Add DOIs (#971)

* fix slugs

* add doi

content/blog/2012-11-26-is-invasive.md

@@ -6,6 +6,8 @@ author: Ignasi Bartomeus
 tags:
   - taxize
   - ecology
+params:
+  doi: "10.59350/q9qm8-wn123"
 ---
 
 The following was a guest post from [Ignasi Bartomeus](http://www.bartomeus.cat/es/ignasi/), originally [posted](https://ibartomeus.wordpress.com/2012/11/26/is-invasive/) on [his blog](https://ibartomeus.wordpress.com/) on 26 Nov, 2012. Check out a related blog post [here](https://sckott.github.com/2012/12/is-invasive/). Note the functionality discussed in this post is now in our [taxize](https://github.com/ropensci/taxize_) package under the function [`gisd_isinvasive`](https://github.com/ropensci/taxize_/blob/master/R/gisd_isinvasive.R). We hacked out a quick [Shiny](https://www.rstudio.com/shiny/) app so you can play around with the below function in taxize on the web to get invasive status and plot it on a phylogeny. Check it out [here](http://glimmer.rstudio.com/ropensci/taxize_invasive/).

content/blog/2013-03-08-ropensci-collaboration.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - GitHub
   - API
+params:
+  doi: "10.59350/3e5z4-vzm13"
 ---
 
 We have been writing code for R packages for a couple years, so it is time to take a look back at the data. What data you ask? The commits data from GitHub ~ data that records who did what and when.

content/blog/2013-03-14-ropensci-challenge.md

@@ -4,6 +4,8 @@ title: The 2013 rOpenSci challenge
 date: '2013-03-14'
 author:
   - Karthik Ram
+params:
+  doi: "10.59350/8gfs7-4d877"
 ---
 
 At rOpenSci we're very passionate about engaging with our community and getting more people on board with open science and open data. There are many challenges to be overcome before this practice becomes mainstream. Even when researchers  see the value in engaging more openly, the learning curve associated with various aspects of the workflow can seem daunting. To identify some of these challenges and barriers, we launched an open science challenge at the start of the year. If any researchers were interesting is using the suite of tools we've built so far, we offered to help them through the technical challenges they might encounter. We're excited to report that we'll be working closely with [Simon Queenborough](https://www.simonqueenborough.com/) and [Julien Colomb](http://lab.brembs.net/author/julien//) on this effort. Below are brief summaries of their work. Stay tuned for updates.

content/blog/2013-03-15-r-metadata.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - metadata
   - API
+params:
+  doi: "10.59350/k3kr3-q6f96"
 ---
 
 Scholarly metadata - the meta-information surrounding articles - can be super useful.  Although metadata does not contain the full content of articles, it contains a lot of useful information, including title, authors, abstract, URL to the article, etc.

content/blog/2013-04-12-rgbif-genus.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - rgbif
   - API
+params:
+  doi: "10.59350/6sqk2-6cy70"
 ---
 
 Real use cases from people using our software are awesome. They are important for many reasons: 1) They make the code more useable because we may change code to make the interace and output easier to understand; 2) They may highlight bugs in our code; and 3) They show us what functions users care the most about (if we can assume number of questions equates to use).

content/blog/2013-04-22-usgs_app.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - shiny
   - API
+params:
+  doi: "10.59350/36ry6-12147"
 ---
 
 Many US federal agencies are now running app competitions to highlight their web services (see [here](https://challenge.gov/)), and hopefully get people to build cool stuff using government data (see [Data.gov](https://www.data.gov/) for more). See [here](https://github.com/GSA/slash-developer-pages#readme) for a nice list of the US government's web services.

content/blog/2013-05-10-introducing-befdata.md

@@ -6,6 +6,8 @@ author: Karthik Ram
 tags:
   - packages
   - biodiversity
+params:
+  doi: "10.59350/n396e-zap95"
 ---
 
