Publications by rOpenSci Blog - R
rOpenSci developer meeting in March
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 tools. These include tools for reading, ...
2732 sym
Caching Encyclopedia of Life API calls
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 one does: EOL, or Encyclopedia of Life. EOL allows you to set the amount of time (in ...
2045 sym R (824 sym/4 pcs) 4 img
Changed and new things in the new version of rgbif, v0.5
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 files are now available on CRAN. There are a few new functions: count_facet,...
3389 sym R (3299 sym/7 pcs)
AntWeb – programmatic interface to ant biodiversity data
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 of AntWeb, I cam...
4997 sym R (4807 sym/11 pcs) 4 img
New features in the most recent taxize update, v0.2
We just released a new version of taxize – version 0.2.0. This release contains a number of new features, and bug fixes. Here is a run down of some of the changes: First, install and load taxize install.packages("rgbif") library(taxize) New things New functions: class2tree Sometimes you just want to have a visual of the taxonomic relationship...
3331 sym R (8386 sym/10 pcs) 2 img
dvn – Sharing Reproducible Research from R
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 i...
5784 sym R (4130 sym/12 pcs)
rnoaa – Access to NOAA National Climatic Data Center data
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 us can create clients for different programming languages to access their da...
3014 sym R (7274 sym/19 pcs) 6 img
Species occurrence data
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...
6738 sym R (3885 sym/10 pcs) 6 img
Accessing iNaturalist data
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 users turn casual observations into meanin...
4740 sym R (3983 sym/8 pcs) 4 img
The ins and outs of interacting with web APIs
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 the past. Common problems include passing incorrect paths, files b...
9301 sym