Chapter 16 Documentation for Reproducibility
R software products such as this markdown document should be simple to reproduce, if the code file or code are available. But it is also important to document the exact versions of the R installation, the OS, and the R packages in place when the document is created.
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18362)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.1252
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] yhat_2.0-2 UsingR_2.0-6 Hmisc_4.4-0
## [4] Formula_1.2-3 HistData_0.8-6 tseries_0.10-47
## [7] sandwich_2.5-1 rmarkdown_2.3 rcompanion_2.3.25
## [10] plyr_1.8.6 plot3Drgl_1.0.1 rgl_0.100.54
## [13] plot3D_1.3 psych_2.0.7 olsrr_0.5.3
## [16] nortest_1.0-4 moments_0.14 lmtest_0.9-37
## [19] zoo_1.8-8 knitr_1.29 HH_3.1-40
## [22] gridExtra_2.3 multcomp_1.4-13 TH.data_1.0-10
## [25] MASS_7.3-51.6 survival_3.2-3 mvtnorm_1.1-1
## [28] latticeExtra_0.6-29 lattice_0.20-41 gt_0.2.1
## [31] gvlma_1.0.0.3 ggthemes_4.2.0 ggExtra_0.9
## [34] GGally_2.0.0 ggplot2_3.3.2 car_3.0-8
## [37] carData_3.0-4 broom_0.7.0.9000 boot_1.3-25
## [40] bcdstats_0.0.0.9002 BayesFactor_0.9.12-4.2 Matrix_1.2-18
## [43] coda_0.19-3
##
## loaded via a namespace (and not attached):
## [1] readxl_1.3.1 backports_1.1.8 miscTools_0.6-26
## [4] splines_4.0.2 gmp_0.6-0 crosstalk_1.1.0.1
## [7] digest_0.6.25 htmltools_0.5.0 yacca_1.1.1
## [10] magrittr_1.5 checkmate_2.0.0 cluster_2.1.0
## [13] openxlsx_4.1.5 matrixStats_0.56.0 xts_0.12-0
## [16] jpeg_0.1-8.1 colorspace_1.4-1 haven_2.3.1
## [19] xfun_0.16 dplyr_1.0.0 libcoin_1.0-5
## [22] crayon_1.3.4 jsonlite_1.7.0 Exact_2.0
## [25] glue_1.4.1 gtable_0.3.0 webshot_0.5.2
## [28] MatrixModels_0.4-1 Rmpfr_0.8-1 quantmod_0.4.17
## [31] abind_1.4-5 SparseM_1.78 scales_1.1.1
## [34] miniUI_0.1.1.1 Rcpp_1.0.5 isoband_0.2.2
## [37] plotrix_3.7-8 xtable_1.8-4 htmlTable_2.0.1
## [40] tmvnsim_1.0-2 foreign_0.8-80 stats4_4.0.2
## [43] vcd_1.4-7 htmlwidgets_1.5.1 RColorBrewer_1.1-2
## [46] modeltools_0.2-23 acepack_1.4.1 ellipsis_0.3.1
## [49] farver_2.0.3 pkgconfig_2.0.3 reshape_0.8.8
## [52] multcompView_0.1-8 nnet_7.3-14 labeling_0.3
## [55] tidyselect_1.1.0 rlang_0.4.7 manipulateWidget_0.10.1
## [58] reshape2_1.4.4 later_1.1.0.1 munsell_0.5.0
## [61] cellranger_1.1.0 tools_4.0.2 generics_0.0.2
## [64] EMT_1.1 evaluate_0.14 shinyBS_0.61
## [67] stringr_1.4.0 fastmap_1.0.1 yaml_2.2.1
## [70] goftest_1.2-2 zip_2.0.4 purrr_0.3.4
## [73] coin_1.3-1 pbapply_1.4-2 nlme_3.1-148
## [76] mime_0.9 quantreg_5.61 leaps_3.1
## [79] compiler_4.0.2 rstudioapi_0.11 curl_4.3
## [82] png_0.1-7 e1071_1.7-3 tibble_3.0.3
## [85] DescTools_0.99.37 stringi_1.4.6 highr_0.8
## [88] forcats_0.5.0 vctrs_0.3.2 pillar_1.4.6
## [91] lifecycle_0.2.0 data.table_1.13.0 conquer_1.0.1
## [94] httpuv_1.5.4 R6_2.4.1 bookdown_0.20
## [97] promises_1.1.1 KernSmooth_2.23-17 rio_0.5.16
## [100] codetools_0.2-16 gtools_3.8.2 withr_2.2.0
## [103] mnormt_2.0.1 mgcv_1.8-31 expm_0.999-5
## [106] parallel_4.0.2 hms_0.5.3 quadprog_1.5-8
## [109] rpart_4.1-15 tidyr_1.1.0 class_7.3-17
## [112] misc3d_0.8-4 Cairo_1.5-12.2 TTR_0.23-6
## [115] shiny_1.5.0 base64enc_0.1-316.1 Revision History
Ver1.2 April 7, 2020
Converted the document to bookdown
Added many sections and updated many code chunks
Ver 1.1 Jan. 29, 2018
ver 1.0 Feb. 2, 2017