* using log directory ‘/srv/hornik/tmp/CRAN/DImodelsMulti.Rcheck’ * using R Under development (unstable) (2024-01-14 r85805) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (3) Debian flang-new version 17.0.6 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘DImodelsMulti/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DImodelsMulti’ version ‘1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Laura Byrne ’ New submission Found the following (possibly) invalid URLs: URL: https://dimodels.com From: DESCRIPTION Status: Error Message: server certificate verification failed. CAfile: none CRLfile: none (Status without verification: OK) * 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 ‘DImodelsMulti’ can be installed ... [2s/2s] 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [4s/4s] 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [7s/7s] ERROR Running examples in ‘DImodelsMulti-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: simMV > ### Title: The simulated multivariate "simMV" dataset > ### Aliases: simMV > ### Keywords: datasets > > ### ** Examples > > ################################################################################################### > ################################################################################################### > > ## Don't show: > ## Set up for R markdown for crayon and cli output if user has packages installed > > if(requireNamespace("fansi", quietly = TRUE) & + requireNamespace("crayon", quietly = TRUE) & + requireNamespace("cli", quietly = TRUE)) + { + options(crayon.enabled = TRUE) + ansi_aware_handler <- function(x, options) + { + paste0( + "
",
+       fansi::sgr_to_html(x = x, warn = FALSE, term.cap = "256"),
+       "
" + ) + } + old_hooks <- fansi::set_knit_hooks(knitr::knit_hooks, + which = c("output", "message", "error", "warning")) + knitr::knit_hooks$set( + output = ansi_aware_handler, + message = ansi_aware_handler, + warning = ansi_aware_handler, + error = ansi_aware_handler + ) + } > ## End(Don't show) > > ## Modelling Example > > # For a more thorough example of the workflow of this package, please see vignette > # DImulti_workflow using the following code: > > ## Not run: > ##D vignette("DImodelsMulti") > ## End(Not run) > > # We use head() to view the dataset > head(simMV) plot p1 p2 p3 p4 p5 p6 treat Y1 Y2 Y3 Y4 1 1 1 0 0 0 0 0 0 1.880817 5.108158 -1.9712356 4.8247704 2 2 1 0 0 0 0 0 0 7.103477 5.183822 -4.0598298 3.1094539 3 3 0 1 0 0 0 0 0 -1.444736 6.900983 6.3342200 4.9055054 4 4 0 1 0 0 0 0 0 -1.756776 4.784160 5.2155726 5.3583856 5 5 0 0 1 0 0 0 0 5.311257 4.258924 -0.4694982 -2.3078377 6 6 0 0 1 0 0 0 0 5.975319 3.148215 1.9509040 -0.6064387 > > > # We can use the function DImulti() to fit a multivariate DI model, with an intercept for "treat" > # for each ecosystem function. The dataset is wide, so the Y columns are all entered through 'y' > # and the first index of eco_func is "NA". We fit the average interaction structure and use "ML" > # so that we can perform model comparisons with varying fixed effects > MVmodel <- DImulti(y = paste0("Y", 1:4), eco_func = c("NA", "UN"), unit_IDs = 1, + prop = paste0("p", 1:6), data = simMV, DImodel = "AV", extra_fixed = ~ treat, + method = "ML") > print(MVmodel) Note: Method Used = ML Correlation Structure Used = UN Average Term Model Theta value(s) = 1 Generalized least squares fit by maximum likelihood Model: value ~ 0 + func:((p1_ID + p2_ID + p3_ID + p4_ID + p5_ID + p6_ID + AV) + treat) AIC BIC logLik 5602.953 5827.104 -2759.476 Multivariate Correlation Structure: General Formula: ~0 | plot Parameter estimate(s): Correlation: 1 2 3 2 -0.108 3 -0.019 -0.033 4 0.041 0.241 -0.104 Table: Fixed Effect Coefficients Beta Std. Error t-value p-value Signif -------------- ------- ----------- -------- ----------- ------- funcY1:p1_ID +6.659 0.554 12.025 7.253e-32 *** funcY2:p1_ID +5.023 0.299 16.784 4.393e-58 *** funcY3:p1_ID -1.110 0.434 -2.557 0.01065 * funcY4:p1_ID +4.637 0.331 14.015 4.946e-42 *** funcY1:p2_ID -0.007 0.558 -0.013 0.9897 funcY2:p2_ID +4.288 0.301 14.229 3.382e-43 *** funcY3:p2_ID +4.405 0.437 10.082 3.539e-23 *** funcY4:p2_ID +5.353 0.333 16.070 9.468e-54 *** funcY1:p3_ID +6.948 0.597 11.640 4.808e-30 *** funcY2:p3_ID +4.395 0.323 13.624 6.109e-40 *** funcY3:p3_ID +1.325 0.468 2.831 0.004695 ** funcY4:p3_ID -0.614 0.357 -1.722 0.08536 + funcY1:p4_ID +2.581 0.545 4.733 2.422e-06 *** funcY2:p4_ID +1.993 0.295 6.763 1.93e-11 *** funcY3:p4_ID +5.873 0.427 13.745 1.384e-40 *** funcY4:p4_ID +5.400 0.326 16.577 8.141e-57 *** funcY1:p5_ID -1.034 0.581 -1.779 0.07552 + funcY2:p5_ID +4.733 0.314 15.070 6.646e-48 *** funcY3:p5_ID +1.448 0.455 3.180 0.001505 ** funcY4:p5_ID +7.225 0.347 20.810 9.933e-85 *** funcY1:p6_ID +4.374 0.533 8.203 4.99e-16 *** funcY2:p6_ID +7.332 0.288 25.441 4.79e-119 *** funcY3:p6_ID +6.508 0.418 15.571 8.463e-51 *** funcY4:p6_ID -0.146 0.319 -0.458 0.6471 funcY1:AV +2.215 1.085 2.041 0.04144 * funcY2:AV +7.502 0.586 12.791 1.228e-35 *** funcY3:AV +2.470 0.850 2.905 0.003727 ** funcY4:AV +0.037 0.648 0.058 0.9541 funcY1:treat1 +3.368 0.214 15.702 1.447e-51 *** funcY2:treat1 -0.449 0.116 -3.875 0.0001113 *** funcY3:treat1 +5.602 0.168 33.329 7.422e-183 *** funcY4:treat1 -1.002 0.128 -7.821 9.78e-15 *** Signif codes: 0-0.001 '***', 0.001-0.01 '**', 0.01-0.05 '*', 0.05-0.1 '+', 0.1-1.0 ' ' Degrees of freedom: 1536 total; 1504 residual Residual standard error: 2.079496 Marginal variance covariance matrix Y1 Y2 Y3 Y4 Y1 4.324300 -0.253190 -0.063976 0.10660 Y2 -0.253190 1.263000 -0.059597 0.33650 Y3 -0.063976 -0.059597 2.655800 -0.21084 Y4 0.106600 0.336500 -0.210840 1.54340 Standard Deviations: 2.0795 1.1238 1.6297 1.2423 > > # We can adjust the previous model to now cross "treat" with each other ID effect. We also specify > # different values of theta for each ecosystem function and use the "REML" method to get unbiased > # estimates. > > # We can now use any S3 method compatible with a gls object, for example, predict() > > predict(MVmodel_theta, newdata = simMV[which(simMV$plot == 1), ]) Error: object 'MVmodel_theta' not found Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [10s/10s] OK Running ‘testthat.R’ [10s/10s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/15s] OK * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character − (U+2212) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: There's no line here to end. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: There's no line here to end. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘DImodelsMulti-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 2 NOTEs