Use of some ropensci packages on GitHub

[sckott]

Hi all, Was browsing a bit on GitHub, and thought I’d check for use of some of our packages on GitHub :

taxize

• https://github.com/davharris/tutoR
• https://github.com/EDiLD/restax
• https://github.com/asmeurer/cran-conda-recipes
• https://github.com/bw4sz/Maquipicuna
• https://github.com/GioBo/TR8
• https://github.com/balhoff/species-vulnerability-traits
• https://github.com/arundurvasula/scripts-n-scraps
• https://github.com/HajkD/biomartr
• https://github.com/chnops/TempleTexas - usage indicated at https://github.com/chnops/TempleTexas#get_valid_taxar
• https://github.com/dfalster/baad
• https://github.com/arundurvasula/FPS-repository
• https://github.com/kgturner/InvasionSyndicate
• https://github.com/nate-d-olson/genomic_purity
• https://github.com/nate-d-olson/peprr
• https://github.com/snaketron/GenPhen
• https://github.com/pedroj/FRUBASE
• https://github.com/maudbv/Post-doc-lincoln
• https://github.com/mauriemma/395-Git
• https://github.com/licaschiou/RoadkillViz
• https://github.com/QUICC-FOR/QUICCSQL
• https://github.com/SEEG-Oxford/ebola_zoonotic
• https://github.com/psmits/taxon_coverage
• https://github.com/bomeara/omearatenure
• https://github.com/slarge/ices
• https://github.com/eunices/Useful
• https://github.com/dmasaki/bisonr
• https://github.com/paulmcbride/lifemine
• https://github.com/ChrKoenig/World-Floras-Database
• https://github.com/wcornwell/TaxonLookup/blob/master/createlookup.R w/ https://github.com/wcornwell/TaxonLookup/blob/master/remake.yml
• https://github.com/grunwaldlab/metacoder
• https://github.com/jonesor/compadreDB
• https://github.com/fmichonneau/inat-poster
• https://github.com/PoisotLab/2015_ms_datamining (uses taxize to check if names are valid)
• https://github.com/PeteCowman/DIPnet
• https://github.com/wcornwell/sTEP_overlap

rgbif

• https://github.com/mkoo/BITW
• https://github.com/galius/gbif_app
• https://github.com/PauloEduardoCardoso/map_spdistribution
• https://github.com/ahhurlbert/brubertlab/blob/master/explore_rgbif.R
• https://github.com/kevinthenaturalist/finalproject
• https://github.com/ndimhypervol/wallace
• https://github.com/unhcr-jordan/communication
• https://github.com/RILAB/historical_genomics
• https://github.com/sarahsupp/hb-migration
• https://github.com/Terradue/dcs-r-gbifsst
• https://github.com/chgrl/leafletR/blob/79f822a1b7f0c31fdec08c3dd35dedd38add126f/R/fileToGeoJSON.R
• https://github.com/bsevansunc/Community_analysis
• https://github.com/Edouard-Legoupil/from-Excel-R
• https://github.com/BiologicalRecordsCentre/sparta
• https://github.com/jmprietob/rapps
• https://github.com/ecfarrer/SIGC
• https://github.com/RILAB/historical_genomics
• https://github.com/dagendresen/trait-mining/blob/master/R/gbif_example.R
• https://github.com/raquamaps/raquamaps - rgbif an import in this pkg
• https://github.com/ndimhypervol/wallace - a Shiny app using rgbif
• https://github.com/jakubecp/Article_1 - rgbif used in article looking at Nicrophorinae

rplos

• https://github.com/antagomir/scripts
• https://github.com/articlemetrics/plosOpenR
• https://github.com/Rnewbie/Bokeh
• https://github.com/qgeissmann/citaugur
• https://github.com/naupaka/open_sci_manuscript_figure
• https://github.com/jhollist/bloggingTweeting
• https://github.com/PLOS/plosr
• https://github.com/sagarnikam123/learnNPratice
• https://github.com/jonesor/compadreDB
• https://github.com/blmoore/blogR
• https://github.com/williamgunn/SciSentiment

