knitr::opts_chunk$set(comment = NA)
library(broom)
library(car)
library(DescTools)
library(Epi)
library(fivethirtyeight)
library(GGally)
library(glmnet)
library(ggdist)
library(ggmice)
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) |
|---|---|---|---|
| 17, 19, 22 | broom | Summarize key information about models into tibbles | Website |
| 7, 9, 17, 19-22 | car | Box-Cox transformations, Companion to Applied Regression |
PDF manual, related book |
| 9 | DescTools | Bonferroni and Tukey HSD CIs after ANOVA | Website |
| 13 | Epi | twoby2(), Epidemiological Analysis with R | Website |
| Appendix | fivethirtyeight | bechdel data set | Website |
| 10, 19 | GGally | scatterplot matrix through ggpairs() | Website |
| 2, 6-9 | ggdist | Rain cloud plots, Visualizations of distributions and uncertainty | Website |
| 22 | ggmice | Visualizations for mice with ggplot2 | Website |
| 2, 10 | ggpubr | add fitted equation to scatterplot | Website |
| 10 | ggstatsplot | Adding Summaries to ggplot-based plots | Website |
| 21-22 | glmnet | LASSO and Elastic Net models | Website |
| 2, 10-11 | glue | working with strings and R results | Website |
| 11, 16, 21 | haven | read and write various data formats | Website |
| 5-7 | infer | tidy statistical inference | Website |
| 2-4, 7-11, 14, 17, 20-22 | janitor | clean_names(), tabyl(), for cleaning and exploring | Overview |
| 2-11, 13-14, 15-22 | knitr | kable(), report generation | Website |
| 13 | medicaldata | data sets for teaching reproducible medical research | Website |
| 17, 22 | mice | Multivariate Imputation by Chained Equations | Website, van Buuren (2021) |
| 6-7 | MKinfer | bootstrap testing | Website |
| 2-3, 5, 7-11, 13-14, 15-22 | naniar | Tidy ways to summarize missingness | Website |
| 20-22 | olsrr | building OLS models, including best subsets | Website |
| 2-3 | palmerpenguins | Palmer Penguins data | Website, Horst et al. (2020) |
| 2, 5-7, 9-11, 16-17, 21-22 | patchwork | Combining separate ggplots into one graphic | Website |
| 15 | pwr | Basic functions for power analysis | Website |
| 6 | readxl | get data out of Excel and into R | Website |
| 5-11, 16-22 | rstanarm | Bayesian Applied Regression Modeling via STAN | Website |
| all | styler | non-invasive code formatting for pretty printing | Website Tidyverse Style Guide |
| 19 | 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) |
|---|---|---|---|
| 2-11, 13-14, 15-22 | easystats | An R Framework for Easy Statistical Modeling, Visualization and Reporting | Website, Lüdecke et al. (2022) |
| 2-11, 13-14, 15-22 | tidyverse | R packages for Data Science | Website |
A.2 Loading all of these R packages
A.3 Session Information
xfun::session_info()R version 4.6.1 (2026-06-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
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_1.5.1 arrangements_1.1.10
askpass_1.2.1 backports_1.5.1 base_4.6.1
base64enc_0.1-6 BayesFactor_0.9.12.4.8 bayesplot_1.15.0
bayestestR_0.18.1 BH_1.90.0.1 bit_4.6.0
bit64_4.8.2 blob_1.3.0 boot_1.3-32
broom_1.0.13 bslib_0.11.0 BWStest_0.2.3
cachem_1.1.0 callr_3.8.0 car_3.1-5
carData_3.0-6 cellranger_1.1.0 checkmate_2.3.4
class_7.3-23 cli_3.6.6 clipr_0.8.1
cmprsk_2.2-12 coda_0.19-4.1 codetools_0.2-20
colorspace_2.1.3 colourpicker_1.3.0 commonmark_2.0.0
compiler_4.6.1 conflicted_1.2.0 contfrac_1.1.12
correlation_0.8.8 corrplot_0.95 cowplot_1.2.0
cpp11_0.5.5 crayon_1.5.3 crosstalk_1.2.2
curl_7.1.0 data.table_1.18.4 datasets_4.6.1
datawizard_1.3.1 DBI_1.3.0 dbplyr_2.6.0
Deriv_4.3.0 desc_1.4.3 DescTools_0.99.60
