knitr::opts_chunk$set(comment = NA)
library(broom)
library(car)
library(emmeans)
library(Epi)
library(fivethirtyeight)
library(GGally)
library(ggdist)
library(ggpubr)
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) |
|---|---|---|---|
| 17-18, 22 | broom | Summarize key information about models into tibbles | Website |
| 7, 10, 17-18, 20-22 | 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 |
| 11, 18 | GGally | scatterplot matrix through ggpairs() | Website |
| 2, 6-7, 9-10 | ggdist | Rain cloud plots, Visualizations of distributions and uncertainty | Website |
| 2, 11 | ggpubr | add fitted equation to scatterplot | Website |
| 21-22 | glmnet | LASSO and Elastic Net models | Website |
| 2, 11-12 | glue | working with strings and R results | Website |
| 8, 12, 16, 21 | haven | read and write various data formats | Website |
| 5-7 | infer | tidy statistical inference | Website |
| 2-4, 7, 9-12, 14, 17, 20-22 | janitor | clean_names(), tabyl(), for cleaning and exploring | Overview |
| 2-14, 16-23 | knitr | kable(), report generation | Website |
| 13 | medicaldata | data sets for teaching reproducible medical research | Website |
| 17, 22-23 | mice | Multivariate Imputation by Chained Equations | Website, van Buuren (2021) |
| 6-7 | MKinfer | bootstrap testing | Website |
| 2-3, 5, 7-14, 16-23 | 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, Hill, and Gorman (2020) |
| 2, 5-7, 10-12, 16-17, 21-22 | patchwork | Combining separate ggplots into one graphic | Website |
| 6 | readxl | get data out of Excel and into R | Website |
| 5-7, 9-12, 16-23 | 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) |
|---|---|---|---|
| 2-14, 16-23 | easystats | An R Framework for Easy Statistical Modeling, Visualization and Reporting | Website, Lüdecke et al. (2022) |
| 2-14, 16-23 | tidyverse | R packages for Data Science | Website |
A.2 Loading all of these R packages
A.3 Session Information
xfun::session_info()R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
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 arrangements_1.1.9 askpass_1.2.1
backports_1.5.0 base64enc_0.1-3 bayesplot_1.11.1
bayestestR_0.15.0 BH_1.84.0.0 bit_4.5.0
bit64_4.5.2 blob_1.2.4 boot_1.3-31
broom_1.0.7 bslib_0.8.0 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_3.6.3
clipr_0.8.0 cmprsk_2.2-12 coda_0.19-4.1
codetools_0.2-20 colorspace_2.1-1 colourpicker_1.3.0
commonmark_1.9.2 compiler_4.4.2 conflicted_1.2.0
correlation_0.8.6 corrplot_0.95 cowplot_1.1.3
cpp11_0.5.0 crayon_1.5.3 credentials_2.0.2
crosstalk_1.2.1 curl_6.0.1 data.table_1.16.2
datasets_4.4.2 datawizard_0.13.0 DBI_1.2.3
dbplyr_2.5.0 Deriv_4.1.6 desc_1.4.3
digest_0.6.37 distributional_0.5.0 doBy_4.6.24
dplyr_1.1.4 DT_0.33 dtplyr_1.3.1
dygraphs_1.1.1.6 easystats_0.7.3 effectsize_0.8.9
emmeans_1.10.5 Epi_2.56 estimability_1.5.1
