Last updated: 2021-07-01
Checks: 2 0
Knit directory: wildlife-bacteria/
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<<<<<<< HEAD Repository version: 76cd179
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<<<<<<< HEAD The results in this page were generated with repository version 76cd179. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files. ======= 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. >>>>>>> 939f8bd0220b7c36ec94acff0d2dac574ce1dd5b
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Unstaged changes:
Modified: analysis/_site.yml
Modified: analysis/index.Rmd
>>>>>>> 939f8bd0220b7c36ec94acff0d2dac574ce1dd5b
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 | <<<<<<< HEAD 76cd179 | siobhon-egan | 2021-07-01 | workflowr::wflow_publish(files = c("_workflowr.yml“,”analysis/_site.yml", |
| html | 76cd179 | siobhon-egan | 2021-07-01 | workflowr::wflow_publish(files = c("_workflowr.yml“,”analysis/_site.yml", |
| Rmd | 5f4c86d | siobhon-egan | 2021-05-23 | restructure pages |
| html | 5f4c86d | siobhon-egan | 2021-05-23 | restructure pages |
| Rmd | ======= >>>>>>> 939f8bd0220b7c36ec94acff0d2dac574ce1dd5b 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 European nucleotide archive the project accession number PRJEB46006 (ERP130188), which includes the following sample accession numbers:
Raw Illumina MiSeq data is available at NCBI SRA project XXXXXX
>>>>>>> 939f8bd0220b7c36ec94acff0d2dac574ce1dd5bNucleotide 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()