R

I’ve been working on a little thing called httping - a small R package that started as a pkg to Ping urls and time requests. It’s a port of the Ruby gem httping. The httr package is in Depends in this package, so its functions can be called directly, without having to load httr explicitly yourself. In addition to timing requests, I’ve been tinkering with how to make http requests, with curl options accepting and returning the same object so they can be chained together, and then that object passed to a http verb like GET. Maybe this is a bad idea, but maybe not. ...

We’ve (ropensci) been working on an R client for interacting with Elasticsearch for a while now, first commit was November 2013. Elasticsearch is a document database built on the JVM. elastic interacts with the Elasticsearch HTTP API, and includes functions for setting connection details to Elasticsearch instances, loading bulk data, searching for documents with both HTTP query variables and JSON based body requests. In addition, elastic provides functions for interacting with APIs for indices, documents, nodes, clusters, an interface to the cat API, and more. ...

I maintain, along with other awesome people, the taxize R package - a taxonomic toolbelt for R, for interacting with taxonomic data sources on the web. Taxonomy data is not standardized, but there are a lot of common elements, and there is a finite list of taxonomic ranks, and finite number of major taxonomic data sets. Thus, I’ve been interested in attempting to define a pseudo standard for expressing taxonomic data in R. The conversation started a while back in a GitHub issue, and hasn’t moved very far. ...

Discourse is a great discussion forum application. It’s another thing from Jeff Atwood, the co-founder of Stackoverflow/Stackexchange. The installation is epecially easy with their dockerized installation setup on DigitalOcean ([instructions here][https://www.digitalocean.com/community/tutorials/how-to-install-discourse-on-ubuntu-14-04]). In rOpenSci, we’ve been using a Google Groups mailing list, which is sufficient I guess, but doesn’t support Markdown, and we all know Google can kill products any day, so it makes sense to use something with which we have more control. We’ve set up our own Discourse installation to have rOpenSci discussions - find it at discuss.ropensci.org. Check it out if you want to discuss anything rOpenSci related, or general open science, open source software, etc. You can login with email, Mozilla Persona, Twitter, or GitHub. ...

At rOpenSci we’ve been working on an R package (geojsonio) to make converting R data in various formats to geoJSON and topoJSON, and vice versa. We hope to do this one job very well, and handle all reasonable use cases. Functions in this package are organized first around what you’re working with or want to get, geojson or topojson, then convert to or read from various formats: geojson_list()/topojson_list() - convert to geojson/topojson as R list format geojson_json()/topojson_json() - convert to geojson/topojson as json geojson_read()``topojson_read() - read a geojson/topojson file from file path or URL geojson_write()/topojson_write() - write a geojson/topojson file locally Each of the above functions have methods for various objects/classes, including numeric, data.frame, list, SpatialPolygons, SpatialPolygonsDataFrame, SpatialLines, SpatialLinesDataFrame, SpatialPoints, SpatialPointsDataFrame. ...

GitHub has this site https://gist.github.com/ in which we can share code, text, images, maps, plots, etc super easily, without having to open up a repo, etc. GitHub gists are a great way to throw up an example use case to show someone, or show code that’s throwing errors to a support person, etc. In addition, there’s API access, which means we can interact with Gists not just from their web interface, but from the command line, or any programming language. There are clients for Node.js, Ruby, Python, and on and on. But AFAIK there wasn’t one for R. Along with Ramnath and others, we’ve been working on an R client for gists. v0.1 is now on CRAN. Below is an overview. ...

I was in San Francisco last week for an altmetrics conference at PLOS. While there, I visited the Asian Art Museum, just the Roads of Arabia exhibition. It was a great exhibit. While I was looking at the pieces, I read many labels, and thought, “hey, what if someone wants this metadata”? Since we have an R package in development for scraping museum metadata (called musemeta), I just started some scraping code for this museum. Unfortunately, I don’t think the pieces from the Roads of Arabia exhibit are on their site, so no metadata to get. But they do have their main collection searchable online at https://www.asianart.org/collections/collection. Examples follow. ...

The Lagotto application is a Rails app that collects and serves up via RESTful API article level metrics data for research objects. So far, this application has only been applied to scholarly articles, but will see action on datasets soon. Martin Fenner has lead the development of Lagotto. He recently set up a discussion site if you want to chat about it. The application has a nice GUI interface, and a quite nice RESTful API. ...

The Lagotto application is a Rails app that collects and serves up via RESTful API article level metrics data for research objects. So far, this application has only been applied to scholarly articles, but will see action on datasets soon. Martin Fenner has lead the development of Lagotto. He recently set up a discussion site if you want to chat about it. The application has a nice GUI interface, and a quite nice RESTful API. ...

At rOpenSci we occasssionally hear from our users that they run into an error like: Error in function (type, msg, asError = TRUE) : easy handled already used in multi handle This error occurs in the httr package that we use to do http requests to sources of data on the web. It happens when e.g., you make a lot of requests to a resource, then it gets interrupted somehow - then you make another call, and you get the error above. Let’s try it with the an version of httr (v0.5): ...