workflowr

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Last updated: 2025-02-27

Checks: 7 0

Knit directory: analysis-user-group/

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.

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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(1337)

The command set.seed(1337) 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

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

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

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

Repository version: c05aafe

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 c05aafe. 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:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/data/
    Ignored:    analysis/figure/

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/adit/custom.css
    Modified:   workflow.R

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.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/0_contacts.Rmd) and HTML (docs/0_contacts.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	c05aafe	DrThomasOneil	2025-02-27	wflow_publish(c("analysis/*.Rmd"))
html	c7f5738	DrThomasOneil	2025-02-24	Build site.
html	79d09b1	DrThomasOneil	2025-02-24	Build site.
html	a5c9f2c	DrThomasOneil	2025-02-24	Build site.
html	ca2c086	DrThomasOneil	2025-02-24	Build site.
html	fca0503	DrThomasOneil	2025-02-24	Build site.
html	af42fba	DrThomasOneil	2025-02-24	Build site.
html	1aeefc7	DrThomasOneil	2025-02-20	Build site.
html	5fe30de	DrThomasOneil	2025-02-20	Build site.
html	5ef4f12	DrThomasOneil	2025-02-11	Build site.
html	f48f4f0	DrThomasOneil	2025-02-10	Build site.
html	3bfe847	DrThomasOneil	2025-02-10	Build site.
html	b14f3b5	DrThomasOneil	2025-02-10	Build site.
html	bfba3e0	DrThomasOneil	2025-02-07	Build site.
html	f3d6f87	DrThomasOneil	2025-02-04	Build site.
Rmd	525ffe6	DrThomasOneil	2025-02-04	wflow_publish(c("analysis/*.Rmd"))
html	f654b8d	DrThomasOneil	2025-02-04	Build site.
Rmd	e6ea78d	DrThomasOneil	2025-02-04	wflow_publish(c("analysis/*.Rmd"))
html	4968925	DrThomasOneil	2025-01-30	Build site.
html	299ff3d	DrThomasOneil	2025-01-28	Build site.
Rmd	272b312	DrThomasOneil	2025-01-28	wflow_publish(c("analysis/*"))
html	023005d	DrThomasOneil	2025-01-07	Build site.
Rmd	0ecb65d	DrThomasOneil	2025-01-07	Updated Getting Started in R. Chapter 1 completed
html	c893d70	DrThomasOneil	2025-01-06	Build site.
Rmd	8eec2ce	DrThomasOneil	2025-01-06	Initial Deployment
html	660b0f8	DrThomasOneil	2025-01-06	Build site.
Rmd	7cb1531	DrThomasOneil	2025-01-06	Initial Deployment
html	2e79a1d	DrThomasOneil	2025-01-06	Build site.
Rmd	451a21f	DrThomasOneil	2025-01-06	Initial Deployment

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Digital Research Skills Network
Committee Members

Committee Chair Thomas O’Neil PostDoc thomas.oneil@sydney.edu.au I have been with the Mucosal Immunity lab at WIMR since my honours year in 2018. I completed my PhD in 2023 and am now a post-doc in the same lab. Initially, my studies involved characterising anogenital T cells by flow cytometry, but having learned analytic programming during COVID, I now study all aspects of human tissue immunology via high-parameter proteomic and transcriptomic bioinformatic approaches. Specifically, I’ve been involved in identifying rare immune cell subsets and defining their roles in initial HIV infection. Recently, I’ve been developing and applying bioinformatic methods to investigate immune cells in inflamed and uninflamed human tissues using spatial technologies (IMC, Xenium & Visium).	Secretary Harry Robertson PhD Candidate Harry Robertson is a research student and aspiring bioinformatician at WIMR who was recently awarded a Fulbright Future Scholarship (Postgraduate) hosted by Harvard University. His Fulbright research focuses on identifying biomarkers for organ transplant health using advanced imaging techniques. Unlike traditional biomarkers, which often require expensive sequencing and are inaccessible to many, Harry’s innovative approach leverages machine learning to analyse imaging data, aiming to develop a universally available, non-invasive diagnostic tool for transplant recipients. Harry envisions a future where healthcare decisions are informed by comprehensive patient data: ‘my goal is to make this vision a reality by developing accessible biomarkers for organ transplant health.’	Communications Lead Vacant NA NA
Communications Deputy Elizabeth Dunn PhD Candidate NA	Events Coordinator Sifan Zhang PhD Candidate NA	Content Coordinator Yuchen Li PhD Candidate NA
Level 2 Representative Vacant NA NA	Level 3 Representative Vacant NA NA	Level 4 Representative Vacant NA NA
Level 5 Representative Jennifer Li PostDoc NA	Level 6 Representative Nicole Fewings PostDoc NA	Level 7 Representative Vacant NA NA
External Representative Erin Coll PhD Candidate NA	External Representative Shreya Rajesh Rao PhD Candidate NA	External Representative Givanna Putri PostDoc NA

Session information

sessionInfo()

R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.3

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: Australia/Sydney
tzcode source: internal

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

other attached packages:
[1] readr_2.1.5     dplyr_1.1.4     workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] bit_4.5.0.1       jsonlite_1.8.9    crayon_1.5.3      compiler_4.4.0   
 [5] promises_1.3.2    tidyselect_1.2.1  Rcpp_1.0.14       stringr_1.5.1    
 [9] git2r_0.35.0      parallel_4.4.0    callr_3.7.6       later_1.4.1      
[13] jquerylib_0.1.4   yaml_2.3.10       fastmap_1.2.0     R6_2.5.1         
[17] generics_0.1.3    knitr_1.49        tibble_3.2.1      rprojroot_2.0.4  
[21] tzdb_0.4.0        bslib_0.9.0       pillar_1.10.1     rlang_1.1.5      
[25] cachem_1.1.0      stringi_1.8.4     httpuv_1.6.15     xfun_0.50        
[29] getPass_0.2-4     fs_1.6.5          sass_0.4.9        bit64_4.6.0-1    
[33] cli_3.6.3         magrittr_2.0.3    ps_1.8.1          digest_0.6.37    
[37] processx_3.8.4    vroom_1.6.5       rstudioapi_0.17.1 hms_1.1.3        
[41] lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.3    glue_1.8.0       
[45] whisker_0.4.1     rmarkdown_2.29    httr_1.4.7        tools_4.4.0      
[49] pkgconfig_2.0.3   htmltools_0.5.8.1

Creators
Thomas O'Neil
Harry Robertson
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