We just released v0.3 of taxize. For details on the update, see the release notes.
Some new features
New function iplant_resolve() to do name resolution using the iPlant name resolution service. Note, this is different from http://taxosaurus.org/ that is wrapped in the tnrs() function.
New function ipni_... [Read more...]
The rOpenSci project is a poster child for the fluid collaboration that has become increasingly common these days thanks to platforms like Twitter and GitHub. It has been really inspring to see open discussions take shape as rough ideas, which rapidly turn into prototype research software, all of which are ... [Read more...]
One of the goals of the rOpenSci is to facilitate interoperability between different data sources around web with our tools. We can achieve this by providing functionality within our packages that converts data coming down via web api's in one format (often a provider specific schema) into a standard format. ... [Read more...]
Editor's note: This is a guest post from Matt Sundquist form the Plot.ly team.
You can access the source code for this post at https://gist.github.com/sckott/10991885
Ggplotly and Plotly's R API let you make ggplot2 plots, add py$ggplotly(), and make your plots interactive, online, and ... [Read more...]
Editor's note: This is the first in a series of posts from rOpenSci's recent hackathon.
I recently had the pleasure of participating in rOpenSci's hackathon. To be honest, I was quite nervous to work among such notables, but I immediately felt welcome thanks to a warm and personable group. Alyssa ... [Read more...]
We've received a number of questions from our users about dealing with the finer details of data sources on the web. Whether you're reading data from local storage such as a csv file, a .Rdata store, or possibly a proprietary file format, you've most likely run into some issues in ... [Read more...]
The iNaturalist project is a really cool way to both engage people in citizen science and collect species occurrence data. The premise is pretty simple, users download an app for their smartphone, and then can easily geo reference any specimen they see, uploading it to the iNaturalist website. It let's ... [Read more...]
The rOpenSci projects aims to provide programmatic access to scientific data repositories on the web. A vast majority of the packages in our current suite retrieve some form of biodiversity or taxonomic data. Since several of these datasets have been georeferenced, it provides numerous opportunities for visualizing species distributions, building ... [Read more...]
We recently pushed the first version of rnoaa to CRAN - version 0.1. NOAA has a lot of data, some of which is provided via the National Climatic Data Center, or NCDC. NOAA has provided access to NCDC climate data via a RESTful API - which is great because people like ... [Read more...]
Reproducible research involves the careful, annotated preservation of data, analysis code, and associated files, such that statistical procedures, output, and published results can be directly and fully replicated. As the push for reproducible research has grown, the R community has responded with an increasingly large set of tools for engaging ... [Read more...]
Data on more than 10,000 species of ants recorded worldwide are available through from California Academy of Sciences' AntWeb, a repository that boasts a wealth of natural history data, digital images, and specimen records on ant species from a large community of museum curators.
Digging through some of the earliest announcements ... [Read more...]
rgbif is an R package to search and retrieve data from the Global Biodiverity Information Facilty (GBIF). rgbif wraps R code around the [GBIF API][gbifapi] to allow you to talk to GBIF from R.
We just pushed a new verion of rgbif to cran - v0.5.0. Source and binary ... [Read more...]
In a recent blog post we discussed caching calls to the web offline, on your own computer. Just like you can cache data on your own computer, a data provider can do the same thing. Most of the data providers we work with do not provide caching. However, at least ... [Read more...]
Our team has been cranking out a large number of tools over the past several months. As regular readers are aware, our software packages provide programmatic access to a diverse and extensive trove of scientific data. More recently we’ve expanded our efforts to build more general purpose and cross-domain ... [Read more...]
I've recently heard the idea of "offline first" via especially Hood.ie. We of course don't do web development, but primarily build R interfaces to data on the web. Internet availablility is increasinghly ubiqutous, but there still are times and places where you don't have internet, but need to get ... [Read more...]
Natural history museums have long been valuable repositories of data on species diversity. These data have been critical for fostering and shaping the development of fields such as biogeography and systematics. The importance of these data repositories is becoming increasingly important, especially in the context of climate change, where a ... [Read more...]
A number of the APIs we interact with (e.g., PLOS full text API, and USGS's BISON API in rplos and rbison, respectively) expose Solr endpoints. Solr is an Apache hosted project - it is a powerful search server. Given that at least two, and possibly more in the future, ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]