library(data.table)

A dependency graph for all GitHub repos that use the rworkflows GitHub Action.

Create

Here is the code for creating the plot.

Install required packages

if(!require("echodeps"))remotes::install_github("RajLabMSSM/echodeps",
                                                dependencies = TRUE)

Create graph

res <- echodeps::dep_graph(pkg = "rworkflows",
                           method_seed = "github",
                           exclude = c("neurogenomics_rworkflows",
                                       "neurogenomics_r_workflows"),
                           #node_size = "total_downloads", 
                           reverse = TRUE,
                           save_path = here::here("reports","rworkflows_depgraph.html"))

Save data

## Save network plot as PNG
echodeps::visnet_save(res$save_path)

## Save all data and plots
saveRDS(res, here::here("reports","dep_graph_res.rds"))

Count stars/clones/views

knitr::kable(res$report)

Show

rworkflow depgraph

Hover over each node to show additional metadata.

Identify highly downloaded packages

Identify the CRAN/Bioc R packages with the most number of downloads. This guides which packages would be the most useful to focus on implementing rworkflows in.

pkgs <- echogithub::r_repos_downloads(which = c("CRAN","Bioc"))

#### Get top 10 per R repository ####
pkgs_top <- pkgs[, tail(.SD, 10), by="r_repo"] 
methods::show(pkgs_top)

Assess R repository usage

This demonstrates the need for using rworkflows, as there are 25,000 R packages that are exclusively distributes via GitHub (which may or may not have code/documentation checks).

r_repos_res <- echogithub::r_repos(save_path = here::here("reports","r_repos_upset.pdf"), width=12)

Session Info

utils::sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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-r0.3.26.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=C              
##  [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] data.table_1.16.2 rworkflows_1.0.3  rmarkdown_2.28   
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        jsonlite_1.8.9      renv_1.0.11        
##  [4] BiocManager_1.30.25 dplyr_1.1.4         compiler_4.4.1     
##  [7] tidyselect_1.2.1    jquerylib_0.1.4     rvcheck_0.2.1      
## [10] scales_1.3.0        yaml_2.3.10         fastmap_1.2.0      
## [13] here_1.0.1          ggplot2_3.5.1       R6_2.5.1           
## [16] generics_0.1.3      knitr_1.48          yulab.utils_0.1.7  
## [19] tibble_3.2.1        desc_1.4.3          dlstats_0.1.7      
## [22] maketools_1.3.1     rprojroot_2.0.4     munsell_0.5.1      
## [25] bslib_0.8.0         pillar_1.9.0        RColorBrewer_1.1-3 
## [28] rlang_1.1.4         utf8_1.2.4          cachem_1.1.0       
## [31] badger_0.2.4        xfun_0.49           fs_1.6.5           
## [34] sass_0.4.9          sys_3.4.3           cli_3.6.3          
## [37] magrittr_2.0.3      digest_0.6.37       grid_4.4.1         
## [40] lifecycle_1.0.4     vctrs_0.6.5         evaluate_1.0.1     
## [43] glue_1.8.0          buildtools_1.0.0    fansi_1.0.6        
## [46] colorspace_2.1-1    tools_4.4.1         pkgconfig_2.0.3    
## [49] htmltools_0.5.8.1

Dependency graph