Chapter 14 Reproducibility

Version 1.5 Mar 1, 2021 Reorganized and expanded the effect size chapter.

Reworked the sequence of ggplot graphs in the EDA section.

Updated some syntax styles and improved some wording/layout.

Corrected too many typos.

Version 1.4 Oct 16, 2020

Added a chapter on unequal sample size implications.

Updated some syntax styles and improved some wording.

Version 1.3 Oct 13, 2020

updated some syntax styles and emphasized using summary.lm on `aov` objects

Cleaned up some wording and layout issues.

Version 1.2 Sept. 16, 2020

updated for some R version 4 compatibility issues, including stringsAsFactors in read.csv.

Also edited some wording.

Version 1.1 April 9, 2020

converted to bookdown format, added multiple sections:

new graphs, contrast analysis details, nonparametrics, permutation, bootstrapping, etc.

Version 1.0 Feb 25, 2019

sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18363)
## 
## 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] parallel  tcltk     stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] dplyr_1.0.4               WRS2_1.1-1               
##  [3] userfriendlyscience_0.7.2 sjstats_0.18.1           
##  [5] sciplot_1.2-0             Rmisc_1.5                
##  [7] rcompanion_2.3.27         pwr_1.3-0                
##  [9] psych_2.0.12              plyr_1.8.6               
## [11] plotrix_3.8-1             pgirmess_1.6.9           
## [13] outliers_0.14             nortest_1.0-4            
## [15] mutoss_0.1-12             multtest_2.44.0          
## [17] Biobase_2.48.0            BiocGenerics_0.34.0      
## [19] multcomp_1.4-16           TH.data_1.0-10           
## [21] MASS_7.3-53.1             mvtnorm_1.1-1            
## [23] lsr_0.5                   lmPerm_2.1.0             
## [25] lmboot_0.0.1              lawstat_3.4              
## [27] lattice_0.20-41           knitr_1.31               
## [29] KScorrect_1.4.0           gt_0.2.2                 
## [31] gridExtra_2.3             granova_2.1              
## [33] ggstatsplot_0.7.0         ggthemes_4.2.4           
## [35] ggplot2_3.3.3             DTK_3.5                  
## [37] ez_4.4-0                  emmeans_1.5.4            
## [39] effectsize_0.4.3          dunn.test_1.3.5          
## [41] coin_1.4-1                survival_3.2-7           
## [43] car_3.0-10                carData_3.0-4            
## [45] beeswarm_0.2.3            BayesFactor_0.9.12-4.2   
## [47] coda_0.19-4               asbio_1.6-7              
## [49] afex_0.28-1               lme4_1.1-26              
## [51] Matrix_1.3-2             
## 
## loaded via a namespace (and not attached):
##   [1] estimability_1.3          GGally_2.1.0             
##   [3] lavaan_0.6-7              tidyr_1.1.2              
##   [5] data.table_1.13.6         doParallel_1.0.16        
##   [7] generics_0.1.0            combinat_0.0-8           
##   [9] DiagrammeR_1.0.6.1        correlation_0.6.0        
##  [11] httpuv_1.5.5              assertthat_0.2.1         
##  [13] viridis_0.5.1             xfun_0.21                
##  [15] hms_1.0.0                 data.tree_1.0.0          
##  [17] evaluate_0.14             promises_1.2.0.1         
##  [19] readxl_1.3.1              htmlwidgets_1.5.3        
##  [21] DBI_1.1.1                 tmvnsim_1.0-2            
##  [23] pixmap_0.4-12             reshape_0.8.8            
##  [25] kSamples_1.2-9            stats4_4.0.3             
##  [27] Rmpfr_0.8-2               paletteer_1.3.0          
##  [29] spdep_1.1-5               purrr_0.3.4              
##  [31] ellipsis_0.3.1            backports_1.2.1          
##  [33] bookdown_0.21             pbivnorm_0.6.0           
##  [35] insight_0.13.0            prismatic_1.0.0          
##  [37] ggcorrplot_0.1.3          gbRd_0.4-11              
##  [39] libcoin_1.0-8             deldir_0.2-9             
##  [41] vctrs_0.3.6               sjlabelled_1.1.7         
##  [43] abind_1.4-5               cachem_1.0.4             
##  [45] withr_2.4.1               checkmate_2.0.0          
