All posts (Page 116 of 122)
Upcoming Book on Open Science with R
We’re pleased to announce that the rOpenSci core team has just signed a contract with CRC Press/Taylor and Francis R series to publish a new book on practical ways to implement open science into your own research using R. Given all the talk about the importance of open science, the discussion often lacks practical suggestions on how one might actually incorporate these practices into their day to day research workflow.
...rplos is an R package to facilitate easy search and full-text retrieval from all Public Library of Science (PLOS) articles, and we have a little feature which aren’t sure if is useful or not. I don’t actually do any text-mining for my research, so perhaps text-mining folks can give some feedback.
You can quickly get a lot of results back using rplos, so perhaps it is useful to quickly browse what you got. What better tool than a browser to browse? Enter highplos and highbrow. highplos uses the Solr capabilities of the PLOS search API, and lets you get back a string with the term you searched for highlighted (by default with <em> tag for italics).
The Global Biodiversity Information Facility (GBIF) is a warehouse of species occurrence data - collecting data from a lot of different sources. Our package rgbif allows you to interact with GBIF from R. We interact with GBIF via their Application Programming Interface, or API. Our last version on CRAN (v0.3) interacted with the older version of their API - this version interacts with the new version of their API. However, we also retained functions that interact with the old API....
We are building a taxonomic toolbelt for R called taxize - which gives you programmatic access to many sources of taxonomic data on the web. We just pushed a new version to CRAN (v0.1.5) with a lot of changes (see here for a rundown). Here are a few highlights of the changes.
Note: the windows binary may not be available yet…
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Install and load taxize
install.packages("taxize")
library(taxize)
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Taxonomic identifiers
Each taxonomic service has their own unique ID for a taxon. We had a way to get ITIS and NCBI identifiers before - we now have functions for Tropicos, EOL, and the Catalogue of Life.
...We have previously written about creating interactive maps on the web from R, with the interactive maps on Github. See here, here, here, and here.
A different approach is to use CartoDB, a freemium service with sql interface to your data tables that provides a map to visualize data in those tables. They released an R interace to their sql API on Github here - which we can use to make an interactive map from R.
We’ll first get some data from GBIF, ~500 occurrences of Puma concolor in the US, then push that data to a CartoDB table. There are a couple more non-programmatic steps in this workflow than with pushing geojson file to Github as outlined in the previous linked above (i.e., going to the CartoDB site and making a visualization, and making it public).
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