Ross Mounce rossmounce

## 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

## 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"/>

## Elsevier's Diamond OA Conference Day 1.txt
JG Bankier (JGB) highlights an article from a Bepress journal called "The Cat is Out of the Bag: Orientalism, Anti-Blackness,
and White Supremacy in Dr. Seuss's Children's Books" https://sophia.stkate.edu/rdyl/vol1/iss2/4/

PlumX metrics indicate this article been downloaded over 300,000 times. It featured in many news stories.

JGB's tips:
1.) Publish regularly
2.) "Google indexing is critical"
3.) "Important to have accurate reporting and readership tools" [so you can see and demonstrate readership]

## Elsevier's Diamond OA Conference Day 2.txt
Talk 1: Abel Packer, SciELO

92/298 SciELO journals now charge an APC

at article level 22037 articles in total for 2020(?)
42% in APC journals, 58% in non-APC journals

by the end of the year over 50% of the articles will be in APC-charging SciELO journals

SciELO is 'neutral' with regard to journal sustainability model (e.g. APC or non-APC).

## message
Date: Fri, 20 Dec 2019 22:05:03 +0000
Message-ID: <CAJr+OEyZ6kYp=5vLqsEk6CqmYCSNCOMbQrGqT5rnHZ98Fpqzbg@mail.gmail.com>
Subject: Why is ESA lobbying against immediate access to federally funded research?
From: Ross Mounce <ross.mounce@gmail.com>
To: ECOLOG-L@community.esa.org
Content-Type: multipart/alternative; boundary="000000000000b46a71059a29dec3"

--000000000000b46a71059a29dec3
Content-Type: text/plain; charset="UTF-8"

## crossref-retractions.R
install.packages('rcrossref')
install.packages('dplyr')

library(rcrossref)
library(dplyr)


# "total-results": 2309
# Crossref http://api.crossref.org/works?filter=update-type:retraction
# fyi the Retraction Watch database has many more 18969 "Retraction or Other Notices"

## OA-Nobel-with-rorcid-and-roadoi.R
install.packages('rorcid')
install.packages('roadoi')
library(roadoi)
library(rorcid)

#Example ORCID given is that of Carol Greider, American molecular biologist
an.ORCID.ID <- "0000-0002-5494-8126"

#This step gets all works publicly known to ORCID to be associated to this person
out <- works(orcid_id(your.ORCID.ID))

## nested_taxa.Rmd
```{r, echo=FALSE}
knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)
```


# and now, all animals and with nested taxonomic ranks

So, a few people liked [this example](https://gist.github.com/dwinter/8d7bde0579daf7466508)
of using `rentrez` to investigate the taxonomic distribution of sequences in
Genbank. I though it might be fun to extend it a little. Specifically:

## bryprunedultra.tre
(((Coleochaete:212.07930099999998674,Chaetosphaeridium:212.07930099999998674):163.33424199999998905,((Nitella:73.024890999999996666,Tolypella:73.024890999999996666):16.564201000000000619,((Lamprothamnium:10.743121999999999616,Chara:10.743121999999999616):28.257583000000000339,(Lychnothamnus:14.391325999999999397,Nitellopsis:14.391325999999999397):24.609379000000000559):50.588388000000001909):285.82445000000001301):494.6687610000000177,(((((Isoetes:156.72701000000000704,Selaginella:156.72701000000000704):27.453109999999998792,((Lycopodiella:34.541863999999996793,(Diphasiastrum:10.702004000000000516,Lycopodium:10.702004000000000516):23.839860000000001605):21.710502999999999219,Huperzia:56.252366999999999564):127.92775199999999813):232.42645099999998592,(((Danaea:46.076124999999997556,(Christensenia:21.918482999999998384,(Marattia:15.249475999999999587,(Archangiopteris:4.3772560000000000358,Angiopteris:4.3772560000000000358):10.872220000000000439):6.6690069999999996853):24.157641999999999172):338.698598000000004

