Chapter 14 Reproducibility

Version 1.6 Feb 8, 2023

  • Updated defunct function arguments.
  • Updated syntax styles and improved some wording/layout.
  • Corrected a few typos.
  • Clarified some fuzzy discussions in contrast analysis and Bayesian inference.

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 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19044)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United States.utf8 
## [2] LC_CTYPE=English_United States.utf8   
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.utf8    
## 
## attached base packages:
## [1] tcltk     stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] dplyr_1.0.10              WRS2_1.1-4               
##  [3] userfriendlyscience_0.7.2 sjstats_0.18.2           
##  [5] sciplot_1.2-0             Rmisc_1.5.1              
##  [7] rcompanion_2.4.18         pwr_1.3-0                
##  [9] psych_2.2.9               plyr_1.8.8               
## [11] plotrix_3.8-2             pgirmess_2.0.0           
## [13] outliers_0.15             nortest_1.0-4            
## [15] mutoss_0.1-12             multtest_2.50.0          
## [17] Biobase_2.54.0            BiocGenerics_0.40.0      
## [19] multcomp_1.4-20           TH.data_1.1-1            
## [21] MASS_7.3-58.1             mvtnorm_1.1-3            
## [23] lsr_0.5.2                 lmPerm_2.1.0             
## [25] lmboot_0.0.1              lawstat_3.5              
## [27] lattice_0.20-45           knitr_1.41               
## [29] KScorrect_1.4.0           gt_0.8.0                 
## [31] gridExtra_2.3             granova_2.1              
## [33] ggstatsplot_0.10.0        ggthemes_4.2.4           
## [35] ggplot2_3.4.0             DTK_3.5                  
## [37] ez_4.4-0                  emmeans_1.8.3            
## [39] effectsize_0.8.2          dunn.test_1.3.5          
## [41] coin_1.4-2                survival_3.5-0           
## [43] car_3.1-1                 carData_3.0-5            
## [45] beeswarm_0.4.0            BayesFactor_0.9.12-4.4   
## [47] coda_0.19-4               asbio_1.8-3              
## [49] afex_1.2-1                lme4_1.1-31              
## [51] Matrix_1.5-3             
## 
## loaded via a namespace (and not attached):
##   [1] estimability_1.4.1     GGally_2.1.2           lavaan_0.6-13         
##   [4] tidyr_1.2.1            data.table_1.14.6      doParallel_1.0.17     
##   [7] generics_0.1.3         proxy_0.4-27           correlation_0.8.3     
##  [10] DiagrammeR_1.0.9       wk_0.7.1               assertthat_0.2.1      
##  [13] viridis_0.6.2          xfun_0.36              hms_1.1.2             
##  [16] jquerylib_0.1.4        data.tree_1.0.0        evaluate_0.19         
##  [19] fansi_1.0.3            readxl_1.4.1           DBI_1.1.3             
##  [22] htmlwidgets_1.6.1      pixmap_0.4-12          reshape_0.8.9         
##  [25] kSamples_1.2-9         stats4_4.2.2           Rmpfr_0.8-9           
##  [28] paletteer_1.5.0        spdep_1.2-7            purrr_1.0.1           
##  [31] ellipsis_0.3.2         backports_1.4.1        bookdown_0.31         
##  [34] pbivnorm_0.6.0         insight_0.18.8         prismatic_1.1.1       
##  [37] libcoin_1.0-9          deldir_1.0-6           vctrs_0.5.1           
##  [40] sjlabelled_1.2.0       abind_1.4-5            cachem_1.0.6          
##  [43] withr_2.5.0            mclust_6.0.0           mnormt_2.1.1          
##  [46] ufs_0.5.2              labeling_0.4.2         pkgconfig_2.0.3       
##  [49] SuppDists_1.1-9.7      units_0.8-1            nlme_3.1-161          
##  [52] statsExpressions_1.3.6 rlang_1.0.6            diptest_0.76-0        
##  [55] lifecycle_1.0.3        MatrixModels_0.5-1     sandwich_3.0-2        
##  [58] modelr_0.1.10          Kendall_2.2.1          cellranger_1.1.0      
##  [61] matrixStats_0.63.0     lmtest_0.9-40          datawizard_0.6.5      
##  [64] mc2d_0.1-22            boot_1.3-28.1          zoo_1.8-11            
##  [67] ggridges_0.5.4         viridisLite_0.4.1      PMCMRplus_1.9.6       
##  [70] parameters_0.20.1      rootSolve_1.8.2.3      KernSmooth_2.23-20    
##  [73] visNetwork_2.1.2       pander_0.6.5           MBESS_4.9.2           
##  [76] classInt_0.4-8         stringr_1.5.0          multcompView_0.1-8    
##  [79] s2_1.1.2               gWidgets2_1.0-9        ggsignif_0.6.4        
##  [82] scales_1.2.1           memoise_2.0.1          magrittr_2.0.3        
##  [85] compiler_4.2.2         rstantools_2.2.0       RColorBrewer_1.1-3    
##  [88] cli_3.6.0              lmerTest_3.1-3         patchwork_1.1.2       
##  [91] pbapply_1.7-0          SCRT_1.3.1             mgcv_1.8-41           
##  [94] tidyselect_1.2.0       stringi_1.7.12         forcats_0.5.2         
##  [97] highr_0.10             yaml_2.3.6             ggrepel_0.9.2         
## [100] grid_4.2.2             sass_0.4.4             tools_4.2.2           
## [103] lmom_2.9               parallel_4.2.2         rio_0.5.29            
## [106] rstudioapi_0.14        foreach_1.5.2          foreign_0.8-84        
## [109] GPArotation_2022.10-2  gld_2.6.6              farver_2.1.1          
## [112] scatterplot3d_0.3-42   digest_0.6.31          BWStest_0.2.2         
## [115] Rcpp_1.0.9             broom_1.0.2            performance_0.10.2    
## [118] httr_1.4.4             gWidgets2tcltk_1.0-8   minpack.lm_1.2-2      
## [121] sf_1.0-9               Rdpack_2.4             colorspace_2.0-3      
## [124] XML_3.99-0.13          splines_4.2.2          rematch2_2.1.2        
## [127] expm_0.999-7           sp_1.5-1               Exact_3.2             
## [130] spData_2.2.1           gmp_0.6-9              xtable_1.8-4          
## [133] jsonlite_1.8.4         nloptr_2.0.3           zeallot_0.1.0         
## [136] modeltools_0.2-23      R6_2.5.1               pillar_1.8.1          
## [139] htmltools_0.5.4        glue_1.6.2             fastmap_1.1.0         
## [142] minqa_1.2.5            deSolve_1.34           class_7.3-20          
## [145] codetools_0.2-18       utf8_1.2.2             bslib_0.4.2           
## [148] tibble_3.1.8           numDeriv_2016.8-1.1    BiasedUrn_2.0.8       
## [151] curl_5.0.0             DescTools_0.99.47      zip_2.2.2             
## [154] openxlsx_4.2.5.1       rmarkdown_2.19         munsell_0.5.0         
## [157] e1071_1.7-12           iterators_1.0.14       sjmisc_2.8.9          
## [160] haven_2.5.1            reshape2_1.4.4         gtable_0.3.1          
## [163] bayestestR_0.13.0      rbibutils_2.2.13