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View GitHub Profile
View wordles.r
#N.B. On *ubuntu RCurl may not install for you off the bat. If so read: http://www.omegahat.org/RCurl/FAQ.html & sudo apt-get install libcurl4-openssl-dev
install.packages(c("RCurl","twitteR","wordcloud","tm","stringr"))
library(twitteR); library(wordcloud); library(tm); library(stringr);
# Search for #mooc tweets
mooctweets <- searchTwitter("#mooc", n=2000)
length(mooctweets) # ends up with 713 as of 03-Jan-13 at 15:42 London time
# make into a data.frame
mooctweets_df <- twListToDF(mooctweets)
@rossmounce
rossmounce / CCBYjournals
Created Mar 4, 2013
This is an incomplete list of 'gold' open access journals that use the CC BY licence. Thanks to Cameron Neylon. Please add any you know of that I've missed. Hybrid OA journals are not to be listed here.
View CCBYjournals
Journal Name ISSN
Abstract and Applied Analysis 10853375
Acta Crystallographica Section E 16005368
Acta Electrotechnica et Informatica 13358243
Acta Linguistica Asiatica 22323317
Acta Medica Martiniana 13358421
Acta Societatis Botanicorum Poloniae 16977
Acta Universitaria 1886266
Acta Universitatis Palackianae Olomucensis : Gymnica 12121185
Acta Veterinaria Scandinavica 17510147
@rossmounce
rossmounce / grep_references.sh
Last active Dec 20, 2015
A grep command for all the different Reference List headings encountered in just two years worth of Zootaxa articles. Some post-publication standardization needed me thinks!
View grep_references.sh
egrep "(^Citations$|Cited Literature$|Literature [cC]ited$|Literatures cited$|Literature Cited\:$|References$|^references$|Refrences$|References [cC]ited$|REFERENCES$|Bibliography$|BIBLIOGRAPHY$|LITERATURE CITED$|LITERATURE cited$|REFERENCES CITED$|References \[not in Zootaxa format\]$|^Reference$|^Literature$|^References \(asterisks|^References \(except original descriptions|Litterature cited$|Literture Cited$)"
@rossmounce
rossmounce / Trees2Trees
Created Aug 12, 2013
A _really_ basic script for doing many-to-many tree2tree distance (RF) comparisons in R, using the phangorn package and the function treedist. I should probably use one of the 'apply' functions here, right?
View Trees2Trees
library(phangorn)
#264 REFERENCE trees in phylip format, PAUP numbering hence 2
ref2 <- read.tree("jackr2.tre")
#264 trees in phylip format to pair-wise compare to the reference trees, TNT numbering hence 1
tr2 <- read.tree("jack1.tre")
x <- {}
#all reference trees to one comp tree
for (i in 1:length(tr2)) {
@rossmounce
rossmounce / feeds.xml
Last active Oct 14, 2019
My OPML bundle of academic journal RSS feeds related to my interests (phylogenetics, palaeontology), split into 4 different thematic sections.
View feeds.xml
<?xml version="1.0" encoding="UTF-8"?>
<opml version="1.0">
<head>
<title>Ross's academic journal RSS feed subscriptions</title>
</head>
<body>
<outline text="General Biology Journals" title="General Biology Journals">
<outline type="rss" text="BioEssays" title="BioEssays" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1521-1878" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1002%2F%28ISSN%291521-1878"/>
<outline type="rss" text="Biol J Linn Soc" title="Biol J Linn Soc" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1111/(ISSN)1095-8312" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1111%2F%28ISSN%291095-8312"/>
@rossmounce
rossmounce / trythis
Created Feb 11, 2014
Content Negotiation, example of Internal Server Error
View trythis
curl -g --location --header 'Accept: application/x-bibtex' "http://dx.doi.org/10.1651/0278-0372(2005)025[0159:GR]2.0.CO;2" > test.txt
RETURNS
<h1>Internal Server Error</h1>
(I've encountered about 91 DOIs that appear to give this error)
View gist:9f514d330ac2092200c7
I know I'm doing all types of wrong here:
Source HTML file here: http://mdpi.com/1420-3049/19/4/5150/htm
I want the text for the dc.source:
Molecules 2014, Vol. 19, Pages 5150-5162
Am using beautiful soup, so probably best to do it in that BUT it should also be regex-able. I can do this in bash no problem!