##  [47] rgdal_1.5-23              mclust_5.4.7             
##  [49] mnormt_2.0.2              splancs_2.01-40          
##  [51] ufs_0.4.3                 crayon_1.4.1             
##  [53] labeling_0.4.2            pkgconfig_2.0.3          
##  [55] SuppDists_1.1-9.5         units_0.6-7              
##  [57] nlme_3.1-152              statsExpressions_0.7.1   
##  [59] diptest_0.75-7            rlang_0.4.10             
##  [61] lifecycle_1.0.0           miniUI_0.1.1.1           
##  [63] MatrixModels_0.4-1        sandwich_3.0-0           
##  [65] EMT_1.1                   modelr_0.1.8             
##  [67] Kendall_2.2               cellranger_1.1.0         
##  [69] matrixStats_0.58.0        lmtest_0.9-38            
##  [71] mc2d_0.1-18               raster_3.4-5             
##  [73] boot_1.3-27               zoo_1.8-8                
##  [75] ggridges_0.5.3            viridisLite_0.3.0        
##  [77] PMCMRplus_1.9.0           parameters_0.11.0        
##  [79] rootSolve_1.8.2.1         visNetwork_2.0.9         
##  [81] KernSmooth_2.23-18        pander_0.6.3             
##  [83] ggExtra_0.9               MBESS_4.8.0              
##  [85] classInt_0.4-3            stringr_1.4.0            
##  [87] multcompView_0.1-8        maptools_1.0-2           
##  [89] gWidgets2_1.0-8           ggsignif_0.6.0           
##  [91] scales_1.1.1              memoise_2.0.0            
##  [93] magrittr_2.0.1            gdata_2.18.0             
##  [95] compiler_4.0.3            rstantools_2.1.1         
##  [97] RColorBrewer_1.1-2        LearnBayes_2.15.1        
##  [99] lmerTest_3.1-3            patchwork_1.1.1          
## [101] pbapply_1.4-3             SCRT_1.3.1               
## [103] mgcv_1.8-33               tidyselect_1.1.0         
## [105] stringi_1.5.3             forcats_0.5.1            
## [107] highr_0.8                 yaml_2.2.1               
## [109] ggrepel_0.9.1             grid_4.0.3               
## [111] sass_0.3.1                tools_4.0.3              
## [113] lmom_2.8                  rio_0.5.16               
## [115] rstudioapi_0.13           GPArotation_2014.11-1    
## [117] foreach_1.5.1             foreign_0.8-81           
## [119] ipmisc_6.0.0              gld_2.6.2                
## [121] pairwiseComparisons_3.1.3 farver_2.0.3             
## [123] scatterplot3d_0.3-41      digest_0.6.27            
## [125] rgeos_0.5-5               shiny_1.6.0              
## [127] BWStest_0.2.2             Rcpp_1.0.6               
## [129] broom_0.7.4               performance_0.7.0        
## [131] later_1.1.0.1             gWidgets2tcltk_1.0-6     
## [133] minpack.lm_1.2-1          sf_0.9-7                 
## [135] Rdpack_2.1                colorspace_2.0-0         
## [137] XML_3.99-0.5              splines_4.0.3            
## [139] statmod_1.4.35            rematch2_2.1.2           
## [141] expm_0.999-6              sp_1.4-5                 
## [143] Exact_2.1                 spData_0.3.8             
## [145] xtable_1.8-4              gmp_0.6-2                
## [147] jsonlite_1.7.2            nloptr_1.2.2.2           
## [149] zeallot_0.1.0             modeltools_0.2-23        
## [151] R6_2.5.0                  gmodels_2.18.1           
## [153] pillar_1.4.7              htmltools_0.5.1.1        
## [155] mime_0.10                 glue_1.4.2               
## [157] fastmap_1.1.0             minqa_1.2.4              
## [159] deSolve_1.28              class_7.3-18             
## [161] codetools_0.2-18          tibble_3.0.6             
## [163] numDeriv_2016.8-1.1       BiasedUrn_1.07           
## [165] curl_4.3                  DescTools_0.99.40        
## [167] gtools_3.8.2              zip_2.1.1                
## [169] openxlsx_4.2.3            rmarkdown_2.6            
## [171] munsell_0.5.0             e1071_1.7-4              
## [173] iterators_1.0.13          sjmisc_2.8.6             
## [175] haven_2.3.1               reshape2_1.4.4           
## [177] gtable_0.3.0              bayestestR_0.8.2         
## [179] rbibutils_2.0