From 251c5cb182e28812714dc0337d0a5e834a95c06f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Thu, 13 Feb 2025 13:42:17 +0100 Subject: [PATCH] Add DOIs (#971) * fix slugs * add doi --- content/blog/2012-11-26-is-invasive.md | 2 + .../blog/2013-03-08-ropensci-collaboration.md | 2 + content/blog/2013-03-14-ropensci-challenge.md | 2 + content/blog/2013-03-15-r-metadata.md | 2 + content/blog/2013-04-12-rgbif-genus.md | 2 + content/blog/2013-04-22-usgs_app.md | 2 + .../blog/2013-05-10-introducing-befdata.md | 2 + content/blog/2013-05-16-pyopensci.md | 2 + content/blog/2013-05-20-updates.md | 2 + content/blog/2013-05-27-rbison.md | 2 + content/blog/2013-06-12-sloan.md | 2 + content/blog/2013-06-14-goals-for-year.md | 2 + content/blog/2013-06-19-usgs-app.md | 2 + content/blog/2013-07-04-rbison-geoson.md | 2 + content/blog/2013-07-17-style-geojson.md | 2 + content/blog/2013-07-19-rWBclimate-maps.md | 2 + content/blog/2013-07-29-esa-2013.md | 2 + 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100644 scripts/rogue.R diff --git a/content/blog/2012-11-26-is-invasive.md b/content/blog/2012-11-26-is-invasive.md index 99931f816..46218853a 100644 --- a/content/blog/2012-11-26-is-invasive.md +++ b/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/). diff --git a/content/blog/2013-03-08-ropensci-collaboration.md b/content/blog/2013-03-08-ropensci-collaboration.md index 03eda8fdf..06fbe5b96 100644 --- a/content/blog/2013-03-08-ropensci-collaboration.md +++ b/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. diff --git a/content/blog/2013-03-14-ropensci-challenge.md b/content/blog/2013-03-14-ropensci-challenge.md index ce91f03ed..3ac8b845c 100644 --- a/content/blog/2013-03-14-ropensci-challenge.md +++ b/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. diff --git a/content/blog/2013-03-15-r-metadata.md b/content/blog/2013-03-15-r-metadata.md index 64cb2dfab..df934f0a3 100644 --- a/content/blog/2013-03-15-r-metadata.md +++ b/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. diff --git a/content/blog/2013-04-12-rgbif-genus.md b/content/blog/2013-04-12-rgbif-genus.md index 9b44e9be8..c316397a6 100644 --- a/content/blog/2013-04-12-rgbif-genus.md +++ b/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). diff --git a/content/blog/2013-04-22-usgs_app.md b/content/blog/2013-04-22-usgs_app.md index 1a80867df..92b21f27e 100644 --- a/content/blog/2013-04-22-usgs_app.md +++ b/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. diff --git a/content/blog/2013-05-10-introducing-befdata.md b/content/blog/2013-05-10-introducing-befdata.md index 2e12bd2e7..41f98d44e 100644 --- a/content/blog/2013-05-10-introducing-befdata.md +++ b/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* diff --git a/content/blog/2013-05-16-pyopensci.md b/content/blog/2013-05-16-pyopensci.md index 3ad366685..4de05056b 100644 --- a/content/blog/2013-05-16-pyopensci.md +++ b/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* diff --git a/content/blog/2013-05-20-updates.md b/content/blog/2013-05-20-updates.md index 9bf396561..617c8a5e0 100644 --- a/content/blog/2013-05-20-updates.md +++ b/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 diff --git a/content/blog/2013-05-27-rbison.md b/content/blog/2013-05-27-rbison.md index 627348ac6..d5d03af1c 100644 --- a/content/blog/2013-05-27-rbison.md +++ b/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. diff --git a/content/blog/2013-06-12-sloan.md b/content/blog/2013-06-12-sloan.md index e19ba2b11..a12aea7ea 100644 --- a/content/blog/2013-06-12-sloan.md +++ b/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 Twitter, our [blog](/blog/) ([rss](/feed.xml)) and new mailing list. diff --git a/content/blog/2013-06-14-goals-for-year.md b/content/blog/2013-06-14-goals-for-year.md index 