knitr::opts_chunk$set(comment = NA)
library(broom)
library(car)
library(emmeans)
library(Epi)
library(fivethirtyeight)
library(GGally)
library(ggdist)
library(ggpubr)
library(ggstatsplot)
library(glue)
library(haven)
library(infer)
library(janitor)
library(knitr)
library(medicaldata)
library(mice)
library(MKinfer)
library(naniar)
library(olsrr)
library(palmerpenguins)
library(patchwork)
library(readxl)
library(rstanarm)
library(styler)
library(tidytuesdayR)
library(xfun)
library(easystats)
library(tidyverse)Appendix A — R Packages
A.1 R Packages used in this book
Here is a list of the R packages that are used in this book.
| Chapters | Package | Description | Reference(s) |
|---|---|---|---|
| 16, 18, 21 | broom | Summarize key information about models into tibbles | Website |
| 7, 9, 16, 18, 20-21 | car | Box-Cox transformations, Companion to Applied Regression |
PDF manual, related book |
| 13 | Epi | twoby2(), Epidemiological Analysis with R | Website |
| Appendix | fivethirtyeight | bechdel data set | Website |
| 10, 18 | GGally | scatterplot matrix through ggpairs() | Website |
| 2, 6-9 | ggdist | Rain cloud plots, Visualizations of distributions and uncertainty | Website |
| 2, 10 | ggpubr | add fitted equation to scatterplot | Website |
| 10 | ggstatsplot | Adding Summaries to ggplot-based plots | Website |
| 20-21 | glmnet | LASSO and Elastic Net models | Website |
| 2, 10-11 | glue | working with strings and R results | Website |
| 11-12, 15, 20 | haven | read and write various data formats | Website |
| 5-7 | infer | tidy statistical inference | Website |
| 2-4, 7-11, 14, 16, 19-21 | janitor | clean_names(), tabyl(), for cleaning and exploring | Overview |
| 2-22 | knitr | kable(), report generation | Website |
| 13 | medicaldata | data sets for teaching reproducible medical research | Website |
| 16, 21-22 | mice | Multivariate Imputation by Chained Equations | Website, van Buuren (2021) |
| 6-7 | MKinfer | bootstrap testing | Website |
| 2-3, 5, 7-22 | naniar | Tidy ways to summarize missingness | Website |
| 19-21 | olsrr | building OLS models, including best subsets | Website |
| 2-3 | palmerpenguins | Palmer Penguins data | Website, Horst, Hill, and Gorman (2020) |
| 2, 5-7, 9-11, 15-16, 20-21 | patchwork | Combining separate ggplots into one graphic | Website |
| 6 | readxl | get data out of Excel and into R | Website |
| 5-11, 15-22 | rstanarm | Bayesian Applied Regression Modeling via STAN | Website |
| all | styler | non-invasive code formatting for pretty printing | Website Tidyverse Style Guide |
| 18 | tidytuesdayR | access data from Tidy Tuesday repository | Website |
| Appendix | xfun | for session information, Section A.3 | Website |
A.1.1 Meta-packages
| Chapters | Meta-Package | Description | Reference(s) |
|---|---|---|---|
| 2-22 | easystats | An R Framework for Easy Statistical Modeling, Visualization and Reporting | Website, Lüdecke et al. (2022) |
| 2-22 | tidyverse | R packages for Data Science | Website |
A.2 Loading all of these R packages
A.3 Session Information
xfun::session_info()R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)
Locale:
LC_COLLATE=English_United States.utf8
LC_CTYPE=English_United States.utf8
LC_MONETARY=English_United States.utf8
LC_NUMERIC=C
LC_TIME=English_United States.utf8
Package version:
abind_1.4-8 afex_1.4.1 arrangements_1.1.9
askpass_1.2.1 backports_1.5.0 base64enc_0.1-3
BayesFactor_0.9.12.4.7 bayesplot_1.13.0 bayestestR_0.16.1
BH_1.87.0.1 bit_4.6.0 bit64_4.6.0.1
blob_1.2.4 boot_1.3-31 broom_1.0.9
bslib_0.9.0 BWStest_0.2.3 cachem_1.1.0
callr_3.7.6 car_3.1-3 carData_3.0-5
cellranger_1.1.0 checkmate_2.3.2 cli_3.6.5
clipr_0.8.0 cmprsk_2.2-12 coda_0.19-4.1
