Jan 8, 2019

rOpenSci HQ

We’ve rolled out a change on our website to facilitate exploring blog posts by authors. There’s a landing page for all authors at https://ropensci.org/authors/ that lets you easily navigate to posts by each author. In addition, at the bottom of each blog post you’ll find a link to more content by each author. On the page for each author (e.g., https://ropensci.org/authors/kelly-obriant/) you’ll find a link to their website. Huge thanks to Maëlle Salmon for all the work on this 🚀

Software 📦

CRAN: GitHub:

New packages

• The first version (v0.6.0) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. Checkout the docs to get started. Find the software review at https://github.com/ropensci/software-review/issues/238

New versions

• A new version (v0.2.7) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

  changes for dplyr compatability; bug fix

• A new version (v1.7.4) of neotoma is on CRAN - access the Neotoma Paleoecological Database. See the release notes for changes. Checkout the vignette to get started.

  get_dataset bug fix; fix to allowable dataset types

• A new version (v0.7.0) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes and expanded release notes for changes. Checkout the docs to get started.

  gains retry, verb, and url_fetch methods; new best practices vignette; now get intermediate response headers

• A new version (v0.3.2) of worrms is on CRAN - client for World Register of Marine Species. See the release notes for changes. Checkout the vignette to get started.

  fix hard coded date in a test

• A new version (v0.3.0) of cRegulome is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the release notes for changes. Checkout the vignettes to get started.

  bug fix, changes to cor_igraph, get_tf and get_mir

• A new version (v1.7.5) of RSelenium is on CRAN - R client for Selenium Remote WebDriver. See the release notes for changes. Checkout the docs to get started.

  fix switchToWindow issue in Firefox; new tutorial for running in IE

• A new version (v0.3.2) of taxa is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the release notes for changes. Checkout the vignette to get started.

  parsers now correctly handle zero length inputs; improvement to parse_tax_data param class_col

• A new version (v1.3.1) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.

  fixed non-running examples; update internal DB of station locations

• A new version (v0.0.9) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started.

  new fxn osmdata_sc(); osmdata object modified; add_osm_feature() and osmdata_sf() changes

• A new version (v0.3.2) of osmplotr is on CRAN - Bespoke Images of OpenStreetMap Data. See the release notes for changes. Checkout the docs to get started.

  verbose param of extract_osm_objects() renamed to quiet

• A new version (v0.7.6) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the vignette to get started.

  improve docs for solr fxns; fix search_anymatch() bug

• A new version (v2.0) of spelling is on CRAN - tools for spell checking. See the release notes for changes. Checkout the README to get started.

  spell_check_package() now checks README & NEWS; treat all input as UTF-8

• A new version (v3.0) of hunspell is on CRAN - High-Performance stemmer, tokenizer, and spell checker. See the release notes for changes. Checkout the vignette to get started.

  update bundled libhunspell to v1.7; add RStudio directory to the search path to use dictionaries installed via the RStudio IDE

• A new version (v0.8.6) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the vignette to get started.

  now using vcr for test caching; bold_seq() fixes: remove return chars, band-aid for large request time-outs

• A new version (v0.2.17) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started.

  use utils::download.file to avoid intermittent download issues on debian

• A new version (v1.0.2) of solrium is on CRAN - general purpose R interface to Solr. See the release notes for changes. Checkout the vignettes to get started.

  progress param added to search fxns supporting httr::progress(); new method json_request for Solr JSON request API; returning responseHeader & nextCursorMark when avail.

• A new version (v0.3.6) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.

  fix compatibility with readr v1.3.0 and tibble v2.0.0

• A new version (v1.3.0) of skynet is on CRAN - Bureau of Transport Statistics Data client. See the release notes for changes. Checkout the vignette to get started.

  new fxn download_t100()

• A new version (v2.0) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started.

  update poppler to 0.72.1; enable pdf_data() on systems >= 0.72.1

• A new version (v6.2.1) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.

  fixes for cran checks

• A new version (v0.1.0) of prism is on CRAN - Data from the Oregon State Prism Climate Project. See the release notes for changes. Checkout the vignette to get started. First version under new maintainer Alan Butler

  new fxns del_early_prov, get_prism_station_md; get_prism_dailys gains param check; many bug fixes

• A new version (v0.5.2) of visdat is on CRAN - create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using ggplot2. See the release notes for changes. Checkout the docs to get started.

