Data Analysis , Visualization, and Scientfic Publishing with R & Rstudio
Participant Manual
Participant Manual
November 21, 2022
Preface
Software information and conventions
This training manual was created using the knitr package1 and the bookdown package2. The following is the R session information:
xfun::session_info()## R version 4.2.0 (2022-04-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
##
## Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
##
## Package version:
## abind_1.4-5 acs_2.1.4 agridat_1.21
## askpass_1.1 assertthat_0.2.1 backports_1.4.1
## base64enc_0.1-3 bit_4.0.4 bit64_4.0.5
## bitops_1.0-7 blob_1.2.3 bookdown_0.30
## boot_1.3.28 brew_1.0.8 brio_1.1.3
## broom_1.0.1 bslib_0.4.1 cachem_1.0.6
## callr_3.7.3 car_3.1-1 carData_3.0-5
## cellranger_1.1.0 checkmate_2.1.0 choroplethr_3.7.1
## choroplethrMaps_1.0.1 class_7.3-20 classInt_0.4-8
## cli_3.4.1 clipr_0.8.0 cluster_2.1.4
## codetools_0.2-18 colorspace_2.0-3 colourpicker_1.2.0
## commonmark_1.8.1 compiler_4.2.0 corrplot_0.92
## cowplot_1.1.1 cpp11_0.4.3 crayon_1.5.2
## crosstalk_1.2.0 curl_4.3.3 data.table_1.14.4
## DBI_1.1.3 dbplyr_2.2.1 deldir_1.0-6
## desc_1.4.2 dichromat_2.0-0.1 diffobj_0.3.5
## digest_0.6.30 dplyr_1.0.10 dtplyr_1.2.2
## e1071_1.7-12 ellipsis_0.3.2 evaluate_0.18
## fansi_1.0.3 farver_2.1.1 fastmap_1.1.0
## fontawesome_0.4.0 forcats_0.5.2 foreign_0.8-83
## Formula_1.2-4 fs_1.5.2 gargle_1.2.1
## generics_0.1.3 geojsonsf_2.0.3 geometries_0.2.0
## ggExtra_0.10.0 ggmap_3.0.1 ggplot2_3.4.0
## ggpubr_0.4.0 ggrepel_0.9.2 ggsci_2.9
## ggsignif_0.6.4 ggthemes_4.2.4 glue_1.6.2
## googledrive_2.0.0 googlesheets4_1.0.1 graphics_4.2.0
## grDevices_4.2.0 grid_4.2.0 gridExtra_2.3
## gtable_0.3.1 haven_2.5.1 highr_0.9
## Hmisc_4.7-1 hms_1.1.2 htmlTable_2.4.1
## htmltools_0.5.3 htmlwidgets_1.5.4 httpuv_1.6.6
## httr_1.4.4 ids_1.0.1 interp_1.1-3
## isoband_0.2.6 jpeg_0.1-9 jquerylib_0.1.4
## jsonify_1.2.2 jsonlite_1.8.3 kableExtra_1.3.4
## KernSmooth_2.23-20 knitr_1.40 labeling_0.4.2
## later_1.3.0 lattice_0.20-45 latticeExtra_0.6-30
## lazyeval_0.2.2 leafem_0.2.0 leaflet_2.1.1
## leaflet.providers_1.9.0 leafpop_0.1.0 leafsync_0.1.0
## lifecycle_1.0.3 lme4_1.1.31 lubridate_1.9.0
## lwgeom_0.2-9 magrittr_2.0.3 maptools_1.1-5
## mapview_2.11.0 markdown_1.3 MASS_7.3.58.1
## Matrix_1.5-3 MatrixModels_0.5.1 memoise_2.0.1
## methods_4.2.0 mgcv_1.8.41 mime_0.12
## miniUI_0.1.1.1 minqa_1.2.5 modelr_0.1.10
## munsell_0.5.0 ndjson_0.9.0 nlme_3.1.160
## nloptr_2.0.3 nnet_7.3-18 numDeriv_2016.8.1.1
## openssl_2.0.4 parallel_4.2.0 pbkrtest_0.5.1
## pillar_1.8.1 pkgconfig_2.0.3 pkgload_1.3.1
## plyr_1.8.8 png_0.1-7 polynom_1.4.1
## praise_1.0.0 prettyunits_1.1.1 processx_3.8.0
## progress_1.2.2 promises_1.2.0.1 proxy_0.4-27
## ps_1.7.2 purrr_0.3.5 quantreg_5.94
## R6_2.5.1 rapidjsonr_1.2.0 rappdirs_0.3.3
## raster_3.6-3 RColorBrewer_1.1-3 Rcpp_1.0.9
## RcppEigen_0.3.3.9.3 RCurl_1.98-1.9 readr_2.1.3
## readxl_1.4.1 rematch_1.0.1 rematch2_2.1.2
## reprex_2.0.2 reshape2_1.4.4 rgdal_1.5-32
## RgoogleMaps_1.4.5.3 rjson_0.2.21 rlang_1.0.6
## rmarkdown_2.18 rnaturalearth_0.1.0 rnaturalearthdata_0.1.0
## rpart_4.1.19 rprojroot_2.0.3 rstatix_0.7.1
## rstudioapi_0.14 rticles_0.24 rvest_1.0.3
## s2_1.1.0 sass_0.4.2 satellite_1.0.4
## scales_1.2.1 selectr_0.4.2 servr_0.25
## sf_1.0-8 sfheaders_0.4.0 shiny_1.7.3
## shinyjs_2.1.0 sourcetools_0.1.7 sp_1.5-1
## SparseM_1.81 splines_4.2.0 stars_0.5-6
## stats_4.2.0 stats4_4.2.0 streamR_0.4.5
## stringi_1.7.8 stringr_1.4.1 survival_3.4-0
## svglite_2.1.0 sys_3.4.1 systemfonts_1.0.4
## terra_1.6-17 testthat_3.1.5 tibble_3.1.8
## tidycensus_1.2.3 tidyr_1.2.1 tidyselect_1.2.0
## tidyverse_1.3.2 tigris_1.6.1 timechange_0.1.1
## tinytex_0.42 tmap_3.3-3 tmaptools_3.1-1
## tools_4.2.0 tzdb_0.3.0 units_0.8-0
## utf8_1.2.2 utils_4.2.0 uuid_1.1-0
## vctrs_0.5.1 viridis_0.6.2 viridisLite_0.4.1
## vroom_1.6.0 waldo_0.4.0 WDI_2.7.8
## webshot_0.5.4 widgetframe_0.3.1 withr_2.5.0
## wk_0.7.0 xfun_0.34 XML_3.99-0.12
## xml2_1.3.3 xtable_1.8-4 yaml_2.3.6