All posts (Page 112 of 122)
We’re delighted to announce that we have received additional funding from the Sloan Foundation to continue and expand our efforts from the past year.
We’re grateful for the overwhelming support from the community, especially through engagement at various events we organized and attended this past year. Over the next year we plan to: advance not only the technical infrastructure for accessing, managing, and synthesizing large and heterogeneous data, but also the social infrastructure of research to facilitate collaboration and exchange of data, methods, and ideas so they can be easily reproduced and extended. Over the next several months you can expect to see various tools that allow for seamless data interoperability, a comprehensive spatial and mapping toolkit, and a new suite of tools to support reproducibility.
...Science is reportedly in the middle of a reproducibility crisis. Reproducibility seems laudable and is frequently called for (e.g., nature and science). In general the argument is that research that can be independently reproduced is more reliable than research that cannot be independently reproduced. It is also worth noting that reproducing research is not solely a checking process, and it can provide useful jumping-off points for future research questions. It is difficult to find a counter-argument to these claims, but arguing that reproducibility is laudable in general glosses over the fact that for each research group it is a significant amount of work to make their research (easily) reproducible for independent scientists. While much of the attention has focused on entirely repeating laboratory experiments, there are many simpler forms of reproducibility including, for example, the ability to recompute analyses on known sets of data....
We just released v0.3 of taxize. For details on the update, see the release notes.
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Some new features
- New function
iplant_resolve()to do name resolution using the iPlant name resolution service. Note, this is different from http://taxosaurus.org/ that is wrapped in thetnrs()function. - New function
ipni_search()to search for names in the International Plant Names Index (IPNI). See below for more. - New function
resolve()that unifies name resolution services from iPlant’s name resolution service (viaiplant_resolve()), Taxosaurus’ TNRS (viatnrs()), and GNR’s name resolution service (viagnr_resolve()). - All
get_functions now returning a new uri attribute that is a link to the taxon on the web. If NA is given back (e.g. nothing found), the uri attribute is blank. You can go directly to the uri in your default browser by doing, for example:browseURL(attr(result, "uri")).
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Updating to v0.3
Since taxize is not updated to v0.3 on CRAN yet at the time of writing this, install taxize from GitHub:
The rOpenSci project is a poster child for the fluid collaboration that has become increasingly common these days thanks to platforms like Twitter and GitHub. It has been really inspring to see open discussions take shape as rough ideas, which rapidly turn into prototype research software, all of which are now happening in the order of few days to weeks rather than months to years. The origins of this project itself lead back to a series of serendipitous conversations that occurred over Twitter three years ago. Today we are a rapidly growing community of scientists, students, software developers, and information researchers....
One of the goals of the rOpenSci is to facilitate interoperability between different data sources around web with our tools. We can achieve this by providing functionality within our packages that converts data coming down via web APIs in one format (often a provider specific schema) into a standard format. The new version of rWBclimate that we just posted to CRAN does just that. In an earlier post I wrote about how users could combine data from both rgbif and rWBclimate. Back then I just thought it was pretty cool that you could overlay the points on a nice climate map. Now we’ve come a long way, with the development of an easier to use and more comprehensive package for accessing species occurrence data, spocc, and added conversion functions to create spatial objects out of both climate data maps, and species occurrence data. The result is that you can grab data from both sources, and then extract climate information about your species occurrence data....
