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Last updated: 2021-04-24

Checks: 1 1

Knit directory: wildlife-bacteria/

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: uncommitted changes

The R Markdown file has staged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: a0173d4

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 a0173d4. 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:    analysis/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  NCBI_data/
    Untracked:  analysis/microbiome-viz-extra.Rmd
    Untracked:  analysis/phylogeny.Rmd
    Untracked:  analysis/tois.Rmd
    Untracked:  data/dada2/
    Untracked:  data/dada2_tois/
    Untracked:  data/taxa_trees/
    Untracked:  data/tmp/
    Untracked:  output/beta-div-statistics.txt
    Untracked:  output/plots/
    Untracked:  output/supp_table_pos.xlsx
    Untracked:  tmp/

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   analysis/microbiome-viz.Rmd
    Deleted:    data/ps_bact_samp.RData
    Deleted:    data/ps_dec_bact.RData

Staged changes:
    New:        RData/amp_dec_bact.RData
    New:        RData/amp_raw_bact.RData
    New:        RData/ps_Ecol.RData
    New:        RData/ps_dec_bact.RData
    New:        RData/ps_raw_bact.RData
    New:        RData/taxa_of_interest.RData
    Modified:   analysis/QIIME2.Rmd
    Modified:   analysis/_site.yml
    Modified:   analysis/index.Rmd
    Modified:   analysis/microbiome-viz.Rmd
    Modified:   analysis/phyloseq.Rmd
    New:        analysis/site-map.Rmd
    New:        code/taxa_summary.R
    New:        data/ps_bact_samp.RData
    New:        data/ps_dec_bact.RData
    New:        data/site_map.xlsx

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	a0173d4	siobhon-egan	2021-02-26	Build site.
Rmd	d502188	siobhon-egan	2021-02-26	microbiome visualization
html	7aafdac	siobhon-egan	2021-02-26	Build site.
Rmd	0e683ca	siobhon-egan	2021-02-26	Publish the initial files for myproject
Rmd	681fc13	siobhon-egan	2021-01-29	Start workflowr project.

In the spirit of reproducibility this project website is created that outlines analysis done for the following publication:

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