Project Workflows and Shiny Helpers/addins using thekidsbiostats

Overview

library(thekidsbiostats)

Organising Statistical Workflows

The following section runs through the various functions for automating and/or simplifying regular/routine tasks performed through a project’s workflow. These functions allow you to create a sensible/structured directory for your project as well as simplifying (and standardising) the creation of Quarto templates using The Kids theming.

Step 1: Create folder structure

  • Let’s create the following project:
    • Project is called “Project XYZ”.
    • Set ext_name = "basic", as I will not be leveraging Targets in this project.
    • I would like all “default” folders (i.e. admin, data, data_raw, docs, reports).
    • In addition to the above, I would like custom folders for “protocols” and “papers”.
create_project(project_name = "Project XYZ", 
               ext_name = "basic",
               other_folders = c("protocols", "papers"))
Figure 1: Prompt on selecting overall project folder.
Figure 1: Prompt on selecting overall project folder.



Figure 2: Creation of project file structure.
Figure 2: Creation of project file structure.

Step 2: Create (Quarto) markdown template

Quarto documents are versatile, reproducible file formats that supports Markdown and code chunks, enabling seamless blending of text, code, and outputs for reports, presentations, and interactive documents.

In this case, we would like to name the report “Analysis_Report_v1”.

create_template(file_name = "Analysis_Report_v1",
                ext_name = "html")
Figure 3: Prompt on selecting where to save analysis report.
Figure 3: Prompt on selecting where to save analysis report.



Figure 4: Creation of skeleton report, with associated styling (in /_extensions).
Figure 4: Creation of skeleton report, with associated styling (in /_extensions).



Figure 5: Supporting files created for the themed html document.
Figure 5: Supporting files created for the themed html document.



Figure 6: Rendered html Quarto report.
Figure 6: Rendered html Quarto report.



Enhancing Report Readability Using Add-Ins

Reproducibility Information

sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] thekidsbiostats_1.9.1 extrafont_0.20        flextable_0.10.0     
#>  [4] gtsummary_2.5.1       lubridate_1.9.5       forcats_1.0.1        
#>  [7] stringr_1.6.0         dplyr_1.2.1           purrr_1.2.2          
#> [10] readr_2.2.0           tidyr_1.3.2           tibble_3.3.1         
#> [13] ggplot2_4.0.3         tidyverse_2.0.0       rmarkdown_2.31       
#> 
#> loaded via a namespace (and not attached):
#>  [1] tidyselect_1.2.1        ggfortify_0.4.19        farver_2.1.2           
#>  [4] S7_0.2.2                fastmap_1.2.0           fontquiver_0.2.1       
#>  [7] janitor_2.2.1           promises_1.5.0          broom.helpers_1.22.0   
#> [10] labelled_2.16.0         digest_0.6.39           timechange_0.4.0       
#> [13] mime_0.13               lifecycle_1.0.5         magrittr_2.0.5         
#> [16] compiler_4.6.1          rlang_1.3.0             sass_0.4.10            
#> [19] tools_4.6.1             yaml_2.3.12             data.table_1.18.4      
#> [22] knitr_1.51              labeling_0.4.3          askpass_1.2.1          
#> [25] curl_7.1.0              xml2_1.6.0              RColorBrewer_1.1-3     
#> [28] tinytable_0.17.0        withr_3.0.3             sys_3.4.3              
#> [31] datawizard_1.3.1        grid_4.6.1              shinyFiles_0.9.3       
#> [34] sysfonts_0.8.9          gdtools_0.5.1           xtable_1.8-8           
#> [37] extrafontdb_1.1         scales_1.4.0            MASS_7.3-66            
#> [40] insight_1.5.2           cli_3.6.6               ragg_1.5.2             
#> [43] generics_0.1.4          otel_0.2.0              rstudioapi_0.19.0      
#> [46] tzdb_0.5.0              cachem_1.1.0            vctrs_0.7.3            
#> [49] jsonlite_2.0.0          fontBitstreamVera_0.1.1 hms_1.1.4              
#> [52] patchwork_1.3.2         systemfonts_1.3.2       maketools_1.3.2        
#> [55] jquerylib_0.1.4         glue_1.8.1              stringi_1.8.7          
#> [58] gtable_0.3.6            later_1.4.8             ggeffects_2.3.2        
#> [61] pillar_1.11.1           htmltools_0.5.9         openssl_2.4.2          
#> [64] R6_2.6.1                textshaping_1.0.5       evaluate_1.0.5         
#> [67] shiny_1.14.0            haven_2.5.5             backports_1.5.1        
#> [70] cards_0.8.1             broom_1.0.13            snakecase_0.11.1       
#> [73] fontLiberation_0.1.0    httpuv_1.6.17           bslib_0.11.0           
#> [76] Rcpp_1.1.2              cardx_0.3.4             zip_3.0.1              
#> [79] uuid_1.2-2              gridExtra_2.3.1         Rttf2pt1_1.3.14        
#> [82] officer_0.7.5           xfun_0.60               fs_2.1.0               
#> [85] buildtools_1.0.0        pkgconfig_2.0.3