deSolve_1.42 digest_0.6.39 distributional_0.8.1
doBy_4.7.2 dplyr_1.2.1 DT_0.34.0
dtplyr_1.3.3 dygraphs_1.1.1.6 e1071_1.7-17
easystats_0.7.6 effectsize_1.0.3 elliptic_1.5.1
emmeans_2.0.4 Epi_2.65 estimability_2.0.0
etm_1.1.2 evaluate_1.0.5 Exact_3.3
exactRankTests_0.8-37 expm_1.0-0 farver_2.1.2
fastmap_1.2.0 fivethirtyeight_0.6.2 fontawesome_0.5.3
forcats_1.0.1 foreach_1.5.2 forecast_9.0.2
Formula_1.2-5 fracdiff_1.5.4 fs_2.1.0
gargle_1.6.1 generics_0.1.4 GGally_2.4.0
ggcorrplot_0.3.0 ggdist_3.3.3 ggmice_0.1.1
ggplot2_4.0.3 ggpubr_1.0.0 ggrepel_0.9.8
ggridges_0.5.7 ggsci_5.2.0 ggside_0.4.1
ggsignif_0.6.4 ggstats_0.13.0 ggstatsplot_1.0.0
gh_1.6.1 gitcreds_0.1.2 gld_2.6.8
glmnet_5.0 glue_1.8.1 gmp_0.7-5.1
goftest_1.2-3 googledrive_2.1.2 googlesheets4_1.1.2
graphics_4.6.1 grDevices_4.6.1 grid_4.6.1
gridExtra_2.3.1 gtable_0.3.6 gtools_3.9.5
haven_2.5.5 highr_0.12 hms_1.1.4
htmltools_0.5.9 htmlwidgets_1.6.4 httpuv_1.6.17
httr_1.4.8 httr2_1.3.0 hypergeo_1.2.14
ids_1.0.1 igraph_2.3.3 infer_1.1.0
ini_0.3.1 inline_0.3.21 insight_1.5.2
isoband_0.3.0 iterators_1.0.14 janitor_2.2.1
jomo_2.7-6 jquerylib_0.1.4 jsonlite_2.0.0
knitr_1.51 kSamples_1.2.12 labeling_0.4.3
later_1.4.8 lattice_0.22-9 lazyeval_0.2.3
lifecycle_1.0.5 litedown_0.10 lme4_2.0-6
lmerTest_3.2.1 lmom_3.3 lmtest_0.9.40
loo_2.10.1 lubridate_1.9.5 magrittr_2.0.5
markdown_2.0 MASS_7.3-66 Matrix_1.7-6
MatrixModels_0.5.4 matrixStats_1.5.0 medicaldata_0.2.0
memoise_2.0.1 methods_4.6.1 mgcv_1.9-4
mice_3.19.0 miceadds_3.20-10 mime_0.13
miniUI_0.1.2 minqa_1.2.8 mitml_0.4-5
mitools_2.4 MKdescr_0.9 MKinfer_1.3
modelbased_0.16.0 modelr_0.1.11 multcomp_1.4-31
multcompView_0.1.12 mvtnorm_1.4-2 naniar_1.1.0
nlme_3.1-170 nloptr_2.2.1 nnet_7.3-20
norm_1.0.11.1 nortest_1.0-4 numDeriv_2016.8-1.1
olsrr_0.7.0 openssl_2.4.2 ordinal_2026.7.26
otel_0.2.0 paletteer_1.7.0 palmerpenguins_0.1.1
pan_2.0 parallel_4.6.1 parameters_0.29.2
patchwork_1.3.2 pbapply_1.7.4 pbkrtest_0.5.5
performance_0.17.1 pillar_1.11.1 pkgbuild_1.4.8
pkgconfig_2.0.3 plyr_1.8.9 PMCMRplus_1.9.12
polynom_1.4.1 posterior_1.7.0 prettyunits_1.2.0
prismatic_1.1.2 processx_3.9.0 progress_1.2.3
promises_1.5.0 proxy_0.4-29 ps_1.9.3
purrr_1.2.2 quadprog_1.5.8 quantreg_6.1
QuickJSR_1.10.0 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_1.5.2 rappdirs_0.3.4 rbibutils_2.4.1
RColorBrewer_1.1-3 Rcpp_1.1.2 RcppArmadillo_15.4.2.1
RcppEigen_0.3.4.0.2 RcppParallel_6.2.0 Rdpack_2.6.6
readr_2.2.0 readxl_1.5.0 reformulas_0.4.4
rematch_2.0.0 rematch2_2.1.2 report_0.6.4
reprex_2.1.1 reshape_0.8.10 reshape2_1.4.5
rlang_1.3.0 rmarkdown_2.31 Rmpfr_1.1.2
rootSolve_1.8.2.4 rpart_4.1.27 rprojroot_2.1.1
rstan_2.32.7 rstanarm_2.32.2 rstantools_2.7.0
rstatix_1.1.0 rstudioapi_0.19.0 rvest_1.0.5
S7_0.2.2 sandwich_3.1-2 sass_0.4.10
scales_1.4.0 see_0.14.1 selectr_0.6.0
shape_1.4.6.1 shiny_1.14.0 shinyjs_2.1.1
shinystan_2.7.0 shinythemes_1.2.0 snakecase_0.11.1
sourcetools_0.1.7.2 SparseM_1.84.2 splines_4.6.1
StanHeaders_2.32.10 stats_4.6.1 stats4_4.6.1
statsExpressions_2.0.0 stbl_0.4.0 stringi_1.8.7
stringr_1.6.0 styler_1.11.0 SuppDists_1.1.9.9
survival_3.8-9 sys_3.4.3 systemfonts_1.3.2
tensorA_0.36.2.1 textshaping_1.0.5 TH.data_1.1-5
threejs_0.3.4 tibble_3.3.1 tidyr_1.3.2
tidyselect_1.2.1 tidytuesdayR_1.3.2 tidyverse_2.0.0
timechange_0.4.0 timeDate_4052.112 tinytex_0.60
tools_4.6.1 tzdb_0.5.0 ucminf_1.2.3
UpSetR_1.4.1 urca_1.3.4 utf8_1.2.6
utils_4.6.1 uuid_1.2.2 V8_8.2.0
vctrs_0.7.3 viridis_0.6.5 viridisLite_0.4.3
visdat_0.6.0 vroom_1.7.1 withr_3.0.3
WRS2_1.1.7 xfun_0.60 xml2_1.6.0
xplorerr_0.2.0 xtable_1.8-8 xts_0.14.2
yaml_2.3.12 zoo_1.9-0