Software Review ✔

We accept community contributed packages via our onboarding system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system), and the authors of the packages!

If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.

The following package was recently submitted:

• tradestatistics > Open Trade Statistics API Wrapper and Utility Program
  • Author: Mauricio Vargas
  • Issue: ropensci/onboarding#274
  • Reviewers:
    • Emily Riederer
    • Mark Padgham

On the blog

Software Review

April Wright wrote about her recently rOpenSci reviewed package treestartr, for automated generation of starting trees for total-evidence phylogenetic analyses. Generating reasonable starting trees for complex phylogenetic analyses

Ignasi Baromeus, Kevin Cazelles, and Jonas Geschke wrote about their recently rOpenSci reviewed package rcites for accessing the CITES Speciesplus database. rcites - The story behind the package

tech notes

Jeroen Ooms wrote about a new major release of the pdftools package, with two major improvements: low level text extraction and encoding improvements. pdftools 2.0: powerful pdf text extraction tools

Jeroen Ooms wrote about a new major release of the spelling package, including automatic checking of README and NEWS files, improved Markdown parsing, and more. Spelling 2.0: Improved Markdown and RStudio Support

Use cases

The following 21 works use/cite rOpenSci software:

• West et al. used rfishbase in their paper Improving consumption based accounting for global capture fisheries ¹
• Antão et al. used ecoretriever in their paper β‐diversity scaling patterns are consistent across metrics and taxa ²
• Blankers et al. used RSelenium in their paper 4-Fluoramphetamine in the Netherlands: Text-mining and sentiment analysis of internet forums ³
• O’Dea et al. used rotl in their paper Developmental temperature affects phenotypic means and variability: a meta-analysis of fish data ⁴
• Teixeira & Derudder wrote a paper about their package skynet SKYNET: An R package for generating air passenger networks for urban studies ⁵
• Lewis used cld2 in their paper Playing for keeps: a psychological measure of the probability of retaining a free agent in professional basketball ⁶
• Cholet et al. used rentrez in their paper Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples ⁷
• Die et al. used rentrez in their paper GeneHummus: A pipeline to define gene families and their expression in legumes and beyond ⁸
• Leaf & Oshima used rfishbase in their paper Construction and evaluation of a robust trophic network model for the northern Gulf of Mexico ecosystem ⁹
• Wong et al. used RSelenium in their article Identifying tweets from Syria refugees using a Random Forest classifier ¹⁰
• Tresch et al. used rotl in their paper Litter decomposition driven by soil fauna, plant diversity and soil management in urban gardens ¹¹
• Weismayer & Pezenka used cld2 in their paper Drivers of Emotions in Airbnb-Reviews ¹²
• Sodnomov et al. used MODIStsp in their conference paper Software for analysis of vegetation indices dynamics ¹³
• Maia et al. used magick in their paper pavo 2: new tools for the spectral and spatial analysis of colour in R ¹⁴
• Liu et al. used pdftools in their paper A text mining analysis of proceedings of the New Zealand Agronomy Society 1971-2017 using Natural Language Processing ¹⁵
• Cichosz used hunspell in their paper A case study in text mining of discussion forum posts: classification with bag of words and global vectors ¹⁶
• Mubeen used rdflib in their thesis Harmonizing major pathway databases to compare and evaluate their consensus ¹⁷
• Mioduchowska et al. used rentrez in their paper Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene ¹⁸
• Konkolova & Paralic used RSelenium in their conference paper Active Learning in Data Science Education ¹⁹
• Rehbach et al. used plotly in their paper Bridging Theory and Practice Through Modular Graphical User Interfaces ²⁰
• Singer et al. used plotly in their paper A survey of digitized data from U.S. fish collections in the iDigBio data aggregator ²¹

In the news

Matt Harris used rnoaa to visualize yearly deviation from median precipitation from 1948-2018 at the Philidelphia Internaional Airport. Link to code included.

"It seems to rain a lot around here."
I thought to myself at 3am as the wind whipped outside of the window and my sick kid finally fell back asleep. So, what does one do with such a thought? Make a plot!

code: https://t.co/bXjDbT3kYq
Thx @sckottie for rnoaa 📦 pic.twitter.com/Ia97kBi9bI

— Matt Harris (@Md_Harris) December 17, 2018

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Footnotes