Last updated: 2022-02-28

Checks: 7 0

Knit directory: STUtility_web_site/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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.

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.

The command set.seed(20191031) 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.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

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

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

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 64ae8be. 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:    analysis/.DS_Store
    Ignored:    analysis/manual_annotation.png
    Ignored:    pre_data/

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/Installation.Rmd) and HTML (docs/Installation.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
html d41bcb0 Ludvig Larsson 2022-02-28 Build site.
html 0dafcee Ludvig Larsson 2021-05-06 Build site.
html df62517 Ludvig Larsson 2021-05-06 Build site.
html 88b046f Ludvig Larsson 2021-05-05 Build site.
html 2523b70 Ludvig Larsson 2021-05-05 Changed names of docs
Rmd 363f911 Ludvig Larsson 2021-05-05 Changed names of Rmds


To install STutility from github (currently only option), you need to have devtools installed:


Using devtools, execute the following from the R console to install STutility:


Common issues on Mac OS

If you run into Error in dyn.load(file, DLLpath = DLLpath, ...):, make sure you have XQuartz installed, which can be downloaded from

If you are missing gfortran you can get it from CRAN

Set up conda environment (Mac OS)

Below are instructions for how to set up a conda environment to install STutility.

From the terminal

conda create -n R4.0
conda activate R4.0
conda install -c conda-forge r-essentials r-base r-devtools r-spdep r-hdf5r
conda install -c bioconda r-fftwtools

From R


A work by Joseph Bergenstråhle and Ludvig Larsson


R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS/LAPACK: /Users/ludviglarsson/anaconda3/envs/R4.0/lib/libopenblasp-r0.3.12.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        jquerylib_0.1.3   pillar_1.7.0      compiler_4.0.3   
 [5] bslib_0.2.4       later_1.1.0.1     git2r_0.28.0      tools_4.0.3      
 [9] getPass_0.2-2     digest_0.6.27     jsonlite_1.7.2    evaluate_0.14    
[13] lifecycle_1.0.1   tibble_3.1.6      pkgconfig_2.0.3   rlang_1.0.1      
[17] cli_3.1.1         rstudioapi_0.13   yaml_2.2.1        xfun_0.20        
[21] httr_1.4.2        stringr_1.4.0     knitr_1.31        sass_0.3.1       
[25] fs_1.5.0          vctrs_0.3.8       rprojroot_2.0.2   glue_1.4.2       
[29] R6_2.5.0          processx_3.5.1    fansi_0.4.2       rmarkdown_2.7    
[33] callr_3.7.0       magrittr_2.0.1    whisker_0.4       ps_1.6.0         
[37] promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.1.1 httpuv_1.5.5     
[41] utf8_1.2.1        stringi_1.5.3     crayon_1.4.1