rossmounce

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). 

rossmounce

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]

rossmounce

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 <[email protected]>
To: [email protected]
Content-Type: multipart/alternative; boundary="000000000000b46a71059a29dec3"

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

rossmounce

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"

rossmounce

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))

rossmounce

```{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:

rossmounce

(((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

rossmounce

#!/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)

rossmounce

Microsoft Windows [Version 6.3.9600]
(c) 2013 Microsoft Corporation. All rights reserved.

C:\Users\jing>npm install --global getpapers
npm ERR! Windows_NT 6.3.9600
npm ERR! argv "C:\\Program Files\\nodejs\\node.exe" "C:\\Program Files\\nodejs\\
node_modules\\npm\\bin\\npm-cli.js" "install" "--global" "getpapers"
npm ERR! node v6.9.2
npm ERR! npm  v3.10.9
npm ERR! file C:\Users\jing\AppData\Roaming\npm-cache\supports-color\1.3.1\packa

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