Blog Archives

A drat repository for rOpenSci

August 4, 2015
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We're happy to announce the launch of a CRAN-style repository for rOpenSci at http://packages.ropensci.org This repository contains the latest nightly builds from the master branch of all rOpenSci packages currently on GitHub. This allows users to install development versions of our software without specialized functions such as install_github(), allows dependencies not hosted on CRAN to still be resolved automatically, and...

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The challenge of combining 176 x #otherpeoplesdata to create the Biomass And Allometry Database

June 3, 2015
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The challenge of combining 176 x #otherpeoplesdata to create the Biomass And Allometry Database

Despite the hype around "big data", a more immediate problem facing many scientific analyses is that large-scale databases must be assembled from a collection of small independent and heterogeneous fragments -- the outputs of many and isolated scientific studies conducted around the globe. Collecting and compiling these fragments is challenging at both political and technical levels. The political challenge is...

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Database interfaces

May 20, 2015
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Database interfaces

There are many different databases. The most familiar are row-column SQL databases like MySQL, SQLite, or PostgreSQL. Another type of database is the key-value store, which as a concept is very simple: you save a value specified by a key, and you can retrieve a value by its key. One more type is the document database, which instead of...

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Introducing a Wishlist for Scientific R Packages

March 10, 2015
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There are two things that make R such a wonderful programming environment - the vast number of packages to access, process and interpret data, and the enthusiastic individuals and subcommunities (of which rOpenSci is a great example). One, of course, flows from the other: R programmers write R packages to provide language users with more features, which makes everyone's jobs easier...

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Curling – exploring web request options

December 18, 2014
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rOpenSci specializes in creating R libraries for accessing data resources on the web from R. Most times you request data from the web in R with our packages, you should have no problem. However, you evenutally will run into problems. In addition, there are advanced things you can do modifying requests to web resources that fall in the advanced...

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Growth of open data in biology

November 10, 2014
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Growth of open data in biology

Why open data growth At rOpenSci we try to make it easier for people to use open data and contribute open data to the community. The question often arises: How much open data do we have? Another angle on this topic is: How much is open data growing? We provide access to dozens of data respositories through our various packages. We...

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Introducing Rocker: Docker for R

October 23, 2014
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Introducing Rocker: Docker for R

You only know two things about Docker. First, it uses Linux containers. Second, the Internet won't shut up about it. -- attributed to Solomon Hykes, Docker CEO So what is Docker? Docker is a relatively new open source application and service, which is seeing interest across a number of areas. It uses recent Linux kernel features (containers, namespaces) to shield processes. While its...

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New fiscal sponsorship agreement with NumFocus foundation

October 1, 2014
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New fiscal sponsorship agreement with NumFocus foundation

I’m very pleased to announce that rOpenSci has signed a comprehensive fiscal sponsorship agreement with the NumFocus foundation, a 501(c)3 nonprofit that supports R&D for open source scientific software projects. We are delighted to be in the company of esteemed projects such as IPython and Julia that share our goal of promoting reproducible research practices...

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NCEAS Codefest Follow-up

September 23, 2014
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The week after labor day, we had the pleasure of attending the NCEAS open science codefest event in Santa Barbara. It was great to meet folks like the new arrivals at the expanding Mozilla Science Lab, Bill Mills and Abby Cabunoc (Bill even already has a great post up about the codefest), and see...

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rOpenSci at NESCent Open Tree of Life Hackathon

August 15, 2014
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The Open Tree of Life project aims to synthesize our combined knowledge of how organisms relate to each other, and make the results available to anyone who wants to use them. At present, the project contains data from more than 4,000 published phylogenies, which combine with other data sources to make a tree that covers 2.5...

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