rossmounce’s gists

rossmounce / wordles.r

Last active December 10, 2015 13:58 — forked from sckott/beswordles.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 / CCBYjournals

Created March 4, 2013 17:02

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.

	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 / grep_references.sh

Last active December 20, 2015 09:58

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!

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 / Trees2Trees

Created August 12, 2013 16:59

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?

	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 / feeds.xml

Last active February 28, 2023 15:20

My OPML bundle of academic journal RSS feeds related to my interests (phylogenetics, palaeontology), split into 4 different thematic sections.

	<?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 / trythis

Created February 11, 2014 17:24

Content Negotiation, example of Internal Server Error

	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)

rossmounce / gist:9f514d330ac2092200c7

Created May 28, 2014 09:37

python regex

	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 / reply1.txt

Last active August 29, 2015 14:12

Reply to Rod Page (having technical problems posting this at PeerJ PrePrints)

	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 -

rossmounce / sample.csv

Created May 21, 2015 08:35

Data for gephi

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 / data_err.csv

Created May 23, 2015 15:09

csvclean data.csv ; 70 errors logged to data_err.csv 13666 rows were joined/reduced to 6628 rows after eliminating expected internal line breaks.

	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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