etm_1.1.1 evaluate_1.0.1 exactRankTests_0.8-35
fansi_1.0.6 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_1.6.5
gargle_1.5.2 generics_0.1.3 gert_2.1.4
GGally_2.2.1 ggdist_3.3.2 ggplot2_3.5.1
ggpubr_0.6.0 ggrepel_0.9.6 ggridges_0.5.6
ggsci_3.2.0 ggsignif_0.6.4 ggstats_0.7.0
gh_1.4.1 gitcreds_0.1.2 glmnet_4.1-8
glue_1.8.0 gmp_0.7-5 goftest_1.2-3
googledrive_2.1.1 googlesheets4_1.1.1 graphics_4.4.2
grDevices_4.4.2 grid_4.4.2 gridExtra_2.3
gtable_0.3.6 gtools_3.9.5 haven_2.5.4
highr_0.11 hms_1.1.3 htmltools_0.5.8.1
htmlwidgets_1.6.4 httpuv_1.6.15 httr_1.4.7
httr2_1.0.6 ids_1.0.1 igraph_2.1.1
infer_1.0.7 ini_0.3.1 inline_0.3.20
insight_0.20.5 isoband_0.2.7 iterators_1.0.14
janitor_2.2.0 jomo_2.7-6 jquerylib_0.1.4
jsonlite_1.8.9 knitr_1.49 labeling_0.4.3
later_1.3.2 lattice_0.22-6 lazyeval_0.2.2
lifecycle_1.0.4 lme4_1.1-35.5 loo_2.8.0
lubridate_1.9.3 magrittr_2.0.3 markdown_1.13
MASS_7.3-61 Matrix_1.7-1 MatrixModels_0.5.3
matrixStats_1.4.1 medicaldata_0.2.0 memoise_2.0.1
methods_4.4.2 mgcv_1.9-1 mice_3.16.0
miceadds_3.17-44 microbenchmark_1.5.0 mime_0.12
miniUI_0.1.1.1 minqa_1.2.8 mitml_0.4-5
mitools_2.4 MKdescr_0.8 MKinfer_1.2
modelbased_0.8.9 modelr_0.1.11 multcomp_1.4-26
munsell_0.5.1 mvtnorm_1.3-2 naniar_1.1.0
nlme_3.1-166 nloptr_2.1.1 nnet_7.3-19
norm_1.0.11.1 nortest_1.0-4 numDeriv_2016.8-1.1
olsrr_0.6.1 openssl_2.2.2 ordinal_2023.12.4.1
palmerpenguins_0.1.1 pan_1.9 parallel_4.4.2
parameters_0.23.0 patchwork_1.3.0 pbkrtest_0.5.3
performance_0.12.4 pillar_1.9.0 pkgbuild_1.4.5
pkgconfig_2.0.3 plyr_1.8.9 polynom_1.4.1
posterior_1.6.0 prettyunits_1.2.0 processx_3.8.4
progress_1.2.3 promises_1.3.0 ps_1.8.1
purrr_1.0.2 quadprog_1.5.8 quantreg_5.99
QuickJSR_1.4.0 R.cache_0.16.0 R.methodsS3_1.8.2
R.oo_1.27.0 R.utils_2.12.3 R6_2.5.1
ragg_1.3.3 rappdirs_0.3.3 RColorBrewer_1.1-3
Rcpp_1.0.13-1 RcppArmadillo_14.0.2.1 RcppEigen_0.3.4.0.2
RcppParallel_5.1.9 readr_2.1.5 readxl_1.4.3
rematch_2.0.0 rematch2_2.1.2 report_0.5.9
reprex_2.1.1 reshape2_1.4.4 rlang_1.1.4
rmarkdown_2.29 rpart_4.1.23 rprojroot_2.0.4
rstan_2.32.6 rstanarm_2.32.1 rstantools_2.4.0
rstatix_0.7.2 rstudioapi_0.17.1 rvest_1.0.4
sandwich_3.1-1 sass_0.4.9 scales_1.3.0
see_0.9.0 selectr_0.4.2 shape_1.4.6.1
shiny_1.9.1 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_4.4.2 StanHeaders_2.32.10
stats_4.4.2 stats4_4.4.2 stringi_1.8.4
stringr_1.5.1 styler_1.10.3 survival_3.7-0
sys_3.4.3 systemfonts_1.1.0 tensorA_0.36.2.1
textshaping_0.4.0 TH.data_1.1-2 threejs_0.3.3
tibble_3.2.1 tidyr_1.3.1 tidyselect_1.2.1
tidytuesdayR_1.1.2 tidyverse_2.0.0 timechange_0.3.0
tinytex_0.54 tools_4.4.2 tzdb_0.4.0
ucminf_1.2.2 UpSetR_1.4.0 usethis_3.0.0
utf8_1.2.4 utils_4.4.2 uuid_1.2.1
V8_6.0.0 vctrs_0.6.5 viridis_0.6.5
viridisLite_0.4.2 visdat_0.6.0 vroom_1.6.5
whisker_0.4.1 withr_3.0.2 xfun_0.49
xml2_1.3.6 xplorerr_0.2.0 xtable_1.8-4
xts_0.14.1 yaml_2.3.10 zip_2.3.1
zoo_1.8-12