Last updated: 2022-04-11

Checks: 2 0

Knit directory: Code/

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 ca60b02. 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:    Flexibility Comparisons.nb.html
    Ignored:    Main.nb.html
    Ignored:    PGLS.FullData.nb.html
    Ignored:    PGLSforeachMeasFeature.nb.html
    Ignored:    PGLSwithPCA_Dims.nb.html
    Ignored:    PreppedVertMeas.nb.html
    Ignored:    ProcessCymatogasterFiles.nb.html
    Ignored:    ProcessFCSVfiles.nb.html
    Ignored:    TestingHabitatwithFriedmanData.nb.html
    Ignored:    Trilok_tree.nb.html
    Ignored:    VertLM.nb.html
    Ignored:    VertMeasLDA_Attempt.nb.html
    Ignored:    VertPGLS.nb.html
    Ignored:    VertPairs.nb.html
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/10-VertLM.nb.html
    Ignored:    analysis/20-plot_phylogeny.nb.html
    Ignored:    analysis/21-plot_fits_and_summary.nb.html
    Ignored:    analysis/CheckSpeciesMatch.nb.html
    Ignored:    caper_test.nb.html
    Ignored:    data/.DS_Store
    Ignored:    ggtree_attempt.nb.html
    Ignored:    plot_example_data.nb.html
    Ignored:    plot_fits_and_summary.nb.html
    Ignored:    plot_phylogeny.nb.html
    Ignored:    renv/library/
    Ignored:    renv/staging/
    Ignored:    summarize_vert_meas.nb.html
    Ignored:    test_phylogeny.nb.html
    Ignored:    test_vertebraspace.nb.html
    Ignored:    vert_evol.Rproj

Untracked files:
    Untracked:  Main.html
    Untracked:  ProcessFCSVfiles.Rmd
    Untracked:  VertPGLS.html
    Untracked:  gg_saver.R
    Untracked:  output/BodyDistribution.pdf
    Untracked:  output/MasterVert_Measurements.csv
    Untracked:  output/mean_d_alphaPos_CBL.pdf
    Untracked:  output/pair_plot.pdf
    Untracked:  output/plot_example_data_figure.pdf
    Untracked:  output/stats_table.rtf
    Untracked:  plot_fits_and_summary.Rmd
    Untracked:  summarize_vert_meas.html
    Untracked:  testtree.csv
    Untracked:  vert_tree.csv

Unstaged changes:
    Modified:   CITATION

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/license.Rmd) and HTML (docs/license.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 ca60b02 Eric Tytell 2022-04-11 wflow_publish(“analysis/license.Rmd”)
html 5e4be8c Eric Tytell 2022-04-11 Build site.
Rmd 7983950 Eric Tytell 2022-04-11 wflow_git_commit(c(“analysis/about.Rmd”, “analysis/index.Rmd”,
Rmd b9f4976 Eric Tytell 2021-12-30 Start workflowr project.

Code

Analysis of vertebral morphology using phylogenetic generalized least squares.

Copyright (C) 2022. Eric D. Tytell, Dana Baxter, Karly E. Cohen, Cassandra Donatelli

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Text

Text in these notebooks and the text of the manuscript are licensed under a Creative Commons Attribution License (CC BY). which allows users to copy, distribute and transmit an article, adapt the article and make commercial use of the article. The CC BY license permits commercial and non-commercial re-use of an open access article, as long as the author is properly attributed.