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.
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The results in this page were generated with repository version 3a8e4cd. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
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Unstaged changes:
Modified: analysis/_site.yml
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/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 |
|---|---|---|---|---|
| Rmd | 0d602a3 | siobhon-egan | 2021-05-23 | updates to pages |
| html | 0d602a3 | siobhon-egan | 2021-05-23 | updates to pages |
| 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 XXXXXX
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()