Last updated: 2021-05-23
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.
The R Markdown file has unstaged 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.
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 9ecc095. 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
Ignored: output/plots/.DS_Store
Ignored: output/plots/QC/.DS_Store
Ignored: output/plots/boxplots_select_taxa/.DS_Store
Ignored: output/plots/heatmaps/.DS_Store
Ignored: output/plots/maps/.DS_Store
Ignored: output/plots/tax_prev_abund/.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/supp_table_pos.xlsx
Untracked: tmp/
Unstaged changes:
Modified: README.md
Modified: analysis/_site.yml
Modified: analysis/index.Rmd
Modified: analysis/microbiome-viz.Rmd
Modified: analysis/phyloseq.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/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 | a69dea3 | siobhon-egan | 2021-04-24 | Build site. |
| Rmd | 6ebcc5d | siobhon-egan | 2021-04-24 | updates |
| html | 6ebcc5d | siobhon-egan | 2021-04-24 | updates |
| 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:
The bacterial biome of ticks and their wildlife hosts at the sylvatic urban interface.
Authors: Siobhon L. Egan, Casey L. Taylor, Peter B. Banks, Amy S. Northover, Liisa A. Ahlstrom, Una M. Ryan, Peter J. Irwin, Charlotte L. Oskam.
This publication is also a chpater of my PhD Thesis 2021
Raw Illumina MiSeq data is available at NCBI SRA project XXXXX
Nucleotide sequence data available on Genbank
Anaplasmataceae (long 16S rRNA)
MW633160--MW633167
Borrelia 16S rRNA
MW633074
Bartonella ITS
MW633076--MW633082
ASVs for taxa of interest
XXXXXX-XXXXXX
Data used but not directly produced for this manuscript.
Nucleotide data for identification of ticks
MW665133–MW665150
To build/view webiste locally
wflow_build() and wflow_view()
Status of workflow
wflow_status()
Publish website pages
wflow_publish(c("analysis/index.Rmd", "analysis/first-analysis.Rmd"), "Add my first analysis")
Push website to github
wflow_git_push()