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Last updated: 2023-11-22

Checks: 1 1

Knit directory: Amphibolis_Posidonia_Comparison/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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 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.

Repository version: c347565

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 c347565. 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:    .Rproj.user/
    Ignored:    renv/library/
    Ignored:    renv/staging/

Unstaged changes:
    Modified:   analysis/GO_and_ortho.Rmd
    Modified:   analysis/GOenrichment.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/metagenome.Rmd
    Modified:   data/Lost_present_gene_lists/Genes_only_in_Algae.txt
    Modified:   data/Lost_present_gene_lists/Genes_only_in_Aquatics_and_Seagrasses.txt
    Modified:   data/Lost_present_gene_lists/Genes_only_in_Aquatics_and_Seagrasses_and_Terrestrials.txt
    Modified:   data/Lost_present_gene_lists/Genes_only_in_Duckweeds.txt
    Modified:   data/Lost_present_gene_lists/Genes_only_in_Seagrasses.txt
    Modified:   data/Lost_present_gene_lists/Genes_only_in_Terrestrials.txt
    Modified:   data/Lost_present_gene_lists/Genes_union_of_Seagrass_and_Aquatics_union.txt
    Modified:   data/arabidopsis_gene_level_comparison.xlsx
    Modified:   data/arabidopsis_gene_level_comparison_only_losts.xlsx
    Modified:   data/arabidopsis_gene_level_counts.xlsx
    Modified:   output/GO_results_genes_in_Algae_NOT_Duckweeds_NOT_Seagrasses_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_genes_in_Aquatics_NOT_Seagrasses_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_genes_in_Aquatics_and_Seagrasses_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_genes_in_Duckweeds_NOT_Algae_NOT_Seagrasses_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_genes_in_Seagrasses_NOT_Algae_NOT_Duckweeds_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_genes_in_Seagrasses_NOT_Aquatics_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_genes_in_Terrestrials_NOT_Aquatics_NOT_Seagrasses.csv.png
    Modified:   output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_intersect.csv.png
    Modified:   output/GO_results_genes_in_all_seagrasses_vs_backgroundAll_union.csv.png
    Modified:   output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_intersect.csv.png
    Modified:   output/GO_results_genes_in_all_seagrasses_vs_seagrassesBackground_union.csv.png
    Modified:   output/GO_results_genes_lost_A_antarctica_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_lost_P_australis_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_lost_Z_marina_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_lost_Z_muelleri_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_only_P_australis_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_only_Z_marina_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_only_Z_muelleri_not_other_seagrasses.csv.png
    Modified:   output/GO_results_genes_union_Aquatics_and_Seagrasses_NOT_Terrestrials.csv.png
    Modified:   output/GO_results_terrestrials_vs_union_aquatics_seagrasses.png
    Modified:   output/Lost_GO_terms_in_five_species.PlantSpecific.xlsx
    Modified:   output/Lost_GO_terms_in_five_species.xlsx
    Modified:   output/Seagrasses_shared_lost_genes.xlsx
    Modified:   output/all_GO_plots.Rdata
    Modified:   output/group_venn_image.Rdata
    Modified:   output/seagrass_venn_image.Rdata

Staged changes:
    Modified:   output/patchwork_seagrass_gene_loss.png
    Modified:   output/patchwork_terrestrials_gene_loss.png
    New:        output/patchwork_terrestrials_seagrasses_gene_loss.png

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	1d2eef4	Philipp Bayer	2023-11-20	Build site.
Rmd	27397c0	Philipp Bayer	2023-11-20	fix index links
html	27397c0	Philipp Bayer	2023-11-20	fix index links
Rmd	b5757ac	Philipp Bayer	2023-11-20	Expand metagenome analysis
html	b5757ac	Philipp Bayer	2023-11-20	Expand metagenome analysis
html	71ed61d	Philipp Bayer	2022-03-16	Build site.
Rmd	ef70004	Philipp Bayer	2022-03-16	workflowr:::wflow_publish(files = "analysis/index.Rmd")
html	a994174	Philipp Bayer	2022-03-10	Build site.
html	8886b0e	Philipp Bayer	2022-03-10	Build site.
Rmd	02708fd	Philipp Bayer	2022-03-10	New: fancy MSAs!!
html	1425b09	Philipp Bayer	2022-03-09	Build site.
Rmd	45b4b42	Philipp Bayer	2022-03-09	add better groups
html	2243fa6	Philipp Bayer	2022-02-23	muh files
html	1a19f93	Philipp Bayer	2022-02-23	Build site.
html	9b59467	Philipp Bayer	2022-02-23	Rewrite Orthofinder analysis
html	b8c0df3	Philipp Bayer	2022-02-22	Build site.
Rmd	709a40d	Philipp Bayer	2022-02-22	wflow_publish("analysis/index.Rmd")
html	c0db4a5	Philipp Bayer	2021-10-07	Build site.
Rmd	08b28ea	Philipp Bayer	2021-10-07	wflow_publish(files = c("analysis/*"))
html	76c8918	Philipp Bayer	2021-04-15	Build site.
Rmd	49dcbb8	Philipp Bayer	2021-04-15	wflow_publish(files = list.files("analysis/", pattern = "*Rmd",
Rmd	9e449bb	Philipp Bayer	2021-04-14	Add missing files
html	9e449bb	Philipp Bayer	2021-04-14	Add missing files
html	9e91425	Philipp Bayer	2021-04-14	Build site.
Rmd	fa39572	Philipp Bayer	2021-04-14	wflow_publish(c("analysis/plot.Rmd", "analysis/_site.yml", "analysis/index.Rmd"),
Rmd	a5be915	Philipp Bayer	2021-04-14	Start workflowr project.

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