 *This is a guest post by Class-Thido Pfaff*

content/blog/2013-05-16-pyopensci.md

@@ -8,6 +8,8 @@ tags:
   - Python
   - pyOpenSci
   - API
+params:
+  doi: "10.59350/mk4kh-bfg87"
 ---
 *A guest blog post by Steve Moss*
 

content/blog/2013-05-20-updates.md

@@ -5,6 +5,8 @@ date: '2013-05-20'
 author: Scott Chamberlain
 tags:
   - API
+params:
+  doi: "10.59350/rw33v-yzb13"
 ---
 
 ## We've been busy

content/blog/2013-05-27-rbison.md

@@ -5,6 +5,8 @@ date: '2013-05-27'
 author: Scott Chamberlain
 tags:
   - API
+params:
+  doi: "10.59350/f31qw-58113"
 ---
 
 The USGS recently released a way to search for and get species occurrence records for the USA. The service is called [BISON](https://bison.usgs.gov//) (Biodiversity Information Serving Our Nation). The service has [a web interface](https://bison.usgs.gov//) for human interaction in a browser, and [two APIs](https://bison.usgs.gov//services.html) (application programming interface) to allow machines to interact with their database. One of the APIs allows you to search and retrieve data, and the other gives back maps as either a heatmap or a species occurrence map. The latter is more appropriate for working in a browser, so I'll leave that to the web app folks.

content/blog/2013-06-12-sloan.md

@@ -7,6 +7,8 @@ author:
 tags:
   - open science
   - funding
+params:
+  doi: "10.59350/d5j8x-fdp49"
 ---
 
 Today we are pleased to announce that rOpenSci has been awarded a generous 180K grant from the [Alfred P. Sloan foundation](https://www.sloan.org/). This funding will allow us to develop a whole new suite of tools and provide scientists with general purpose toolkits to access various kinds of scientific data. We will also be traveling a whole bunch this year and running workshops at several conferences and universities. If you'd like us to speak to your research group, please [get in touch](/contact/). We'll be at several events over the coming months including [The Ecological Society of America annual meeting](https://www.nceas.ucsb.edu/news/nceas-leads-hands-primer-ecoinformatics-ecological-society-americas-2013-conference), [The Open knowledge conference](https://okcon.org/), Science Online Climate, [American Geophysical Union](https://www.agu.org/Plan-for-a-Meeting/AGUMeetings/) and several others. Stay tuned for announcements on <a href="https://twitter.com/ropensci">Twitter</a>, our [blog](/blog/) ([rss](/feed.xml)) and new mailing list.

content/blog/2013-06-14-goals-for-year.md

@@ -7,6 +7,8 @@ author:
   - Scott Chamberlain
 tags:
   - funding
+params:
+  doi: "10.59350/wjaar-mfd62"
 ---
 
 At rOpenSci's virtual HQ we're busy planning out several exciting projects for the coming year thanks to the generous [180k grant from Sloan](/blog/2013/06/12/sloan/). In the interest of maintaining transparency with our community here are additional details of what we hope to accomplish and how we'll measure our successes. We have also posted a full copy of our proposal over at [figshare](https://figshare.com/articles/rOpenSci_Open_Tools_to_Facilitate_Data_Driven_Science_in_Ecology_and_Evolution/719786).

content/blog/2013-06-19-usgs-app.md

@@ -10,6 +10,8 @@ tags:
   - rgbif
   - taxize
   - rbison
+params:
+  doi: "10.59350/cvyj4-t2r13"
 ---
 
 R has a reputation of not playing nice on the web. At rOpenSci, we write R pacakages to bring data from around the web into R on your local machine - so we mostly don't do any dev for the web. However, the United States Geological Survey (USGS) recenty held an app competition - it was a good opportunity to play with R on the web. We won best overall app as described in [an earlier post on this blog][usgsold]. Check out our app **TaxaViewer** at <https://ropensci.shinyapps.io/taxaviewer/>. Last week we presented the app to the USGS - a video of the presentation will be coming soon. A screenshot:

content/blog/2013-07-04-rbison-geoson.md

@@ -7,6 +7,8 @@ tags:
   - rbison
   - API
   - geojson
+params:
+  doi: "10.59350/79ps2-cz128"
 ---
 
