All posts (Page 78 of 121)
R package test suites that include HTTP requests are dependent on an internet connection being up, the internet connection speed, changing behavior of the remote server, as well as changing response formats/data from a remote server. We ideally want to test functionality of our package relative to some known data that isn’t intermittently unavailable or changing. Caveat is that we do want to make sure the package fails well, including fails well in response to server failures, but these responses can be cached....
taxize was seven years old this last Saturday!
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What is taxize?
taxize is designed around making working with taxonomic names easier - abstracting away the details of what each of 20 or so taxonomic data sources require for a given use case.
A samping of use cases covered in taxize (all of these across many different data sources):
- Taxonomic identifier from a taxonomic name and vice versa
- Taxonomic name from a vernacular (common) name and vice versa
- Taxonomic hierarchy/classification from identifier or name
- Taxonomic children of an identifier or name
- All taxa downstream to a certain rank from identifier or name
- Taxonomic name synonyms from identifier or name
- Lowest common taxon and rank for an identifier or name
- Resolve taxonomic names, i.e., fix spelling errors
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History
taxize was one of our first packages. Our first commit was on 2011-05-19, uneventfully adding an empty README:
The drake R package is not only a reproducible research solution, but also a serious high-performance computing engine. The package website introduces drake, and this technical note draws from the guides on high-performance computing and timing in the drake manual.
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You can help!
Some of these features are brand new, and others are newly refactored. The GitHub version has all the advertised functionality, but it needs more testing and development before I can submit it to CRAN in good conscience. New issues such as r-lib/processx#113 and HenrikBengtsson/future#226 seem to affect drake, and more may emerge. If you use drake for your own work, please consider supporting the project by field-testing the claims below and posting feedback here.
Phylogenetic trees are commonly used to present evolutionary relationships of species. Newick is the de facto format in phylogenetic for representing tree(s). Nexus format incorporates Newick tree text with related information organized into separated units known as blocks. For the R community, we have ape and phylobase packages to import trees from Newick and Nexus formats. However, analysis results (tree + analysis findings) from widely used software packages in this field are not well supported. Some of them are extended from Newick and Nexus (e.g. RevBayes and BEAST outputs), while some of the others are just log files (e.g. r8s and PAML outputs). Parsing these output files is important for interpreting analysis findings....
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Icons in R
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style=" object-fit: cover; object-position: center; height: 150px; width: 150px; margin-right: 15px"
/>
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The <a href="https://github.com/ropenscilabs/icon">icon</a> package provides a convenient interface for adding icons from popular web fonts to R Markdown documents. The project began at <a href="https://ozunconf17.ropensci.org/">rOpenSci OzUnconf 2017</a>, and was developed by <a href="https://github.com/mitchelloharawild">Mitchell O’Hara-Wild</a>, <a href="https://github.com/earowang">Earo Wang</a> and <a href="https://github.com/timothyhyndman">Timothy Hyndman</a>. The package currently supports icons from <a href="https://fontawesome.com/">Font Awesome</a>, <a href="https://jpswalsh.github.io/academicons/">Academicons</a>, and <a href="https://ionicons.com/">ionicons</a>.
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</figure>
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Icons can be added to your R Markdown documents using short prefixes which identify the font’s library.
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