* using log directory 'd:/RCompile/CRANincoming/R-devel/cotram.Rcheck'
* using R Under development (unstable) (2024-07-15 r86902 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'cotram/DESCRIPTION' ... OK
* this is package 'cotram' version '0.5-0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [13s] NOTE
Maintainer: 'Sandra Siegfried <sandra.siegfried@alumni.uzh.ch>'
New maintainer:
Sandra Siegfried <sandra.siegfried@alumni.uzh.ch>
Old maintainer(s):
Sandra Siegfried <sandra.siegfried@uzh.ch>
* checking package namespace information ... OK
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* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
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* checking whether package 'cotram' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' 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 code 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
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* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
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* checking examples ... OK
* checking differences from 'cotram-Ex.Rout' to 'cotram-Ex.Rout.save' ... OK
157a158,239
> > ## No test:
> > m_PF <- cotram(Pardosa_ferruginea ~ Elevation + Canopy_openess,
> + data = spiders, method = "probit", order = OR)
> Model was fitted to log(Pardosa_ferruginea + 1).
> > m_HL <- cotram(Harpactea_lepida ~ Elevation + Canopy_openess,
> + data = spiders, method = "probit", order = OR)
> Model was fitted to log(Harpactea_lepida + 1).
> > m_CC <- cotram(Callobius_claustrarius ~ Elevation + Canopy_openess,
> + data = spiders, method = "probit", order = OR)
> Model was fitted to log(Callobius_claustrarius + 1).
> > m_CT <- cotram(Coelotes_terrestris ~ Elevation + Canopy_openess,
> + data = spiders, method = "probit", order = OR)
> Model was fitted to log(Coelotes_terrestris + 1).
> > m_PL <- cotram(Pardosa_lugubris ~ Elevation + Canopy_openess,
> + data = spiders, method = "probit", order = OR)
> Model was fitted to log(Pardosa_lugubris + 1).
> > m_PR <- cotram(Pardosa_riparia ~ Elevation + Canopy_openess,
> + data = spiders, method = "probit", order = OR)
> Model was fitted to log(Pardosa_riparia + 1).
> >
> > ### fit dependence parameters
> > mm <- mcotram(m_PF, m_HL, m_CC, m_CT, m_PL, m_PR, data = spiders,
> + M = M, scale = TRUE)
> > logLik(mm)
> 'log Lik.' -2476.198 (df=39)
> >
> > ### Kendall's tau: Dependence of species after accounting
> > ### for elevation and canopy openess in marginal models
> > coef(mm, type = "Kendall")
> , , 1
>
> Pardosa_ferruginea Harpactea_lepida
> Pardosa_ferruginea 1.0000000 -0.25500654
> Harpactea_lepida -0.2550065 1.00000000
> Callobius_claustrarius 0.1486198 -0.15465885
> Coelotes_terrestris 0.4277688 -0.36502236
> Pardosa_lugubris -0.3158523 0.43608652
> Pardosa_riparia 0.1069219 -0.08780907
> Callobius_claustrarius Coelotes_terrestris
> Pardosa_ferruginea 0.14861978 0.42776881
> Harpactea_lepida -0.15465885 -0.36502236
> Callobius_claustrarius 1.00000000 0.06773758
> Coelotes_terrestris 0.06773758 1.00000000
> Pardosa_lugubris -0.20091535 -0.49275900
> Pardosa_riparia 0.26841797 0.10070886
> Pardosa_lugubris Pardosa_riparia
> Pardosa_ferruginea -0.3158523 0.10692192
> Harpactea_lepida 0.4360865 -0.08780907
> Callobius_claustrarius -0.2009153 0.26841797
> Coelotes_terrestris -0.4927590 0.10070886
> Pardosa_lugubris 1.0000000 -0.15911185
> Pardosa_riparia -0.1591119 1.00000000
>
> >
> > ### regress dependencies on elevation and canopy openess
> > mmc <- mcotram(m_PF, m_HL, m_CC, m_CT, m_PL, m_PR, data = spiders,
> + formula = ~ Elevation + Canopy_openess, M = M, scale = TRUE)
> > logLik(mmc)
> 'log Lik.' -2452.546 (df=69)
> >
> > ### weak evidence for such effects
> > pchisq(2 * (logLik(mmc) - logLik(mm)), df = 30, lower.tail = FALSE)
> 'log Lik.' 0.02323324 (df=69)
> >
> > ### plot Kendall's tau for different elevations / openess levels
> > nd <- expand.grid(Elevation = 80:120 * 10, Canopy_openess = 1:10 * 10)
> > KD <- Lower_tri(coef(mmc, newdata = nd, type = "Kendall"))
> > f <- factor(rownames(KD))
> > nd <- cbind(f = rep(f, nrow(nd)), nd[rep(1:nrow(nd), each = nlevels(f)),])
> > nd$KD <- c(KD)
> >
> > if (require("lattice")) {
> + contourplot(KD ~ Elevation + Canopy_openess | f, data = nd,
> + cuts = 18, xlab = "Elevation", ylab = "Canopy openess")
> + }
> >
> > ### for example:
> > ### => constant negative dependence of Pardosa_lugubris and Coelotes_terrestris
> > ### => weak dependence of Harpactea_lepida and Pardosa_ferruginea
> > ### for low elevations, negative dependence increasing with elevation
> >
> > ## End(No test)
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [22s] OK
Running 'checks-Ex.R'
Running 'confband-Ex.R'
Comparing 'confband-Ex.Rout' to 'confband-Ex.Rout.save' ... OK
Running 'models-Ex.R' [11s]
Running 'predict-Ex.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [56s] OK
* checking PDF version of manual ... [28s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 NOTE