Last updated on 2026-06-08 00:52:03 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.3 | 133.45 | 152.39 | 285.84 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.3 | 106.96 | 106.02 | 212.98 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.3 | 163.00 | 543.23 | 706.23 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.3 | 274.00 | 577.57 | 851.57 | OK | |
| r-devel-windows-x86_64 | 1.1.3 | 147.00 | 178.00 | 325.00 | OK | |
| r-patched-linux-x86_64 | 1.1.3 | 127.98 | 138.54 | 266.52 | OK | |
| r-release-linux-x86_64 | 1.1.3 | 141.45 | 140.21 | 281.66 | OK | |
| r-release-macos-arm64 | 1.1.3 | 32.00 | 118.00 | 150.00 | OK | |
| r-release-macos-x86_64 | 1.1.3 | 95.00 | 500.00 | 595.00 | OK | |
| r-release-windows-x86_64 | 1.1.3 | 159.00 | 202.00 | 361.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.3 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.3 | 77.00 | 170.00 | 247.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.3 | 180.00 | 245.00 | 425.00 | OK |
Version: 1.1.3
Check: examples
Result: ERROR
Running examples in ‘phyr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pglmm_compare
> ### Title: Phylogenetic Generalized Linear Mixed Model for Comparative Data
> ### Aliases: pglmm_compare
> ### Keywords: regression
>
> ### ** Examples
>
>
> ## Illustration of `pglmm_compare` with simulated data
>
> # Generate random phylogeny
>
> library(ape)
>
> n <- 100
> phy <- compute.brlen(rtree(n=n), method = "Grafen", power = 1)
>
> # Generate random data and standardize to have mean 0 and variance 1
> X1 <- rTraitCont(phy, model = "BM", sigma = 1)
> X1 <- (X1 - mean(X1))/var(X1)
>
> # Simulate binary Y
> sim.dat <- data.frame(Y = array(0, dim = n), X1 = X1, row.names = phy$tip.label)
> sim.dat$Y <- ape::binaryPGLMM.sim(Y ~ X1, phy = phy, data=sim.dat, s2 = 1,
+ B = matrix(c(0, .25), nrow = 2, ncol = 1),
+ nrep = 1)$Y
>
> # Fit model
> pglmm_compare(Y ~ X1, family = "binomial", phy = phy, data = sim.dat)
Warning: the ‘nobars’ function has moved to the reformulas package. Please update your imports, or ask an upstream package maintainer to do so.
This warning is displayed once per session.
'as(<matrix>, "dgTMatrix")' is deprecated.
Use 'as(as(as(., "dMatrix"), "generalMatrix"), "TsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Generalized linear mixed model for binomial data fit by restricted maximum likelihood
Call:Y ~ X1
logLik AIC BIC
-57.6 123.2 129.0
Phylogenetic random effects variance (s2):
Variance Std.Dev
s2 0.004683 0.06844
Fixed effects:
Value Std.Error Zscore Pvalue
(Intercept) 0.99975 0.28540 3.503 0.0004601 ***
X1 0.24034 0.28510 0.843 0.3992317
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> # Compare with `binaryPGLMM`
> ape::binaryPGLMM(Y ~ X1, phy = phy, data = sim.dat)
Call:Y ~ X1
Random effect (phylogenetic signal s2):
s2 Pr
1 0.04448 0.4384
Fixed effects:
Value Std.Error Zscore Pvalue
(Intercept) 1.00516 0.25935 3.8757 0.0001063 ***
X1 0.26456 0.26826 0.9862 0.3240275
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> # Compare with `phyloglm`
> summary(phylolm::phyloglm(Y ~ X1, phy = phy, data = sim.dat))
Call:
phylolm::phyloglm(formula = Y ~ X1, data = sim.dat, phy = phy)
AIC logLik Pen.logLik
150.11 -72.06 -71.57
Method: logistic_MPLE
Mean tip height: 1
Parameter estimate(s):
alpha: 0.8193869
Coefficients:
Estimate StdErr z.value p.value
(Intercept) 2.25302 1.25590 1.7939 0.07282 .
X1 1.78038 0.77642 2.2931 0.02184 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Note: Wald-type p-values for coefficients, conditional on alpha=0.8193869
>
> # Compare with `glm` that does not account for phylogeny
> summary(glm(Y ~ X1, data = sim.dat, family = "binomial"))
Call:
glm(formula = Y ~ X1, family = "binomial", data = sim.dat)
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.0119 0.2287 4.424 9.67e-06 ***
X1 0.2945 0.2469 1.192 0.233
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 116.65 on 99 degrees of freedom
Residual deviance: 115.20 on 98 degrees of freedom
AIC: 119.2
Number of Fisher Scoring iterations: 4
>
> # Compare with logistf() that does not account
> # for phylogeny but is less biased than glm()
> logistf::logistf(Y ~ X1, data = sim.dat)
Error in loadNamespace(x) : there is no package called ‘logistf’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc