Ross Mounce rossmounce

## 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)

## 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

## 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$|Literture Cited$)"

## 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)) {

## 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"/>

## 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)

## 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!

## 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 -

## sample.csv
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

## 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
	#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)
	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
	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)) {
	<?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"/>
	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)
	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!
	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 -