 We have a number of packages for getting species occurrence data: [rgbif][rgbif] and [rbison][rbison]. The power of R is that you can pull down this occurrence data, manipulate the data, do some analyses, and visualize the data - all in one open source framework.

content/blog/2013-07-17-style-geojson.md

@@ -8,6 +8,8 @@ tags:
   - geojson
   - json
   - maps
+params:
+  doi: "10.59350/pw9zy-vw739"
 ---
 
 [Previously on this blog][ropost] and on [my own personal blog][scottpost], I have discussed how easy it is to create interactive maps on Github using a combination of R, git and Github. This is done using a file format called [*geojson*](https://en.wikipedia.org/wiki/GeoJSON), a file format based on JSON (JavaScript Object Notation) in which you can specify geographic data along with any other metadata.

content/blog/2013-07-19-rWBclimate-maps.md

@@ -7,6 +7,8 @@ tags:
   - API
   - climate
   - maps
+params:
+  doi: "10.59350/ej8hd-7qe09"
 ---
 
 A recent video on the [PBS Ideas Channel](https://video.pbs.org/program/idea-channel/) posited that the discovery of [climate change is humanities greatest scientific achievement](http://www.youtube.com/watch?v=1M1BPz0nY3s). It took synthesizing generations of data from thousands of scientists, hundreds of thousands (if not more) of hours of computer time to run models at institutions all over the world.  But how can the individual researcher get their hands of some this data?  Right now the [World Bank](https://www.worldbank.org) provides access to global circulation model (GCM) output from between 1900 and 2100 in 20 year intervals via their [climate data api](https://data.worldbank.org/developers/climate-data-api).  Using our new package [rWBclimate](https://github.com/ropensci/rWBclimate) you can access model output from 15 different GCM's, ensemble data from all GCM's aggregated, and historical climate data.  This data is available at two different spatial scales, individual countries or watershed basins. On top of access to all this data, the API provides a way to download [KML](https://developers.google.com/kml/documentation/) definitions for each corresponding spatial element (country or basin).  This means with our package it's easy to download climate data and create maps of any of the thousands of datapoints you have access to via the API.

content/blog/2013-07-29-esa-2013.md

@@ -5,6 +5,8 @@ date: '2013-07-29'
 author: Karthik Ram
 tags:
   - conference
+params:
+  doi: "10.59350/ksn7m-n0y09"
 ---
 
 It's the last week in July and this means that ecologists across North America (and elsewhere) are busy returning from the field and  preparing their presentations and posters in anticipation of the annual Ecological Society of America meeting. The entire <a href="/about/#devteam">rOpenSci dev team</a> will be in attendance <a href="https://www.esa.org/minneapolis/">this year</a> and we have several workshops, talks, and events planned out. The topics range from half-day workshops on open data, data visualization, reproducible research, to an entire symposium on open science.

content/blog/2013-07-29-rWBclimate-rgbif.md

@@ -9,6 +9,8 @@ tags:
   - maps
   - GBIF
   - ecology
+params:
+  doi: "10.59350/ct0xn-dm714"
 ---
 
 One of our primary goals at ROpenSci is to wrap as many science API's as possible.  While each package can be used as a standalone interface, there's lots of ways our packages can overlap and complement each other.  Sure [He-Man](https://www.youtube.com/watch?v=7yeA7a0uS3A) usually rode [Battle Cat](https://en.wikipedia.org/wiki/Battle_Cat), but there's no reason he couldn't ride a my little pony sometimes too.  That's the case with our packages for [GBIF](https://www.gbif.org/) and the [worldbank climate data api](https://data.worldbank.org/developers/climate-data-api).  Both packages will give you lots and lots of data, but a shared feature of both is the ability to plot spatial information.  The [rWBclimate](https://github.com/ropensci/rWBclimate) package provides a robust mapping ability on top of access to climate data.  At it's most bare bones, it can be used as alternative to the built in mapping facilities included in [rgbif](https://github.com/ropensci/rgbif/).  Building on the example in the [rgbif tutorial](/tutorials/rgbif_tutorial.html#occurrencelist) we'll plot data for two species in the US and Mexico, the dark eyed junco (*Junco hyemalis*) and the wood duck (*Aix sponsa*).  Here's how you can use the kml interface from rWBclimate to download a map of the US and Mexico and overlay it with data from rgbif.