@rossmounce
rossmounce / reply1.txt
Last active Aug 29, 2015
Reply to Rod Page (having technical problems posting this at PeerJ PrePrints)
View reply1.txt
Thanks for your feedback Rod. I really value it.
I don't pretend to have all the answers. All of the academic content discovery
services are fairly murky about how they actually index things,
as I'm sure you know (Google Scholar perhaps being the most open-ish about how it does things?).
> how comparable are PLoS and Zootaxa from the perspective of search engines?
I am not a search engine. I am a human researcher. Whether a paper is
published in Nature, Science, PLOS ONE or Zootaxa, it is the same to me -
View sample.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 34 columns, instead of 6. in line 1.
img1,Actinokineospora_fastidiosa,Amycolatopsis_alba_DSM_44262,Amycolatopsis_albidoflavus,Amycolatopsis_azurea,Amycolatopsis_balhimycina,Amycolatopsis_benzoatilytica,Amycolatopsis_coloradensis,Amycolatopsis_decaplanina_DSM_44594,Amycolatopsis_echigonensis,Amycolatopsis_kentuckyensis,Amycolatopsis_keratiniphila,Amycolatopsis_keratiniphila_subsp._nogabecina,Amycolatopsis_lexingtonensis,Amycolatopsis_lurida,Amycolatopsis_marina,Amycolatopsis_mediterranei,Amycolatopsis_methanolica_239,Amycolatopsis_nigrescens_CSC17Ta-90,Amycolatopsis_orientalis,Amycolatopsis_palatopharyngis,Amycolatopsis_plumensis,Amycolatopsis_regifaucium,Amycolatopsis_rifamycinica,Amycolatopsis_rubida,Amycolatopsis_saalfeldensis,Amycolatopsis_sacchari,Amycolatopsis_sp.,Amycolatopsis_sulphurea,Amycolatopsis_taiwanensis,Amycolatopsis_thermoflava_N1165,Amycolatopsis_tolypomycina,Amycolatopsis_vancoresmycina,Prauserella_rugosa
img2,Antarctobacter_heliothermus,Donghicola_eburneus,Jannaschia_helgolandensis,Ketogulonicigenium_vulgare,Loktanella_salsila
@rossmounce
rossmounce / data_err.csv
Created May 23, 2015
csvclean data.csv ; 70 errors logged to data_err.csv 13666 rows were joined/reduced to 6628 rows after eliminating expected internal line breaks.
View data_err.csv
line_number msg _id _full_text occurrenceID catalogNumber scientificName scientificNameAuthorship typeStatus locality country waterBody expedition recordedBy collectionCode kingdom phylum class order family genus subgenus specificEpithet infraspecificEpithet higherClassification taxonRank stateProvince continent island islandGroup higherGeography habitat decimalLongitude decimalLatitude geodeticDatum georeferenceProtocol maxError verbatimLongitude verbatimLatitude minimumElevationInMeters maximumElevationInMeters minimumDepthInMeters maximumDepthInMeters recordNumber individualCount lifeStage sex preparations identifiedBy dateIdentified identificationQualifier eventTime day month year earliestEonOrLowestEonothem latestEonOrHighestEonothem earliestEraOrLowestErathem latestEraOrHighestErathem earliestPeriodOrLowestSystem latestPeriodOrHighestSystem earliestEpochOrLowestSeries latestEpochOrHighestSeries earliestAgeOrLowestStage latestAgeOrHighestStage lowestBiostratigraphicZone highestBiostratigraphicZone group
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