Check results for 'diversitree'

using R version 3.0.1 Patched (2013-05-20 r62767)
using platform: x86_64-unknown-linux-gnu (64-bit)
using session charset: UTF-8
checking for file ‘diversitree/DESCRIPTION’ ... OK
this is package ‘diversitree’ version ‘0.9-3’
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
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checking for hidden files and directories ... OK
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checking for sufficient/correct file permissions ... OK
checking whether package ‘diversitree’ can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
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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 namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking loading without being on the library search path ... OK
checking for unstated dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... NOTE
Foreign function calls with ‘PACKAGE’ argument in a different package:
.C("node_depth", ..., PACKAGE = "ape")
.Call("call_lsoda", ..., PACKAGE = "deSolve")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
checking R code for possible problems ... OK
checking Rd files ... OK
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 for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
checking compiled code ... OK
checking examples ... ERROR
Running examples in ‘diversitree-Ex.R’ failed
The error most likely occurred in:

> ### Name: make.bisse
> ### Title: Binary State Speciation and Extinction Model
> ### Aliases: make.bisse starting.point.bisse
> ### Keywords: models
>
> ### ** Examples
>
> pars <- c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01)
> set.seed(4)
> phy <- tree.bisse(pars, max.t=30, x0=0)
>
> ## Here is the 52 species tree with the true character history coded.
> ## Red is state '1', which has twice the speciation rate of black (state
> ## '0').
> h <- history.from.sim.discrete(phy, 0:1)
> plot(h, phy)
>
> lik <- make.bisse(phy, phy$tip.state)
Warning in make.ode.deSolve(info, control) :
diversitree is not known to work with deSolve > 1.10.3
falling back on slow version
> lik(pars) # -159.71
[1] -159.71
>
> ## Heuristic guess at a starting point, based on the constant-rate
> ## birth-death model (uses make.bd).
> p <- starting.point.bisse(phy)
>
> ## Start an ML search from this point. This takes some time (~7s)
> fit <- find.mle(lik, p, method="subplex")
> logLik(fit) # -158.6875
'log Lik.' -158.6875 (df=6)
>
> ## The estimated parameters aren't too far away from the real ones, even
> ## with such a small tree
> rbind(real=pars,
+ estimated=round(coef(fit), 2))
lambda0 lambda1 mu0 mu1 q01 q10
real 0.10 0.20 0.03 0.03 0.01 0.01
estimated 0.14 0.18 0.12 0.04 0.00 0.02
>
> ## Test a constrained model where the speciation rates are set equal
> ## (takes ~4s).
> lik.l <- constrain(lik, lambda1 ~ lambda0)
> fit.l <- find.mle(lik.l, p[-1], method="subplex")
> logLik(fit.l) # -158.7357
'log Lik.' -158.7357 (df=5)
>
> ## Despite the difference in the estimated parameters, there is no
> ## statistical support for this difference:
> anova(fit, equal.lambda=fit.l)
Df lnLik AIC ChiSq Pr(>|Chi|)
full 6 -158.69 329.37
equal.lambda 5 -158.74 327.47 0.096466 0.7561
>
> ## Run an MCMC. Because we are fitting six parameters to a tree with
> ## only 50 species, priors will be needed. I will use an exponential
> ## prior with rate 1/(2r), where r is the character independent
> ## diversificiation rate:
> prior <- make.prior.exponential(1 / (2 * (p[1] - p[3])))
>
> ## This takes quite a while to run, so is not run by default
> ## Not run:
> ##D tmp <- mcmc(lik, fit$par, nsteps=100, prior=prior, w=.1, print.every=0)
> ##D
> ##D w <- diff(sapply(tmp[2:7], range))
> ##D samples <- mcmc(lik, fit$par, nsteps=1000, prior=prior, w=w,
> ##D print.every=100)
> ##D
> ##D ## See profiles.plot for more information on plotting these
> ##D ## profiles.
> ##D col <- c("blue", "red")
> ##D profiles.plot(samples[c("lambda0", "lambda1")], col.line=col, las=1,
> ##D xlab="Speciation rate", legend="topright")
> ## End(Not run)
>
> ## BiSSE reduces to the birth-death model and Mk2 when diversification
> ## is state independent (i.e., lambda0 ~ lambda1 and mu0 ~ mu1).
> lik.mk2 <- make.mk2(phy, phy$tip.state)
> lik.bd <- make.bd(phy)
>
> ## 1. BiSSE / Birth-Death
> ## Set the q01 and q10 parameters to arbitrary numbers (need not be
> ## symmetric), and constrain the lambdas and mus to be the same for each
> ## state. The likelihood function now has just two parameters and
> ## will be proprtional to Nee's birth-death based likelihood:
> lik.bisse.bd <- constrain(lik,
+ lambda1 ~ lambda0, mu1 ~ mu0,
+ q01 ~ .01, q10 ~ .02)
> pars <- c(.1, .03)
> ## These differ by -167.3861 for both parameter sets:
> lik.bisse.bd(pars) - lik.bd(pars)
[1] -167.3861
> lik.bisse.bd(2*pars) - lik.bd(2*pars)
[1] -167.3861
>
> ## 2. BiSSE / Mk2
> ## Same idea as above: set all diversification parameters to arbitrary
> ## values (but symmetric this time):
> lik.bisse.mk2 <- constrain(lik,
+ lambda0 ~ .1, lambda1 ~ .1,
+ mu0 ~ .03, mu1 ~ .03)
> ## Differ by -150.4740 for both parameter sets.
> lik.bisse.mk2(pars) - lik.mk2(pars)
[1] -150.474
> lik.bisse.mk2(2*pars) - lik.mk2(2*pars)
[1] -150.474
>
> ## 3. Sampled BiSSE / Birth-Death
> ## Pretend that the tree is only .6 sampled:
> lik.bd2 <- make.bd(phy, sampling.f=.6)
> lik.bisse2 <- make.bisse(phy, phy$tip.state, sampling.f=c(.6, .6))
Warning in make.ode.deSolve(info, control) :
diversitree is not known to work with deSolve > 1.10.3
falling back on slow version
> lik.bisse2.bd <- constrain(lik.bisse2,
+ lambda1 ~ lambda0, mu1 ~ mu0,
+ q01 ~ .01, q10 ~ .01)
>
> ## Difference of -167.2876
> lik.bisse2.bd(pars) - lik.bd2(pars)
[1] -167.2876
> lik.bisse2.bd(2*pars) - lik.bd2(2*pars)
[1] -167.2876
>
> ## 4. Unresolved clade BiSSE / Birth-Death
> set.seed(1)
> unresolved <- data.frame(tip.label=I(sample(phy$tip.label, 5)),
+ Nc=sample(2:10, 5), n0=0, n1=0)
> unresolved.bd <- structure(unresolved$Nc, names=unresolved$tip.label)
> lik.bisse3 <- make.bisse(phy, phy$tip.state, unresolved)
Warning in make.ode.deSolve(info, control) :
diversitree is not known to work with deSolve > 1.10.3
falling back on slow version
> lik.bisse3.bd <- constrain(lik.bisse3,
+ lambda1 ~ lambda0, mu1 ~ mu0,
+ q01 ~ .01, q10 ~ .01)
> lik.bd3 <- make.bd(phy, unresolved=unresolved.bd)
>
> ## Difference of -167.1523
> lik.bisse3.bd(pars) - lik.bd3(pars)
At line 125 of file dsexpvi.f
Fortran runtime error: Index '212' of dimension 1 of array 'w' above upper bound of 211