content/blog/2013-08-01-altmetrics.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - altmetrics
   - PLOS
+params:
+  doi: "10.59350/tbj2b-8wh87"
 ---
 
 We recently had a paper come out in [a special issue](https://www.niso.org/niso-io/isq/2013/06/information-standards-quarterly-summer-2013) on *article-level metrics* in the journal Information Standards Quarterly. Our paper basically compared article-level metrics provided by different aggregators. The other papers covered various article-level metrics topics from folks at PLOS, Mendeley, and more. [Get our paper](https://www.niso.org/niso-io/isq/2013/06/information-standards-quarterly-summer-2013/chamberlain).

content/blog/2013-08-05-noaa-sparklines.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - ecology
   - API
+params:
+  doi: "10.59350/va339-g5578"
 ---
 
 We have started a new R package interacting with NOAA climate data called **rnoaa**. You can find our package in development [here](https://github.com/ropensci/rnoaa) and documentation for NOAA web services [here](https://www.ncdc.noaa.gov/cdo-web/webservices). It is still early days for this package, but we wanted to demo what you can do with the package.

content/blog/2013-08-18-sciordata.md

@@ -7,6 +7,8 @@ tags:
   - climate change
   - phenology
   - API
+params:
+  doi: "10.59350/qn1hz-mtt61"
 ---
 
 I recently attended [ScienceOnline Climate][sciocweb], a conference in Washington, D.C. at AAAS. You may have heard of the [ScienceOnline annual meeting in North Carolina][sciox] - this was one of their topical meetings focused on Climate Change. I moderated a session on [working with data from the web in R][sciordata], focusing on climate data. Search Twitter for \#scioClimate for tweets from the conference, and \#sciordata for tweets from the session I ran. The following is an abbreviated demo of what I did in the workshop showing some of what you can do with climate data in R using our packages.

content/blog/2013-09-10-usecases.md

@@ -6,6 +6,8 @@ author:
   - Scott Chamberlain
 tags:
   - R
+params:
+  doi: "10.59350/jk446-9b744"
 ---
 
 Good discovery tools for sotware are important as they can facilitate the pace of software development, bugs are found and squashed and new features added more quickly, and users find software they need faster. We have a page on our website for [our packages](/packages/) that provides an overview of the packages we have, with descriptions and links.

content/blog/2013-09-11-taskview.md

@@ -6,6 +6,8 @@ author:
   - Scott Chamberlain
 tags:
   - R
+params:
+  doi: "10.59350/ek7gj-zj221"
 ---
 
 There is an increasing set of R packages for interacting with the web from R, whether it be the low level tools to interact with the web via http (see [RCurl][RCurl] and [httr][httr]), parsing data from the web (like [RJSONIO][RJSONIO] and [XML][XML]), or wrappers to web APIs that provide data (like [twitteR][twitteR]).

content/blog/2013-10-03-tutorials.md

@@ -5,6 +5,8 @@ date: '2013-10-03'
 author: Scott Chamberlain
 tags:
   - help
+params:
+  doi: "10.59350/sagq9-pny57"
 ---
 
 To help you use rOpenSci packages we put tutorials up on our site at [/tutorials](/tutorials). Up to now, we created them with combination of raw html + converting code blocks to html and inserting them, etc. -- it was a slow process to update them when changes happened in our packages.

content/blog/2013-10-03-uptaskview.md

@@ -5,6 +5,8 @@ date: '2013-10-03'
 author: Scott Chamberlain
 tags:
   - help
+params:
+  doi: "10.59350/pcksy-kpa65"
 ---
 
 Just a quick note that the Task View we have been working on with others **Web Technologies and Services** is up on CRAN now. Find it here [https://cran.r-project.org/web/views/WebTechnologies.html](https://cran.r-project.org/web/views/WebTechnologies.html).

