Last updated: 2023-06-20

Checks: 2 0

Knit directory: dgrp-starve/

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.

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.

Repository version: e0e44f1

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 e0e44f1. 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:    code/snake/
    Ignored:    data/snake/

Untracked files:
    Untracked:  .snakemake/
    Untracked:  Rplot.pdf
    Untracked:  analysis/linearReg.Rmd
    Untracked:  bglr-f.R
    Untracked:  code/PCA/
    Untracked:  code/data-prep/
    Untracked:  code/fabio/
    Untracked:  code/gBayesC.R
    Untracked:  code/id_bank_creation.R
    Untracked:  code/intro-starve/
    Untracked:  code/methodComp/
    Untracked:  code/regress/
    Untracked:  colorCode
    Untracked:  data/bayesF.rds
    Untracked:  data/bayesM.rds
    Untracked:  data/bglr-f-130k.rds
    Untracked:  data/bglr-f.rds
    Untracked:  data/bglr-m-130k.rds
    Untracked:  data/bglr-m.rds
    Untracked:  data/corLoop-f-minus.rds
    Untracked:  data/corLoop-f.rds
    Untracked:  data/corLoop-m-Minus.rds
    Untracked:  data/corLoop-m-minus.rds
    Untracked:  data/corLoop-m.rds
    Untracked:  data/fRegress.txt
    Untracked:  data/fRegress_adj.txt
    Untracked:  data/fm.burglar
    Untracked:  data/gbayesC-f.Rds
    Untracked:  data/gbayesC-m.Rds
    Untracked:  data/gbayesC.Rds
    Untracked:  data/gbayes_100k-f.Rds
    Untracked:  data/gbayes_100k-m.Rds
    Untracked:  data/goGroups.txt
    Untracked:  data/id_bank
    Untracked:  data/id_bank.Rds
    Untracked:  data/mPart.txt
    Untracked:  data/mRegress.txt
    Untracked:  data/mRegress_adj.txt
    Untracked:  data/multiReg.rData
    Untracked:  data/pheno_f
    Untracked:  data/pheno_m
    Untracked:  data/starve-f.txt
    Untracked:  data/starve-m.txt
    Untracked:  data/xp-f.txt
    Untracked:  data/xp-m.txt
    Untracked:  data/xp_f
    Untracked:  data/xp_m
    Untracked:  data/y_save.txt
    Untracked:  f-cor.png
    Untracked:  figure/
    Untracked:  junk/
    Untracked:  m-cor.png
    Untracked:  notes/
    Untracked:  posterPlots.R
    Untracked:  runtime.png
    Untracked:  snake/

Unstaged changes:
    Modified:   .Rprofile
    Modified:   .gitattributes
    Modified:   .gitignore
    Modified:   README.md
    Modified:   _workflowr.yml
    Modified:   analysis/_site.yml
    Modified:   analysis/about.Rmd
    Deleted:    analysis/gremlo.R
    Modified:   analysis/license.Rmd
    Modified:   analysis/linReg.Rmd
    Deleted:    analysis/methodComp-f.Rmd
    Deleted:    analysis/methodComp-m.Rmd
    Modified:   analysis/methodComp.Rmd
    Modified:   analysis/methodPred.Rmd
    Modified:   analysis/multiComp.Rmd
    Modified:   analysis/multiReg.Rmd
    Modified:   analysis/pca.Rmd
    Modified:   analysis/predict.Rmd
    Modified:   analysis/recap.Rmd
    Modified:   analysis/rewrite.Rmd
    Modified:   analysis/starve.Rmd
    Deleted:    analysis/stepwise-f.Rmd
    Deleted:    analysis/stepwise-m.Rmd
    Deleted:    analysis/testing.R
    Deleted:    analysis/tips.Rmd
    Modified:   analysis/trace.Rmd
    Modified:   code/README.md
    Deleted:    code/baseScript-lineComp.R
    Deleted:    code/combineSNP.R
    Deleted:    code/four-comp.76979.err
    Deleted:    code/four-comp.76979.out
    Deleted:    code/four-comp.sbatch
    Deleted:    code/fourLinePrep.R
    Deleted:    code/line_avgMinus.R
    Deleted:    code/line_avgPlus.R
    Deleted:    code/line_difMinus.R
    Deleted:    code/line_difPlus.R
    Deleted:    code/snpGene.R
    Deleted:    code/starveDataPrep.R
    Modified:   data/README.md
    Modified:   data/avgMinus-result.txt
    Modified:   data/avgMinus.txt
    Modified:   data/avgPlus-result.txt
    Modified:   data/avgPlus.txt
    Modified:   data/difMinus-result.txt
    Modified:   data/difMinus.txt
    Modified:   data/difPlus-result.txt
    Modified:   data/difPlus.txt
    Modified:   data/geneHits.txt
    Modified:   data/snpList.txt
    Modified:   data/starve.csv
    Modified:   dgrp-starve.Rproj
    Modified:   output/README.md
    Modified:   output/avgMinus-result.txt
    Modified:   output/avgPlus-result.txt
    Modified:   output/difMinus-result.txt
    Modified:   output/difPlus-result.txt

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/index.Rmd) and HTML (docs/index.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 790a201 nklimko 2023-05-30 Build site.
Rmd 19e444b nklimko 2023-05-30 wflow_publish("analysis/index.Rmd")
html 1eea604 nklimko 2023-04-10 Build site.
Rmd d075224 nklimko 2023-04-10 wflow_publish("analysis/index.Rmd")
html 50b5899 nklimko 2023-03-05 Build site.
Rmd 6d91368 nklimko 2023-03-05 wflow_publish("analysis/index.Rmd")
html 3d4bedc nklimko 2023-01-22 Build site.
Rmd 3277dc5 nklimko 2023-01-22 wflow_publish("analysis/index.Rmd")
html 64c9c72 nklimko 2023-01-10 Build site.
Rmd 8b91e57 nklimko 2023-01-10 wflow_publish("analysis/index.Rmd")
html 94ee8ea nklimko 2023-01-10 Build site.
Rmd fb9edde nklimko 2023-01-10 wflow_publish("analysis/index.Rmd")
html 036d3cc nklimko 2023-01-10 Build site.
Rmd b2c1969 nklimko 2023-01-10 wflow_publish("analysis/index.Rmd")
html 736d53e nklimko 2023-01-10 Build site.
Rmd 5cc6e18 nklimko 2023-01-10 wflow_publish("analysis/*")
html 9e86f56 nklimko 2023-01-08 Build site.
Rmd 951799a nklimko 2023-01-08 wflow_publish("analysis/*")
html 3751eb8 nklimko 2022-12-14 Build site.
html 88ee9ec nklimko 2022-11-29 Build site.
html 37278c9 nklimko 2022-11-22 Build site.
html f09779e nklimko 2022-11-22 Build site.
html f1d6437 nklimko 2022-11-15 Build site.
html 79e98ca nklimko 2022-11-15 Build site.
html d23d7f7 nklimko 2022-11-11 Build site.
Rmd 3a282f1 nklimko 2022-11-11 wflow_publish("analysis/*")
html 0ce7be4 nklimko 2022-11-10 code sync
Rmd b90e540 nklimko 2022-11-09 wflow_git_commit(all = TRUE)
html b90e540 nklimko 2022-11-09 wflow_git_commit(all = TRUE)
html 81037cc nklimko 2022-11-09 html reworking, snp success
html e9314ce nklimko 2022-11-05 wflow_git_commit(all = TRUE)
Rmd 3dab5a8 nklimko 2022-11-01 all files for me
html 3dab5a8 nklimko 2022-11-01 all files for me

Weekly Projects

Resources