datelife?datelife is an R package that allows researchers and the
general audience to obtain open scientific data on the age of any
organism they are interested in. datelife retrieves
organism ages from a database of dated phylogenetic trees (chronograms),
which have been peer-reviewed and published in association with a
scientific research article in an indexed journal (Open Tree of Life’s tree
store). As such, these organism ages constitute state-of-the-art,
peer-reviewed, public scientific knowledge, that can be accessed and
reused by experts and non-experts in the field alike.
datelife?You can install the datelife R package on your own
computer and use it locally.
If you do not want to deal with installation, you can go to DateLife’s interactive website application.
To learn more, please go to datelife’s
documentation website.
datelife R packagedatelife’s most recent stable version can be installed
with:
install.packages("datelife")datelife’s previous stable versions are available for
installation from the CRAN repository. For example, to install
version 0.6.1, you can run:
devtools::install_version("datelife", version="0.6.1")You can install datelife’s development version from its
GitHub repository with:
devtools::install_github("phylotastic/datelife")datelifeIf you use datelife for a publication, please cite the R
package and the accompanying paper:
O’Meara B, Sanchez-Reyes L, Eastman J, Heath T, Wright A, Schliep K, Chamberlain S, Midford P, Harmon L, Brown J, Pennell M, Alfaro M (2022). datelife: Scientific Data on Time of Lineage Divergence for Your Taxa. R package version 0.6.4, https://doi.org/10.5281/zenodo.593938.
Sanchez-Reyes L, O’Meara B (2019). “datelife: Leveraging databases and analytical tools to reveal the dated Tree of Life.” bioRxiv, 782094. https://doi.org/10.1101/782094.
You can get these citations and the bibtex entry with:
citation("datelife")
toBibtex(citation("datelife"))We welcome and encourage to post a GitHub
issue with any comments, ideas and questions about
datelife’s software and website. If you want to contribute
with code directly, we welcome and encourage pull
requests.
Package and function documentation was generated with roxygen2:
roxygen2::roxygenise()We used the package lintr to check for coding style:
lintr::lint_package()Code coverage was calculated with the package covr:
cov <- covr::package_coverage()
usethis::use_data(cov, overwrite = TRUE)You can see an interactive report of testing coverage:
covr::report(cov)And, find code with zero coverage:
covr::zero_coverage(cov)datelife’s hexsticker:Code used to generate current datelife’s logo hexsticker
is in data-raw/hexsticker-current.R
Vignettes are rendered automatically upon built. However, if you wish
to see how they look rendered before releasing the package, you can do
this with knitr::knit(). The following command renders the
vignette Getting_started_with_datelife as html:
knitr::knit("vignettes/Getting_started_with_datelife.Rmd")Using pkgdown for this is quite straightforward and
fun:
usethis::use_pkgdown()
pkgdown::build_site()To be able to release to CRAN, the first step is to pass the checks
locally. To run a local check, you can use the command
R CMD check from your terminal. For that, change
directories to the one above your working clone of the
datelife repo:
cd ../Generate a tar ball for your package by running
R CMD build package-name:
R CMD build datelifeFinally, run R CMD check package-tar-ball on the tar
ball that you just generated:
R CMD check --as-cran datelife_0.6.0.tar.gzIf you do not have access to different OS to test your package on, the rhub package allows remote testing on a variety of OS with the command:
rhub::check_for_cran()To submit to CRAN call devtools::release() and answer
the prompted questions. If the answer to all of these is yes,
the package will be submitted to CRAN :rocket:
This package is free and open source software, licensed under GPL.
datelife has been developed as part of the phylotastic (NSF-funded) project, and
is still under development.