codetools_0.2-20 colourpicker_1.3.0 commonmark_2.0.0
compiler_4.5.1 conflicted_1.2.0 contfrac_1.1.12
correlation_0.8.8 corrplot_0.95 cowplot_1.2.0
cpp11_0.5.2 crayon_1.5.3 crosstalk_1.2.1
curl_6.4.0 data.table_1.17.8 datasets_4.5.1
datawizard_1.2.0 DBI_1.2.3 dbplyr_2.5.0
Deriv_4.2.0 desc_1.4.3 deSolve_1.40
digest_0.6.37 distributional_0.5.0 doBy_4.7.0
dplyr_1.1.4 DT_0.33 dtplyr_1.3.1
dygraphs_1.1.1.6 easystats_0.7.5 effectsize_1.0.1
elliptic_1.4.0 emmeans_1.11.2 Epi_2.60
estimability_1.5.1 etm_1.1.2 evaluate_1.0.4
exactRankTests_0.8-35 farver_2.1.2 fastmap_1.2.0
fivethirtyeight_0.6.2 fontawesome_0.5.3 forcats_1.0.0
foreach_1.5.2 Formula_1.2-5 fs_1.6.6
gargle_1.5.2 generics_0.1.4 GGally_2.3.0
ggcorrplot_0.1.4.1 ggdist_3.3.3 ggplot2_3.5.2
ggpubr_0.6.1 ggrepel_0.9.6 ggridges_0.5.6
ggsci_3.2.0 ggside_0.3.1 ggsignif_0.6.4
ggstats_0.10.0 ggstatsplot_0.13.1 gh_1.5.0
gitcreds_0.1.2 glmnet_4.1-10 glue_1.8.0
gmp_0.7-5 goftest_1.2-3 googledrive_2.1.1
googlesheets4_1.1.1 graphics_4.5.1 grDevices_4.5.1
grid_4.5.1 gridExtra_2.3 gtable_0.3.6
gtools_3.9.5 haven_2.5.5 highr_0.11
hms_1.1.3 htmltools_0.5.8.1 htmlwidgets_1.6.4
httpuv_1.6.16 httr_1.4.7 httr2_1.2.1
hypergeo_1.2.14 ids_1.0.1 igraph_2.1.4
infer_1.0.9 ini_0.3.1 inline_0.3.21
insight_1.3.1 isoband_0.2.7 iterators_1.0.14
janitor_2.2.1 jomo_2.7-6 jquerylib_0.1.4
jsonlite_2.0.0 knitr_1.50 kSamples_1.2.10
labeling_0.4.3 later_1.4.2 lattice_0.22-7
lazyeval_0.2.2 lifecycle_1.0.4 litedown_0.7
lme4_1.1-37 lmerTest_3.1.3 loo_2.8.0
lubridate_1.9.4 magrittr_2.0.3 markdown_2.0
MASS_7.3-65 Matrix_1.7-3 MatrixModels_0.5.4
matrixStats_1.5.0 medicaldata_0.2.0 memoise_2.0.1
methods_4.5.1 mgcv_1.9-3 mice_3.18.0
miceadds_3.17-44 microbenchmark_1.5.0 mime_0.13
miniUI_0.1.2 minqa_1.2.8 mitml_0.4-5
mitools_2.4 MKdescr_0.8 MKinfer_1.2
modelbased_0.12.0 modelr_0.1.11 multcomp_1.4-28
multcompView_0.1.10 mvtnorm_1.3-3 naniar_1.1.0
nlme_3.1-168 nloptr_2.2.1 nnet_7.3-20
norm_1.0.11.1 nortest_1.0-4 numDeriv_2016.8-1.1
olsrr_0.6.1 openssl_2.3.3 ordinal_2023.12.4.1
paletteer_1.6.0 palmerpenguins_0.1.1 pan_1.9
parallel_4.5.1 parameters_0.27.0 patchwork_1.3.1
pbapply_1.7.4 pbkrtest_0.5.5 performance_0.15.0
pillar_1.11.0 pkgbuild_1.4.8 pkgconfig_2.0.3
plyr_1.8.9 PMCMRplus_1.9.12 polynom_1.4.1
posterior_1.6.1 prettyunits_1.2.0 prismatic_1.1.2
processx_3.8.6 progress_1.2.3 promises_1.3.3
ps_1.9.1 purrr_1.1.0 quadprog_1.5.8
quantreg_6.1 QuickJSR_1.8.0 R.cache_0.17.0
R.methodsS3_1.8.2 R.oo_1.27.1 R.utils_2.13.0
R6_2.6.1 ragg_1.4.0 rappdirs_0.3.3
rbibutils_2.3 RColorBrewer_1.1-3 Rcpp_1.1.0
RcppArmadillo_14.6.0.1 RcppEigen_0.3.4.0.2 RcppParallel_5.1.10
Rdpack_2.6.4 readr_2.1.5 readxl_1.4.5
reformulas_0.4.1 rematch_2.0.0 rematch2_2.1.2
report_0.6.1 reprex_2.1.1 reshape_0.8.10
reshape2_1.4.4 rlang_1.1.6 rmarkdown_2.29
Rmpfr_1.1.1 rpart_4.1.24 rprojroot_2.1.0
rstan_2.32.7 rstanarm_2.32.1 rstantools_2.4.0
rstatix_0.7.2 rstudioapi_0.17.1 rvest_1.0.4
S7_0.2.0 sandwich_3.1-1 sass_0.4.10
scales_1.4.0 see_0.11.0 selectr_0.4.2
shape_1.4.6.1 shiny_1.11.1 shinyjs_2.1.0
shinystan_2.6.0 shinythemes_1.2.0 snakecase_0.11.1
sourcetools_0.1.7.1 SparseM_1.84.2 splines_4.5.1
StanHeaders_2.32.10 stats_4.5.1 stats4_4.5.1
statsExpressions_1.7.1 stringi_1.8.7 stringr_1.5.1
styler_1.10.3 SuppDists_1.1.9.9 survival_3.8-3
sys_3.4.3 systemfonts_1.2.3 tensorA_0.36.2.1
textshaping_1.0.1 TH.data_1.1-3 threejs_0.3.4
tibble_3.3.0 tidyr_1.3.1 tidyselect_1.2.1
tidytuesdayR_1.2.1 tidyverse_2.0.0 timechange_0.3.0
tinytex_0.57 tools_4.5.1 tzdb_0.5.0
ucminf_1.2.2 UpSetR_1.4.0 utf8_1.2.6
utils_4.5.1 uuid_1.2.1 V8_6.0.5
vctrs_0.6.5 viridis_0.6.5 viridisLite_0.4.2
visdat_0.6.0 vroom_1.6.5 withr_3.0.2
WRS2_1.1.7 xfun_0.52 xml2_1.3.8
xplorerr_0.2.0 xtable_1.8-4 xts_0.14.1
yaml_2.3.10 zeallot_0.2.0 zoo_1.8-14