content/blog/2013-10-08-shutdown.md

@@ -5,6 +5,8 @@ date: '2013-10-08'
 author: Scott Chamberlain
 tags:
   - help
+params:
+  doi: "10.59350/ry8d3-j7v47"
 ---
 
 With the US government shut down, many of the federal government provided data APIs are down. We write R packages to interact with many of these APIs. We have been tweeting about what APIs that are down related to R pacakges we make, but we thought we would write up a proper blog post on the issue.

content/blog/2013-10-15-altmetrics-conf.md

@@ -5,6 +5,8 @@ date: '2013-10-15'
 author: Scott Chamberlain
 tags:
   - altmetrics
+params:
+  doi: "10.59350/dpdag-xmv75"
 ---
 
 I attended the recent [ALM Workshop 2013][almworkshop] and [data challenge][datachal] hosted by Public Library of Science (PLOS) in San Francisco. The workshop covered various issues having to do with altmetrics, or article-level metrics (ALM). The same workshop last year definitely had a feeling of **we don't know x, y, and z**, while the workshop this year felt like we know a lot more. There were many great talks - you can see the list of speakers [here][talks]. I was there representing rOpenSci as altmetrics is one of the types of data for which we make R libraries ([rAltmetric][raltmetric] for Altmetric.com data, and [alm][alm] for the PLOS altmetrics data).

content/blog/2013-10-22-oaweek-rplos.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - rplos
   - textmining
+params:
+  doi: "10.59350/w4jr7-pmt65"
 ---
 
 Open access week is here!  We love open access, and think it's extremely important to publish in open access journals. One of the many benefits of open access literature is that we likely can use the text of articles in OA journals for many things, including text-mining.

content/blog/2013-10-23-style-geojson-polygon.md

@@ -9,6 +9,8 @@ tags:
   - geojson
   - json
   - maps
+params:
+  doi: "10.59350/2b2h5-5hf56"
 ---
 
 Previously on this blog we have discussed making geojson maps and uploading to Github for interactive visualization [with USGS BISON data][ropost], and [with GBIF data][ropost2], and on [my own personal blog][scottpost]. This is done using a file format called [*geojson*](https://en.wikipedia.org/wiki/GeoJSON), a file format based on JSON (JavaScript Object Notation) in which you can specify geographic data along with any other metadata.

content/blog/2013-11-04-data-to-cartodb.md

@@ -8,6 +8,8 @@ tags:
   - API
   - cartodb
   - maps
+params:
+  doi: "10.59350/z7ycs-vgk43"
 ---
 
 We have previously written about creating interactive maps on the web from R, with the interactive maps on Github. See [here](/blog/2013/10/23/style-geojson-polygon/), [here](/blog/2013/07/17/style-geojson/), [here](/blog/2013/07/04/rbison-geoson/), and [here](https://recology.info/2013/06/geojson/).

content/blog/2013-11-19-taxize-changes.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - taxonomy
   - API
+params:
+  doi: "10.59350/84ejb-q7a63"
 ---
 
 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)](https://cran.r-project.org/web/packages/taxize/index.html) with a lot of changes (see [here](https://github.com/ropensci/taxize#notes-on-the-itis-api) for a rundown). Here are a few highlights of the changes.

content/blog/2013-11-21-rgbif-changes.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - taxonomy
   - API
+params:
+  doi: "10.59350/g8ph1-ah536"
 ---
 
 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.

content/blog/2013-12-01-open-science-with-R.md

@@ -7,6 +7,8 @@ tags:
   - book
   - reproducible research
   - open science
+params:
+  doi: "10.59350/wmyt2-7cd29"
 ---
 
 **Upcoming Book on Open Science with R**

content/blog/2013-12-02-rplos-highlights.md

@@ -7,6 +7,8 @@ tags:
   - textmining
   - API
   - PLOS
+params:
+  doi: "10.59350/hhc04-p9x84"
 ---
 
 `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.

content/blog/2014-01-27-solr.md

@@ -6,6 +6,8 @@ author: Scott Chamberlain
 tags:
   - textmining
   - API
+params:
+  doi: "10.59350/6ttrs-n2f07"
 ---