Last updated: 2024-08-29

Checks: 7 0

Knit directory: muse/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200712)

The command set.seed(20200712) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

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Repository version: 128229e

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 128229e. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/pbmc3k.csv
    Ignored:    data/pbmc3k.csv.gz
    Ignored:    data/pbmc3k/
    Ignored:    r_packages_4.3.3/
    Ignored:    r_packages_4.4.0/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/styler.Rmd) and HTML (docs/styler.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 128229e Dave Tang 2024-08-29 Non-invasive pretty printing of R code

Install.

install.packages("styler")

Load.

library(styler)

Create badly formated function.

add<-function(a,b){
a+b
}

dump(list = 'add', file = "add.R")

Check it out.

cat add.R
add <-
function(a,b){
a+b
}

Style it.

style_file("add.R")
Styling  1  files:
 add.R ℹ 
────────────────────────────────────────
Status  Count   Legend 
✔   0   File unchanged.
ℹ   1   File changed.
✖   0   Styling threw an error.
────────────────────────────────────────
Please review the changes carefully!

Check it out again!

cat add.R
add <-
  function(a, b) {
    a + b
  }

Remove file.

unlink("add.R")

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 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-r0.3.20.so;  LAPACK version 3.10.0

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] styler_1.10.3   bench_1.1.3     workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8    compiler_4.4.0    promises_1.3.0    Rcpp_1.0.12      
 [5] stringr_1.5.1     git2r_0.33.0      callr_3.7.6       later_1.3.2      
 [9] jquerylib_0.1.4   yaml_2.3.8        fastmap_1.2.0     R6_2.5.1         
[13] knitr_1.47        tibble_3.2.1      rprojroot_2.0.4   R.cache_0.16.0   
[17] bslib_0.7.0       pillar_1.9.0      R.utils_2.12.3    rlang_1.1.4      
[21] utf8_1.2.4        cachem_1.1.0      stringi_1.8.4     httpuv_1.6.15    
[25] xfun_0.44         getPass_0.2-4     fs_1.6.4          sass_0.4.9       
[29] cli_3.6.3         withr_3.0.1       magrittr_2.0.3    ps_1.7.6         
[33] digest_0.6.37     processx_3.8.4    rstudioapi_0.16.0 lifecycle_1.0.4  
[37] R.oo_1.26.0       R.methodsS3_1.8.2 vctrs_0.6.5       evaluate_0.24.0  
[41] glue_1.7.0        whisker_0.4.1     fansi_1.0.6       purrr_1.0.2      
[45] rmarkdown_2.27    httr_1.4.7        tools_4.4.0       pkgconfig_2.0.3  
[49] htmltools_0.5.8.1