7fad403bb..19608297a 100644 --- a/content/blog/2013-06-14-goals-for-year.md +++ b/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). diff --git a/content/blog/2013-06-19-usgs-app.md b/content/blog/2013-06-19-usgs-app.md index ba8f1feb5..92023f160 100644 --- a/content/blog/2013-06-19-usgs-app.md +++ b/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 . Last week we presented the app to the USGS - a video of the presentation will be coming soon. A screenshot: diff --git a/content/blog/2013-07-04-rbison-geoson.md b/content/blog/2013-07-04-rbison-geoson.md index 6601ab59d..a47c8f83a 100644 --- a/content/blog/2013-07-04-rbison-geoson.md +++ b/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. diff --git a/content/blog/2013-07-17-style-geojson.md b/content/blog/2013-07-17-style-geojson.md index 4c48a6938..8181dfaa4 100644 --- a/content/blog/2013-07-17-style-geojson.md +++ b/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. diff --git a/content/blog/2013-07-19-rWBclimate-maps.md b/content/blog/2013-07-19-rWBclimate-maps.md index 5d4efa910..28ef57717 100644 --- a/content/blog/2013-07-19-rWBclimate-maps.md +++ b/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. diff --git a/content/blog/2013-07-29-esa-2013.md b/content/blog/2013-07-29-esa-2013.md index 4928ddb6c..a7201609d 100644 --- a/content/blog/2013-07-29-esa-2013.md +++ b/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 rOpenSci dev team will be in attendance this year 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. diff --git a/content/blog/2013-07-29-rWBclimate-rgbif.md b/content/blog/2013-07-29-rWBclimate-rgbif.md index 09e683302..6932d9399 100644 --- a/content/blog/2013-07-29-rWBclimate-rgbif.md +++ b/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. diff --git a/content/blog/2013-08-01-altmetrics.md b/content/blog/2013-08-01-altmetrics.md index 361d0de12..4462677b4 100644 --- a/content/blog/2013-08-01-altmetrics.md +++ b/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). diff --git a/content/blog/2013-08-05-noaa-sparklines.md b/content/blog/2013-08-05-noaa-sparklines.md index 32de6df0b..f45893d5e 100644 --- a/content/blog/2013-08-05-noaa-sparklines.md +++ b/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. diff --git a/content/blog/2013-08-18-sciordata.md b/content/blog/2013-08-18-sciordata.md index 82c91e37a..7d30fcff5 100644 --- a/content/blog/2013-08-18-sciordata.md +++ b/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. diff --git a/content/blog/2013-09-10-usecases.md b/content/blog/2013-09-10-usecases.md index cdb76753c..bbbd863a1 100644 --- a/content/blog/2013-09-10-usecases.md +++ b/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. diff --git a/content/blog/2013-09-11-taskview.md b/content/blog/2013-09-11-taskview.md index bfb74ffd3..5a95b5782 100644 --- a/content/blog/2013-09-11-taskview.md +++ b/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]). diff --git a/content/blog/2013-10-03-tutorials.md b/content/blog/2013-10-03-tutorials.md index d7cff4fbb..f5fd3a467 100644 --- a/content/blog/2013-10-03-tutorials.md +++ b/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. diff --git a/content/blog/2013-10-03-uptaskview.md b/content/blog/2013-10-03-uptaskview.md index 9326944cc..b52f44491 100644 --- a/content/blog/2013-10-03-uptaskview.md +++ b/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). diff --git a/content/blog/2013-10-08-shutdown.md b/content/blog/2013-10-08-shutdown.md index 80a8787b2..2294f70f9 100644 --- a/content/blog/2013-10-08-shutdown.md +++ b/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. diff --git a/content/blog/2013-10-15-altmetrics-conf.md b/content/blog/2013-10-15-altmetrics-conf.md index 382230c9f..81fa9c81c 100644 --- a/content/blog/2013-10-15-altmetrics-conf.md +++ b/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). diff --git a/content/blog/2013-10-22-oaweek-rplos.md b/content/blog/2013-10-22-oaweek-rplos.md index 091f6bbe7..38788eff8 100644 --- a/content/blog/2013-10-22-oaweek-rplos.md +++ b/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. diff --git a/content/blog/2013-10-23-style-geojson-polygon.md b/content/blog/2013-10-23-style-geojson-polygon.md index 4db3d0c87..612cce76e 100644 --- a/content/blog/2013-10-23-style-geojson-polygon.md +++ b/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. diff --git a/content/blog/2013-11-04-data-to-cartodb.md b/content/blog/2013-11-04-data-to-cartodb.md index 849578d09..a46145c03 100644 --- a/content/blog/2013-11-04-data-to-cartodb.md +++ b/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/). diff --git a/content/blog/2013-11-19-taxize-changes.md b/content/blog/2013-11-19-taxize-changes.md index 71408e864..426a19e67 100644 --- a/content/blog/2013-11-19-taxize-changes.md +++ b/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. diff --git a/content/blog/2013-11-21-rgbif-changes.md b/content/blog/2013-11-21-rgbif-changes.md index 9222d85b7..fc6b309ab 100644 --- a/content/blog/2013-11-21-rgbif-changes.md +++ b/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. diff --git a/content/blog/2013-12-01-open-science-with-R.md b/content/blog/2013-12-01-open-science-with-R.md index ceb04488b..96b77bd45 100644 --- a/content/blog/2013-12-01-open-science-with-R.md +++ b/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** diff --git a/content/blog/2013-12-02-rplos-highlights.md b/content/blog/2013-12-02-rplos-highlights.md index 7f84679c9..33047277c 100644 --- a/content/blog/2013-12-02-rplos-highlights.md +++ b/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. diff --git a/content/blog/2014-01-27-solr.md b/content/blog/2014-01-27-solr.md index c7a5e0d05..ab22248ec 100644 --- a/content/blog/2014-01-27-solr.md +++ b/content/blog/2014-01-27-solr.md @@ -6,6 +6,8 @@ author: Scott Chamberlain tags: - textmining - API +params: + doi: "10.59350/6ttrs-n2f07" --- diff --git a/content/blog/2014-01-30-ecoengine.md b/content/blog/2014-01-30-ecoengine.md index 6ecf60537..113773e1e 100644 --- a/content/blog/2014-01-30-ecoengine.md +++ b/content/blog/2014-01-30-ecoengine.md @@ -8,6 +8,8 @@ tags: - museums - biodiversity - informatics +params: + doi: "10.59350/61t3f-8ya07" --- 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 strong understanding of how species responded to past climate is key to understanding their responses in the future. Leading the way in opening up such valuable data is a new effort by the [ Berkeley Initiative in Global Change Biology](https://globalchange.berkeley.edu/ecoinformatics-engine) called the [Ecoengine](https://ecoengine.berkeley.edu/). diff --git a/content/blog/2014-02-03-caching-offline.md b/content/blog/2014-02-03-caching-offline.md index fa5392ac0..f7de443b5 100644 --- a/content/blog/2014-02-03-caching-offline.md +++ b/content/blog/2014-02-03-caching-offline.md @@ -5,6 +5,8 @@ date: '2014-02-03' author: Scott Chamberlain tags: - API +params: + doi: "10.59350/v74zb-9tt10" --- I've recently heard the idea of "offline first" via especially [Hood.ie](http://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 work done. diff --git a/content/blog/2014-02-10-ropensci-hackathon.md b/content/blog/2014-02-10-ropensci-hackathon.md index b4940c8a1..0c84be242 100644 --- a/content/blog/2014-02-10-ropensci-hackathon.md +++ b/content/blog/2014-02-10-ropensci-hackathon.md @@ -8,6 +8,8 @@ tags: - meetings - unconf - unconf14 +params: + doi: "10.59350/5f3vs-z0749" --- 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, writing, integrating and publishing data, a unit testing platform for data, and a mapping engine that can visualize various kinds of spatial data. Many of our projects are inspired by ad hoc discussions with other scientists and software developers both online (often on [Twitter](https://twitter.com/ropensci) and [GitHub](https://github.com/ropensci)) and offline. Several of these folks are now [regular contributors](/community/) to the project. To foster more such collaborations and drive new software innovations, we are excited to announce our first developer meeting next month at GitHub’s headquarters in San Francisco. This meeting is made possible by support from the Alfred P. Sloan foundation and GitHub. diff --git a/content/blog/2014-02-12-caching-with-api.md b/content/blog/2014-02-12-caching-with-api.md index 0ef09c1ac..c371f6f23 100644 --- a/content/blog/2014-02-12-caching-with-api.md +++ b/content/blog/2014-02-12-caching-with-api.md @@ -6,6 +6,8 @@ author: Scott Chamberlain tags: - API - EOL +params: + doi: "10.59350/pb2br-k4t21" --- In [a recent blog post][cacheoff] 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][eol], or Encyclopedia of Life. EOL allows you to set the amount of time (in seconds) that the call is cached, within which time you can make the same call and get the data back faster. We have a number of functions to interface with EOL in our `taxize` package. diff --git a/content/blog/2014-02-17-rgbif-update.md b/content/blog/2014-02-17-rgbif-update.md index 6986d7a52..f75f1e3d0 100644 --- a/content/blog/2014-02-17-rgbif-update.md +++ b/content/blog/2014-02-17-rgbif-update.md @@ -6,6 +6,8 @@ author: Scott Chamberlain tags: - API - GBIF +params: + doi: "10.59350/9vh5m-c3e32" --- `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. diff --git a/content/blog/2014-02-18-antweb.md b/content/blog/2014-02-18-antweb.md index a8326be43..0dacacd93 100644 --- a/content/blog/2014-02-18-antweb.md +++ b/content/blog/2014-02-18-antweb.md @@ -7,6 +7,8 @@ tags: - taxonomy - biodiversity - informatics +params: + doi: "10.59350/911zq-81w92" --- diff --git a/content/blog/2014-02-19-taxize-update.md b/content/blog/2014-02-19-taxize-update.md index 7f1576a11..ada83f901 100644 --- a/content/blog/2014-02-19-taxize-update.md +++ b/content/blog/2014-02-19-taxize-update.md @@ -7,6 +7,8 @@ tags: - API - taxize - taxonomy +params: + doi: "10.59350/czbbh-qz045" --- 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: diff --git a/content/blog/2014-02-21-dvn-dataverse-network.md b/content/blog/2014-02-21-dvn-dataverse-network.md index 61393df4d..c23719723 100644 --- a/content/blog/2014-02-21-dvn-dataverse-network.md +++ b/content/blog/2014-02-21-dvn-dataverse-network.md @@ -8,6 +8,8 @@ tags: - reproducible research - data - archiving +params: + doi: "10.59350/wweve-rt950" --- diff --git a/content/blog/2014-03-13-rnoaa.md b/content/blog/2014-03-13-rnoaa.md index 5c17eae74..cc2436521 100644 --- a/content/blog/2014-03-13-rnoaa.md +++ b/content/blog/2014-03-13-rnoaa.md @@ -6,6 +6,8 @@ author: Scott Chamberlain tags: - API - climate +params: + doi: "10.59350/549ga-0vh52" --- 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](https://www.ncdc.noaa.gov//), 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 data programatically. If you are so inclined to write a bit of R code, this means you can get to NCDC data in the R environment where your workflow is reproducible, and you can connect data acquisition to a suite of tools for data manipulation (e.g., `plyr`), visualization (e.g., `ggplot2`), and statistics (e.g., `lme4`, etc.). diff --git a/content/blog/2014-03-17-spocc.md b/content/blog/2014-03-17-spocc.md index f51b538ff..fb394a16f 100644 --- a/content/blog/2014-03-17-spocc.md +++ b/content/blog/2014-03-17-spocc.md @@ -8,6 +8,8 @@ tags: - biodiversity - species - occurrence +params: + doi: "10.59350/z9cvk-99y79" ---