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 4.4.1 (2024-06-14 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_1.4-5 arrangements_1.1.9 askpass_1.2.0
backports_1.5.0 base64enc_0.1-3 bayesplot_1.11.1
bayestestR_0.14.0 BH_1.84.0.0 bit_4.0.5
bit64_4.0.5 blob_1.2.4 boot_1.3-31
broom_1.0.6 broom.helpers_1.17.0 bslib_0.8.0
cachem_1.1.0 callr_3.7.6 car_3.1-2
carData_3.0-5 cards_0.2.2 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_1.9.1
compiler_4.4.1 conflicted_1.2.0 correlation_0.8.5
corrplot_0.94 cowplot_1.1.3 cpp11_0.5.0
crayon_1.5.3 credentials_2.0.1 crosstalk_1.2.1
curl_5.2.2 data.table_1.16.0 datasets_4.4.1
datawizard_0.12.3 DBI_1.2.3 dbplyr_2.5.0
Deriv_4.1.3 desc_1.4.3 digest_0.6.37
distributional_0.4.0 doBy_4.6.22 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_1.10.4
Epi_2.53 estimability_1.5.1 etm_1.1.1
evaluate_0.24.0 exactRankTests_0.8-35 fansi_1.0.6
farver_2.1.2 fastmap_1.2.0 fivethirtyeight_0.6.2
fontawesome_0.5.2 forcats_1.0.0 foreach_1.5.2
fs_1.6.4 gargle_1.5.2 generics_0.1.3
gert_2.1.1 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_0.6.0 gh_1.4.1 gitcreds_0.1.2
glmnet_4.1-8 glue_1.7.0 gmp_0.7-5
goftest_1.2-3 googledrive_2.1.1 googlesheets4_1.1.1
graphics_4.4.1 grDevices_4.4.1 grid_4.4.1
gridExtra_2.3 gtable_0.3.5 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_1.0.3 ids_1.0.1
igraph_2.0.3 infer_1.0.7 ini_0.3.1
inline_0.3.19 insight_0.20.4 isoband_0.2.7
iterators_1.0.14 janitor_2.2.0 jomo_2.7-6
jquerylib_0.1.4 jsonlite_1.8.8 knitr_1.48
labeling_0.4.3 labelled_2.13.0 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_1.7-0 MatrixModels_0.5.3 matrixStats_1.4.0
medicaldata_0.2.0 memoise_2.0.1 methods_4.4.1
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_0.8.8
modelr_0.1.11 multcomp_1.4-26 munsell_0.5.1
mvtnorm_1.3-1 naniar_1.1.0 nlme_3.1-164
nloptr_2.1.1 nnet_7.3-19 norm_1.0.11.1
nortest_1.0-4 numDeriv_2016.8-1.1 olsrr_0.6.0
openssl_2.2.1 ordinal_2023.12.4.1 palmerpenguins_0.1.1
pan_1.9 parallel_4.4.1 parameters_0.22.2
patchwork_1.2.0 pbkrtest_0.5.3 performance_0.12.3
pillar_1.9.0 pkgbuild_1.4.4 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_1.7.7 purrr_1.0.2
quadprog_1.5.8 quantreg_5.98 QuickJSR_1.3.1
R.cache_0.16.0 R.methodsS3_1.8.2 R.oo_1.26.0
R.utils_2.12.3 R6_2.5.1 ragg_1.3.2
rappdirs_0.3.3 RColorBrewer_1.1-3 Rcpp_1.0.13
RcppArmadillo_14.0.0.1 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_2.28
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_0.16.0 rvest_1.0.4 sandwich_3.1-0
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_4.4.1 StanHeaders_2.32.10 stats_4.4.1
stats4_4.4.1 stringi_1.8.4 stringr_1.5.1
styler_1.10.3 survival_3.7-0 sys_3.4.2
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_0.52
tools_4.4.1 tzdb_0.4.0 ucminf_1.2.2
UpSetR_1.4.0 usethis_3.0.0 utf8_1.2.4
utils_4.4.1 uuid_1.2.1 V8_5.0.0
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_3.0.1 xfun_0.47 xml2_1.3.6
xplorerr_0.1.2 xtable_1.8-4 xts_0.14.0
yaml_2.3.10 zip_2.3.1 zoo_1.8-12