## checking-Wellcome-DOIs.R
#!/usr/bin/env Rscript
#install.packages("dplyr")
#install.packages("httr")
library(dplyr, warn.conflicts=FALSE)
library(httr)
uniquedois <- read.csv(file="wellcomeDOIs.txt",header=F,stringsAsFactors = F)
uniquedois <- as.data.frame(uniquedois)
vec <- vector("list",length(uniquedois$V1))
for (doi in (seq(1,length(uniquedois$V1)))){
  vec[doi] <- try(http_status(GET(uniquedois$V1[doi], timeout(6), user_agent("Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.0; Trident/5.0; Trident/5.0)")))$message)
	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
	<?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"/>
	JG Bankier (JGB) highlights an article from a Bepress journal called "The Cat is Out of the Bag: Orientalism, Anti-Blackness,
	and White Supremacy in Dr. Seuss's Children's Books" https://sophia.stkate.edu/rdyl/vol1/iss2/4/

	PlumX metrics indicate this article been downloaded over 300,000 times. It featured in many news stories.

	JGB's tips:
	1.) Publish regularly
	2.) "Google indexing is critical"
	3.) "Important to have accurate reporting and readership tools" [so you can see and demonstrate readership]
	Talk 1: Abel Packer, SciELO

	92/298 SciELO journals now charge an APC

	at article level 22037 articles in total for 2020(?)
	42% in APC journals, 58% in non-APC journals

	by the end of the year over 50% of the articles will be in APC-charging SciELO journals

	SciELO is 'neutral' with regard to journal sustainability model (e.g. APC or non-APC).
	Date: Fri, 20 Dec 2019 22:05:03 +0000
	Message-ID: <CAJr+OEyZ6kYp=5vLqsEk6CqmYCSNCOMbQrGqT5rnHZ98Fpqzbg@mail.gmail.com>
	Subject: Why is ESA lobbying against immediate access to federally funded research?
	From: Ross Mounce <ross.mounce@gmail.com>
	To: ECOLOG-L@community.esa.org
	Content-Type: multipart/alternative; boundary="000000000000b46a71059a29dec3"

	--000000000000b46a71059a29dec3
	Content-Type: text/plain; charset="UTF-8"
	install.packages('rcrossref')
	install.packages('dplyr')

	library(rcrossref)
	library(dplyr)


	# "total-results": 2309
	# Crossref http://api.crossref.org/works?filter=update-type:retraction
	# fyi the Retraction Watch database has many more 18969 "Retraction or Other Notices"
	install.packages('rorcid')
	install.packages('roadoi')
	library(roadoi)
	library(rorcid)

	#Example ORCID given is that of Carol Greider, American molecular biologist
	an.ORCID.ID <- "0000-0002-5494-8126"

	#This step gets all works publicly known to ORCID to be associated to this person
	out <- works(orcid_id(your.ORCID.ID))
	```{r, echo=FALSE}
	knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)
	```


	# and now, all animals and with nested taxonomic ranks

	So, a few people liked [this example](https://gist.github.com/dwinter/8d7bde0579daf7466508)
	of using `rentrez` to investigate the taxonomic distribution of sequences in
	Genbank. I though it might be fun to extend it a little. Specifically:
	#!/usr/bin/env Rscript
	#install.packages("dplyr")
	#install.packages("httr")
	library(dplyr, warn.conflicts=FALSE)
	library(httr)
	uniquedois <- read.csv(file="wellcomeDOIs.txt",header=F,stringsAsFactors = F)
	uniquedois <- as.data.frame(uniquedois)
	vec <- vector("list",length(uniquedois$V1))
	for (doi in (seq(1,length(uniquedois$V1)))){
	vec[doi] <- try(http_status(GET(uniquedois$V1[doi], timeout(6), user_agent("Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.0; Trident/5.0; Trident/5.0)")))$message)