Last updated: 2022-03-07
Checks: 2 0
Knit directory: wildlife-ticks/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
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 7b4fd7e. 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: analysis/_footer.html
Ignored: output/.DS_Store
Ignored: output/plots/.DS_Store
Untracked files:
Untracked: .Rprofile
Untracked: ENA_submission/
Untracked: NCBI_submission/
Untracked: analysis/images/
Untracked: data/
Untracked: experiments/
Untracked: flex.Rmd
Untracked: flex.html
Untracked: list.csv
Untracked: output/plots/allmap1.pdf
Untracked: output/plots/allmap2.pdf
Untracked: output/plots/allmapala1.pdf
Untracked: output/plots/allmapala2.pdf
Untracked: output/plots/combined-map5.pdf
Untracked: output/plots/combined-map6.pdf
Untracked: output/plots/combined-map7.pdf
Untracked: output/plots/combined-map8.pdf
Untracked: output/plots/map-ala.html
Untracked: output/plots/map-ala_files/
Untracked: output/plots/map-all-ala.html
Untracked: output/plots/map-all-ala_files/
Untracked: output/plots/map-all-curated.html
Untracked: output/plots/map-all-curated_files/
Untracked: output/plots/map-atrig-facet-edit.pdf
Untracked: output/plots/map-atrig-facet-edit.png
Untracked: output/plots/map-atrig-facet-edit.svg
Untracked: output/plots/map-atrig-subspecies1.pdf
Untracked: output/plots/map-atrig-subspecies2.pdf
Untracked: output/plots/map-atrig1.pdf
Untracked: output/plots/map-atrig2.pdf
Untracked: output/plots/map-ixhol1-edit.pdf
Untracked: output/plots/map-ixhol1-edit.png
Untracked: output/plots/map-ixhol1-edit.svg
Untracked: output/plots/map-ixtas1-edit.pdf
Untracked: output/plots/map-ixtas1-edit.png
Untracked: output/plots/map-ixtas1-edit.svg
Untracked: output/plots/maplegend-ala.pdf
Untracked: output/plots/maplegend-edit.pdf
Untracked: output/plots/maplegend-edit.png
Untracked: output/plots/maplegend-edit.svg
Untracked: output/plots/maplegend.pdf
Untracked: speciesNames.csv
Untracked: temp/
Unstaged changes:
Modified: README.md
Modified: analysis/_site.yml
Deleted: analysis/mapping.Rmd
Deleted: output/plots/combined-map.pdf
Modified: output/plots/combined-map1.pdf
Modified: output/plots/combined-map2.pdf
Modified: output/plots/combined-map3.pdf
Modified: output/plots/combined-map4.pdf
Deleted: output/plots/map-atrig-comb-nolegend.pdf
Deleted: output/plots/map-atrig-comb.pdf
Modified: output/plots/map-atrig-facet.pdf
Deleted: output/plots/map-atrig-simple1.pdf
Deleted: output/plots/map-atrig-simple2.pdf
Modified: output/plots/map-ixhol1.pdf
Modified: output/plots/map-ixhol2.pdf
Modified: output/plots/map-ixtas1.pdf
Modified: output/plots/map-ixtas2.pdf
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 | 7b4fd7e | Siobhon Egan | 2022-03-07 | Update prj website |
| html | cbb925a | Siobhon Egan | 2022-02-19 | Build site. |
| Rmd | cf0cae8 | Siobhon Egan | 2022-02-19 | Publish |
| Rmd | 4d29a72 | Siobhon Egan | 2022-02-19 | re-build to consolidate related data |
| html | 4d29a72 | Siobhon Egan | 2022-02-19 | re-build to consolidate related data |
In the spirit of reproducibility this project website is created that outlines analysis done relating to analysis of Australian ticks.
Project website available here http://siobhonlegan.com/wildlife-ticks/ and source code is available at https://github.com/siobhon-egan/wildlife-ticks/
Illumina MiSeq data generated from the metabarcoding of ticks targeting the 12S rRNA locus has been deposited in the European nucleotide archive under the project accession number PRJEB46056 (ERP130244), which includes the following sample accession numbers: ERS6635126–ERS6635348 (BioSample # SAMEA8952359–SAMEA8952582)
Nucleotide data for subset of zOTUs generated are available in for the molecular identification of ticks has been uploaded to GenBank under accession numbers MW665133–MW665150.
Nucleotide data for MSLT barcode sequence data produced by Sanger sequencing has been deposited in GenBank under the following accession numbers