rentrez

• https://github.com/gschofl/rmisc
• https://github.com/e3bo/2015phylo
• https://github.com/gschofl/gsmisc
• https://github.com/rOpenHealth/rpubmed
• https://github.com/Angel001/More-pubmed-terms
• https://github.com/massyah/PdbMine
• https://github.com/naupaka/open_sci_manuscript_figure
• https://github.com/e3bo/e3bo
• https://github.com/Wuandmu/statGeneticStuff
• https://github.com/snaketron/GenPhen
• https://github.com/glynnsc/whisky
• https://github.com/NBRAYKO/StaphRotation
• https://github.com/ls233/widget
• https://github.com/rnivelle4550/DataBase_Scripts_R
• https://github.com/izhbannikov/CoPubNet
• https://github.com/kaneplusplus/akde-pubmed
• https://github.com/rozeggo/ncbiTools
• https://github.com/VascoElbrecht/PrimerMiner - e.g., use in PrimerMiner/R/Download_mito.R - goal: download sequence information for specied groups, which then can be used to generate DNA barcoding primers or mini-barcodes for applications like DNA & eDNA metabarcoding.

rebird

• https://github.com/asmeurer/cran-conda-recipes
• https://github.com/ateucher/crd_rare_bird_bot
• https://github.com/STAT545-UBC/STAT545-UBC.github.io
• https://github.com/dmcglinn/quant_methods
• https://github.com/rocker-org/ropensci
• https://github.com/SixByNine/hitrun-scripts
• https://github.com/kenlau177/cpsc547
• https://github.com/crubba/Wiley-ADCR
• https://github.com/patricktoohey/GitHubR

rnoaa

• https://github.com/albre116/Weather_CHR
• https://github.com/dlebauer/bety-documentation
• https://github.com/ahhurlbert/brubertlab
• https://github.com/jcrb/RWeather
• https://github.com/rocker-org/ropensci
• https://github.com/MacHu-GWU/WB_working
• https://github.com/chadtopaz/ClimateApp
• https://github.com/flycat1989/RFinalProject
• https://github.com/ibreckhe/code
• https://github.com/ibreckhe/MORA_microclimate
• https://github.com/RENCI-Ecohydro/OSS-2014
• https://github.com/bsevansunc/Community_analysis
• https://github.com/crubba/Wiley-ADCR
• https://github.com/Pakillo/Rpackages_dir
• https://github.com/rmendels/xtractomatic
• https://github.com/marc28/Tech-Fundamentals
• https://github.com/rabravo/ws2pgdb
• https://github.com/potterzot/cbcct
• https://github.com/dkmehrmann/rnoaa_projects

git2r

• https://github.com/OHI-Science/ohi-webapps Ocean Health Index web apps
• https://github.com/ohibc/britishcolumbia Similar to above
• https://github.com/eddelbuettel/drat Drat R Archive Template by Dirk
• https://github.com/pghalliday/shiny-jira-project-analysis
• https://github.com/trosendal/gitcheckout Example use of git2r
• https://github.com/jefferislab/nat.flybrains
• https://github.com/stewid/gix An R package to search a Git repository - by the git2r creator
• https://github.com/rgrannell1/fresh Command-line tool for gathering statistics on the age of a git code-base
• https://github.com/rgrannell1/kea Composable Functional Programming in R
• https://github.com/dgrtwo/rgallery - Build a Gallery of R Snippets (e.g. http://varianceexplained.org/broom-gallery/)
• https://github.com/rdatsci/rt - R tools for the command line
• https://github.com/ropensci/ggit - Git visualization tools for git2r
• https://github.com/trosendal/giraffe - view the changes of a csv file in a git repo
• https://github.com/Mullefa/locallib - looking to create virtualenv for R

gender

• https://github.com/kathleenleeper/open-access-representation
• https://github.com/scottkosty/genderAnalysis Analysis of gender of R users
• https://github.com/phantom04/data-science-tools Collection of data science tools
• https://github.com/mdlincoln/caa_2015_data
• https://github.com/cblevins/Texas_Postmasters Postmaster appointments from TX
• https://github.com/seenya/HealthHack-ResearchFunding Hackathon project from http://www.healthhack.com.au/locations/melbourne/challenge5/
• https://github.com/NoiKristinsson/filmandgenderproject Gender and filmmakers
• https://github.com/blmoore/blogR Celebrity twitter demographics by gender

gistr

• https://github.com/cpsievert/LDAvis
• https://github.com/tdhock/animint
• https://github.com/gmbecker/switchrGist
• modulr package in the gist_gear() function
• https://github.com/WeihuaLei/textdatamining
• https://github.com/LewBurton/kitchen-sink-R

rwbclimate

• https://github.com/nicolegoebel/WorldBank_RstudioShinyApp World Bank Shiny app
• https://github.com/mkao006/sws_wasate
• https://github.com/mingjerli/rWBData
• https://github.com/ibreckhe/deltaC

rfigshare

• https://github.com/dfalster/Falster_2005_JEcol_data
• https://github.com/jcolomb/CeTrAn
• https://github.com/zoonproject/modules
• https://github.com/phantom04/coursera_getting_and_cleaning_data
• https://github.com/ecjbosu/RQuantInstall

spocc

• https://github.com/byam/Online-Courses
• https://github.com/jarioksa/natto An extreme vegan package of random, experimental and alien code
• https://github.com/bsevansunc/Community_analysis Community data of DC birds
• https://github.com/latif003/Phenology_Project
• https://github.com/tziol001/Geoscripting-Phenology-Project
• https://github.com/zoonproject/modules/blob/master/R/SpOcc.R - a module used in the zoon package
• https://github.com/jsgosnell/ratlantis - used as in import in the package, for collecting species occ. data
• https://github.com/jakubecp/sciodrepoides

rfishbase

• https://github.com/cddesja/R4Atlantis
• https://github.com/benjamincarr/Collapse Examination of the Causes of Fisheries Collapse
• https://github.com/colinpmillar/Ignoring-stock-structure presentation on ignoring stock structure in marine fish
• https://github.com/cddesja/rlantis helper functions for creating, manipulating, and viewing Atlantis files from R
• https://github.com/fishnets/fishnets A library of multivariate priors for fish population dynamics parameters
• https://github.com/PeteCowman/DIPnet A set of scripts for a NEScent Project “Diversity in the Indo-Pacific”
• https://github.com/bomeara/ComparativeMethodsInR - Brian O’Meara’s book on Comparative Methods in R
• https://github.com/boopsboops/nhamunda-checklist - code/data from Collins et al. (2015) Biodiversity Data Journal - usage here
• https://github.com/BrianHayden/Niche_scripts - uses rfishbase, rgbif, rglobi - e.g. code

paleobioDB

• https://github.com/ladykiyenz/branchlengths

elastic

• https://github.com/bindaasamit/wForceOptAnalytics
• https://github.com/shaozhifei/elasticsearch
• https://github.com/paulmoto/articleprofileupdate

solr

• https://github.com/lsq921224/tc

traits

• https://github.com/davharris/mistnet
• https://github.com/grunwaldlab/metacoder

rcrossref

• https://github.com/kmanlove/ParticipationInComputing - Explore rate & composition of individuals actively participating in the online statistical computing community
• openAPC - open dataset of APC charges at German universities https://github.com/OpenAPC/openapc-de
• A framework incorporating ropensci modules and several API’s to crawl bibliographic data https://github.com/Bubblbu/crawling-framework

rbison

• https://github.com/cgwillis/geo-scrub - Scrubs geo-referenced data against USDA Plants distribution

ckanr

• https://github.com/dspim/DSPCkan - ckanr is an import
• https://github.com/florianm/arewethereyet - a Shiny app uses ckanr
• https://github.com/florianm/shiny-timeseries - a Shiny app uses ckanr
• https://github.com/florianm/shreadthatsheet - a Shiny app uses ckanr
• https://github.com/datawagovau/ckan-o-sweave
• Eflores89/proyectos - used in a script

aRxiv

• A framework incorporating ropensci modules and several API’s to crawl bibliographic data https://github.com/Bubblbu/crawling-framework

fulltext

• https://github.com/flacomenoide/mapasMentales - actual use here

geojsonlint

• https://github.com/kamermanpr/geojsonBASIC - actual use here

geojsonio

• https://github.com/skgrange/gissr - geojsonio is an import
• https://github.com/Hackout2/repijson - geojsonio was an import (not anymore)
• reaktor/Neliohinnat - used in a script
• https://github.com/safferli/opendataday2016 - [actual use here]
  (https://github.com/safferli/opendataday2016/blob/d967ec90490d577459e88cfeec30ca2c5026abe9/get_shapefile.R)
• https://github.com/cyclestreets/transporthack - e.g., actual use here
• https://github.com/npct/pct - actual use here
• https://github.com/mwhittle91/20_Study - actual use here
• https://github.com/timelyportfolio/mapshaper_htmlwidget - actual use here - geojsonio is an import
• https://github.com/Robinlovelace/Creating-maps-in-R - actual use here
• https://github.com/i40poster/geoFracker - actual use here

geonames

• https://github.com/hadley/nycflights13 - actual use here
• https://github.com/jdrizin/artocarpus-mapping - actual use here

bold

• https://github.com/VascoElbrecht/PrimerMiner - http://onlinelibrary.wiley.com/wol1/doi/10.1111/2041-210X.12687/abstract

[cbogart]

Hi Sckott,

I like the status page; I hadn’t noticed it before.
A couple questions, and a plug for a related tool:

• Did you get these project listings in your message by searching for the name of each package on Github and copying down the interesting ones, or is it some automated search?
• I realize I’m looking at this a month after you posted it, but as of today the status page shows zero r-studio downloads for anything. Do you think rOpenSci package users just get their packages elsewhere, or is something broken?

I have a similar search in place, but not in quite as succinct a format, at http://scisoft-net-map.isri.cmu.edu, where among other things we’re analyzing references to all R packages by all Github projects**. For example we show 48 packages using taxize, shown here: http://scisoft-net-map.isri.cmu.edu/application/taxize/gitprojects. There’s also analyses of what the package is most used with, when github projects were updated, and counts of publications that cite the package.

We’re really interested in making our own software mapping tool more useful***, so it would be awesome if anyone out there is willing to poke around on our site, see what it shows for package(s) they’re familiar with or curious about, and then comment on what we could do to make it more practically useful to you. (either here, via email, or best of all, though the survey link that appears in the sidebar after visiting a few pages on the site (a red label that says “what do you think?”) ).

Thanks!
Chris Bogart

** I look for references to an R package either with a .R file containing “import()”, “requires()”, or a well-formatted DESCRIPTION file that Imports or Depends on a package.

*** My research group is interested in how scientists know the impact of the software they create, qualitatively and quantitatively. So, beyond plugging our own tool, I’m interested in any discussion here about how you all know how your packages get used, and what you do with that information.

[sckott]

@cbogart

Did you get these project listings in your message by searching for the name of each package on Github and copying down the interesting ones, or is it some automated search?

Just used advanced search of the package name, removing a bunch of users like ropensci, cran, etc, and language:R, etc. to narrow down

@cbogart

I realize I’m looking at this a month after you posted it, but as of today the status page shows zero r-studio downloads for anything.

Sorry about that, it’s sometimes not working. paging @karthik

@cbogart

For example we show 48 packages using taxize, shown here: http://scisoft-net-map.isri.cmu.edu/application/taxize/gitprojects.

Awesome! That’s a better solution than what I was doing (manual searching). I’ll definitely look around more on your site.

[karthik]

Yeah, thanks for the reminder on the status page. Metacran is having issues
that I’ll resolve after I finish with a current project.