Setup URLs Episode names Transcripts Summary word usage Sentiment Most common positive and negative words Reply All is a great podcast. I’ve been wanting to learn some text analysis tools, and transcripts from the podcast are on their site. Took some approaches outlined in the tidytext package in this vignette, and used the tokenizers package, and some of the tidyverse. Code on github at sckott/nonoyes Also check out the html version...

This is how I edit videos of talks that I need to incorporate slides and video together I’m on a Mac import to iMovie (using v10 something) drop movie into editing section split pdf slides into individual files pdfseparate foobar.pdf %d.pdf convert individual pdf slides into png sips -s format png --out "${pdf%%.*}.png" "$pdf" import png’s into imovie for each image, drop into editing area where you want it when focused on the png of the slide: select crop, then - choose fit, say okay select “add as overlay” (very most left symbol), then choose picture in picture then choose swap then move inset to where you want it say okay rinse and repeat for all slides export - via File option share to youtube e....

UPDATE: pkg API has changed - updated the post below to work with the current CRAN version, submitted 2016-08-02 I was at a hackathon focused on Ocean Biogeographic Information System (OBIS) data back in November last year in Belgium. One project idea was to make it easier to get at data based on one or more marine regions. I was told that Marineregions.org is often used for shape files to get different regions to then do other work with....

We (rOpenSci) just held our 3rd annual rOpenSci unconference (https://unconf16.ropensci.org/) in San Francisco. There were a lot of ideas, and lots of awesome projects from awesome people came out of the 2 day event. One weird idea I had comes from looking at the Node world, where there are lots of tiny packages, instead of the often larger packages we have in the R world. One reason for tiny in Node is that of course you want a library to be tiny if running in the browser for faster load times (esp....

GenBank IDs, accession numbers and GI identifiers, are the two types of identifiers for entries in GenBank. (see this page for why there are two types of identifiers). Actually, recent news from NCBI is that GI identifiers will be phased out by September this year, which affects what I’ll talk about below. There are a lot of sequences in GenBank. Sometimes you have identifiers and you want to check if they exist in GenBank, or want to get one type from another (accession from GI, or vice versa; although GI phase out will make this use case no longer needed), or just get a bunch of identifiers for software testing purposes perhaps....

GitHub issues are great for humans to correspond over software, or any other project. At rOpenSci we use an issue based software review system (ropensci/onboarding). Software authors and reviewers go back and forth on the software, making a better product in the end. We have a relatively small number of pieces of software under review at any one time compared to e.g., scientific journals - however, even with the small number, we as organizers, and authors and reviewers can forget things....

scrubr is an R library for cleaning species occurrence records. It’s general purpose, and has the following approach: We think using a piping workflow (%>%) makes code easier to build up, and easier to understand. However, you don’t have to use pipes in this package. All inputs and outputs are data.frame’s - which makes the above point easier Records trimmed off due to various filters are retained as attributes, so can still be accessed for later inspection, but don’t get in the way of the data....

request is DSL for http requests for R, and is inspired by the CLI tool httpie. It’s built on httr. The following were driving principles for this package: The web is increasingly a JSON world, so we assume applications/json by default, but give back other types if not The workflow follows logically, or at least should, from, hey, I got this url, to i need to add some options, to execute request - and functions support piping so that you can execute functions in this order Whenever possible, we transform output to data....

The first version of binomen is now up on CRAN. It provides various taxonomic classes for defining a single taxon, multiple taxa, and a taxonomic data.frame. It is designed as a companion to taxize, where you can get taxonomic data on taxonomic names from the web. The classes (S3): taxon taxonref taxonrefs binomial grouping (i.e., classification - used different term to avoid conflict with classification in taxize) For example, the binomial class is defined by a genus, epithet, authority, and optional full species name and canonical version....

I gave two talks recently at the annual Crossref meeting, one of which was a somewhat technical overview of programmatic clients for Crossref APIs. Check out the talk here. I talked about the motivation for working with Crossref data by writing code/etc. rather than going the GUI route, then went over the various clients, with brief examples. We (rOpenSci) have been working on the R client rcrossref for a while now, but I’m also working on the Python and Ruby clients for Crossref....