* using log directory ‘/srv/hornik/tmp/CRAN/cotram.Rcheck’ * using R Under development (unstable) (2024-07-15 r86902) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (1+b1) Debian flang-new version 18.1.8 (1+b1) * running under: Debian GNU/Linux trixie/sid * 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 ... [4s/6s] NOTE Maintainer: ‘Sandra Siegfried ’ New maintainer: Sandra Siegfried Old maintainer(s): Sandra Siegfried * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cotram’ can be installed ... [4s/4s] 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [2s/2s] 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 ... [9s/9s] OK Running ‘checks-Ex.R’ [1s/1s] Running ‘confband-Ex.R’ [2s/2s] Comparing ‘confband-Ex.Rout’ to ‘confband-Ex.Rout.save’ ... OK Running ‘models-Ex.R’ [4s/4s] Running ‘predict-Ex.R’ [2s/2s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/16s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE