License

Last updated: 2021-04-30

Checks: 2 0

Knit directory: CassavaNIRS/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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

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Repository version: 88fee14

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The results in this page were generated with repository version 88fee14. 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:    .Rproj.user/
    Ignored:    Hershberger_CassavaNIRS_2021.zip
    Ignored:    analysis/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    data/Cassavabase_phenotypes_20210419.csv
    Ignored:    data/Corrected_metadata/
    Ignored:    data/README.html
    Ignored:    data/README.txt
    Ignored:    data/Spectra/
    Ignored:    data/TrialNameKey.csv
    Ignored:    data/raw_pheno.csv
    Ignored:    data/raw_scans.csv
    Ignored:    output/.DS_Store
    Ignored:    output/Figure2_DMC_distributions.png
    Ignored:    output/Figure4_within_predictions.png
    Ignored:    output/Figure5_Subsamples.png
    Ignored:    output/Figure6_RF_Importance.png
    Ignored:    output/Figure7_CV_predictions.png
    Ignored:    output/FigureS2_within_trial_prediction_all.png
    Ignored:    output/S1_overlapping_accession_counts.csv
    Ignored:    output/S3_removed_scans.csv
    Ignored:    output/Table2_DMC_statistics.csv
    Ignored:    output/Table3_performance_summary.csv
    Ignored:    output/TableS2_within_trial_predictions.csv
    Ignored:    output/TableS4_cv_results.csv
    Ignored:    output/cv_base.png
    Ignored:    output/cv_results.csv
    Ignored:    output/full_filtered_plots.csv
    Ignored:    output/full_filtered_subsamples.csv
    Ignored:    output/full_filtered_unaggregated.csv
    Ignored:    output/subsampling_prediction_results_2021.csv
    Ignored:    output/within_trial_waves_PLSR.csv
    Ignored:    output/within_trial_waves_RF.csv
    Ignored:    output/within_trial_waves_RF_importance.csv
    Ignored:    output/within_trial_waves_SVM.csv

Unstaged changes:
    Modified:   analysis/index.Rmd

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/license.Rmd) and HTML (docs/license.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	88fee14	Jenna Hershberger	2021-04-30	Build workflowr site
Rmd	8f143af	Jenna Hershberger	2021-04-21	Add content
Rmd	fecea09	Jenna Hershberger	2021-04-19	Start workflowr project.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.