multiple regimes
> my.jive <- make_jive(Anolis_tree, Anolis_traits[,-3], map = Anolis_map,
+  model.priors =list(mean = "BM", logvar = c("OU", "theta", "alpha")))
mean prior model: BM [1]
logvar prior model: OU + theta + alpha [2]
> 
> ## JIVE object to run jive from an ancestral state reconstruction (stochastic mapping)
> # First generate simmap object
> library(phytools)
Loading required package: ape
Loading required package: maps
> n= length(Anolis_tree$tip.label)
> trait = rep(0,n)
> trait[c(4,3,14,16, 6,5)] = 1
> names(trait) =  Anolis_tree$tip.label
> 
> mapped_tree=make.simmap(Anolis_tree, trait, model='SYM')
make.simmap is sampling character histories conditioned on
the transition matrix

Q =
            0           1
0 -0.01156974  0.01156974
1  0.01156974 -0.01156974
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
  0   1 
0.5 0.5 
Done.
> plotSimmap(mapped_tree)
no colors provided. using the following legend:
        0         1 
  "black" "#DF536B" 
> 
> my.jive <- make_jive(mapped_tree, Anolis_traits[,-3]
+ , model.priors = list(mean = "OU" , logvar = c("OU", "theta")))
mean prior model: OU [1]
logvar prior model: OU + theta [2]
>  
>  ## Jive object using another model of trait evolution (EB from mvMORPH)
>  library(mvMORPH)
Error in library(mvMORPH) : there is no package called ‘mvMORPH’
Execution halted
Package suggested but not available for checking: ‘mvMORPH’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Running examples in ‘bite-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_jive
> ### Title: Create a list that can be used as an input to mcmc_bite
> ### Aliases: make_jive
> 
> ### ** Examples
> 
> 
> ## Load test data
> data(Anolis_traits)
> data(Anolis_tree)
> data(Anolis_map)
> 
> ## JIVE object to run jive with single regimes
> my.jive <- make_jive(phy = Anolis_tree, traits = Anolis_traits[,-3],
+  model.priors = list(mean = "BM", logvar= c("OU", "root")))
mean prior model: BM [1]
logvar prior model: OU + root [1]
> 
> ## JIVE object to run jive with multiple regimes
> my.jive <- make_jive(Anolis_tree, Anolis_traits[,-3], map = Anolis_map,
+  model.priors =list(mean = "BM", logvar = c("OU", "theta", "alpha")))
mean prior model: BM [1]
logvar prior model: OU + theta + alpha [2]
> 
> ## JIVE object to run jive from an ancestral state reconstruction (stochastic mapping)
> # First generate simmap object
> library(phytools)
Loading required package: ape
Loading required package: maps
> n= length(Anolis_tree$tip.label)
> trait = rep(0,n)
> trait[c(4,3,14,16, 6,5)] = 1
> names(trait) =  Anolis_tree$tip.label
> 
> mapped_tree=make.simmap(Anolis_tree, trait, model='SYM')
make.simmap is sampling character histories conditioned on
the transition matrix

Q =
            0           1
0 -0.01156974  0.01156974
1  0.01156974 -0.01156974
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
  0   1 
0.5 0.5 
Done.
> plotSimmap(mapped_tree)
no colors provided. using the following legend:
        0         1 
  "black" "#DF536B" 
> 
> my.jive <- make_jive(mapped_tree, Anolis_traits[,-3]
+ , model.priors = list(mean = "OU" , logvar = c("OU", "theta")))
mean prior model: OU [1]
logvar prior model: OU + theta [2]
>  
>  ## Jive object using another model of trait evolution (EB from mvMORPH)
>  library(mvMORPH)
Error in library(mvMORPH) : there is no package called ‘mvMORPH’
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_jive.Rd: make.simmap, as.phylo
  plot_jive.Rd: vioplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.