tests/testthat/fixtures/README.md

In beaver: Bayesian Model Averaging of Covariate Adjusted Negative-Binomial Dose-Response

I attest that all .Rdata and .rds files in this directory are generated and in no way use real study data. They are created by running the three .R files in this directory in the following order:

1. make-nb_datasets.R This program creates negative binomially distributed datasets (without and with covariates) that reflect a dose response.

2. make-nb_mcmc+_objects.R This program fits the datasets generated in step 1 to various (individual) dose-response models using rjags.

3. make-nb_bma_objects.R This program takes the results from step 2 to produce Bayesian Model Averaged objects/results.

Note that the files produced by make-nb_bma_objects.R may show up as superficially different when the code is re-executed. To verify that the content of files (produced by all three R programs) is effectively identical, run the following code:

# Load old data
pkgload::load_all() # from the root directory of the {beaver} source code
env_old <- new.env()
for (file in list.files("tests/testthat/fixtures", pattern = "\\.Rdata$", full.names = TRUE)) {
  load(file, envir = env_old)
}
for (file in list.files("tests/testthat/fixtures", pattern = "\\.rds$", full.names = TRUE)) {
  env_old[[basename(file)]] <- readRDS(file)
}

# Remove old data
unlink(file.path("tests/testthat/fixtures", c("*.Rdata", "*.rds")))

# Recompute data
source("tests/testthat/fixtures/make-nb_datasets.R")
source("tests/testthat/fixtures/make-nb_mcmc+_objects.R")
source("tests/testthat/fixtures/make-nb_bma_objects.R")

# Load new data
env_new <- new.env()
for (file in list.files("tests/testthat/fixtures", pattern = "\\.Rdata$", full.names = TRUE)) {
  load(file, envir = env_new)
}
for (file in list.files("tests/testthat/fixtures", pattern = "\\.rds$", full.names = TRUE)) {
  env_new[[basename(file)]] <- readRDS(file)
}

# Compare data
stopifnot(all(names(env_new) == names(env_old)))
for (name in names(env_new)) {
  stopifnot(identical(env_new[[name]], env_old[[name]]))
}

For reference:

> sessionInfo()
R version 4.2.2 Patched (2022-11-30 r83413)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: [redacted]

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] beaver_0.2.0-1 testthat_3.1.5

loaded via a namespace (and not attached):
 [1] pkgload_1.3.2     tidyr_1.2.1       brio_1.1.3        shiny_1.7.3      
 [5] assertthat_0.2.1  diffobj_0.3.5     remotes_2.4.2     sessioninfo_1.2.2
 [9] pillar_1.8.1      backports_1.4.1   lattice_0.20-45   glue_1.6.2       
[13] digest_0.6.30     promises_1.2.0.1  checkmate_2.1.0   colorspace_2.0-3 
[17] htmltools_0.5.4   httpuv_1.6.6      pkgconfig_2.0.3   devtools_2.4.5   
[21] purrr_0.3.5       xtable_1.8-4      scales_1.2.1      processx_3.8.0   
[25] rjags_4-13        later_1.3.0       tibble_3.1.8      generics_0.1.3   
[29] ggplot2_3.4.0     usethis_2.1.6     ellipsis_0.3.2    cachem_1.0.6     
[33] withr_2.5.0       lazyeval_0.2.2    cli_3.4.1         magrittr_2.0.3   
[37] crayon_1.5.2      mime_0.12         memoise_2.0.1     evaluate_0.18    
[41] ps_1.7.2          fs_1.5.2          fansi_1.0.3       xml2_1.3.3       
[45] pkgbuild_1.4.0    rsconnect_0.8.28  profvis_0.3.7     tools_4.2.2      
[49] prettyunits_1.1.1 cyclocomp_1.1.0   lifecycle_1.0.3   stringr_1.5.0    
[53] munsell_0.5.0     callr_3.7.3       rex_1.2.1         compiler_4.2.2   
[57] covr_3.6.1        rlang_1.0.6       grid_4.2.2        rstudioapi_0.14  
[61] htmlwidgets_1.5.4 miniUI_0.1.1.1    rmarkdown_2.18    waldo_0.4.0      
[65] yodel_1.0.0       gtable_0.3.1      DBI_1.1.3         rematch2_2.1.2   
[69] R6_2.5.1          knitr_1.41        dplyr_1.0.10      fastmap_1.1.0    
[73] utf8_1.2.2        rprojroot_2.0.3   lintr_3.0.2       desc_1.4.2       
[77] stringi_1.7.8     Rcpp_1.0.9        vctrs_0.5.1       xfun_0.35        
[81] tidyselect_1.2.0  urlchecker_1.0.1  coda_0.19-4      

-Hollins Showalter ([e-mail])

beaver documentation built on May 29, 2024, 1:49 a.m.