View 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))
View nested_taxa.Rmd
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 of using rentrez to investigate the taxonomic distribution of sequences in Genbank. I though it might be fun to extend it a little. Specifically:

View 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
View 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)
View cmd console
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
View latlongs.csv
10.38333 98.85
12.08 99.02
13.42306 101.94194
13.61222 104.04528
14.28 99.25
14.43333 101.36667
14.5 101
14.5 104
15.37 100.34
16.04611 99.23
View Angiosperm-orders.tre
(((t37:0.5,(((t64:0.8,t62:0.9):0.9,((t13:0.1,((t36:1,t9:0.1):0.4,(t41:0.4,t31:0.1):0.9):0.2):0.7,t51:0.1):0.001):0.4,((((((t24:0.3,t54:0.2):0.8,t30:0.3):0.9,t32:0.9):0.4,(t63:0.2,t6:0.3):0.9):0.3,(((t45:1,t8:0.4):1,((t48:0.3,t47:0.2):0.8,t17:0.6):0.7):0.9,t39:0.6):0.6):0.6,((t49:0.3,(t14:0.05,t60:0.2):0.5):0.7,((t23:0.3,t12:0.3):0.7,((t56:0.3,t7:0.3):0.2,(t58:0.9,((t43:0.2,t50:0.2):0.7,t4:0.6):0.3):1):0.7):0.4):1):0.6):1):0.1,(((t18:0.3,((t25:0.3,t3:0.7):0.2,t21:0.1):0.2):0.9,((t57:0.1,t10:0.6):0.2,((t46:0.1,t1:0.6):0.07,t34:0.6):0.07):0.004):0.1,(t42:0.8,(((((t15:0.04,t35:0.3):0.9,((t29:0.7,t40:0.02):0.7,(((t53:0.09,t16:0.04):0.01,t2:0.2):0.04,t26:0.5):0.07):0.7):0.4,((t27:0.1,t20:0.08):0.8,(((t22:0.8,t61:0.08):0.1,t59:0.5):0.8,(t33:0.8,t5:0.9):0.9):0.4):0.9):0.5,t19:0.09):0.04,((t28:0.8,(t52:0.3,t44:0.9):0.3):0.9,t38:1):0.3):0.5):0.3):0.4):0.7,t11:0.4);
View failbinoms
Abdulmajidia chaniana
Abdulmajidia maxwelliana
Abromeitiella brevifolia
Abromeitiella lorentziana
Abutilothamnus yaracuyensis
Acanthopeltis hirsuta
Acetabularia caliculus
Acetabularia ryukyuensis
Achasma triorgyale
Acmenosperma pringlei
View uniqgenus
Aa
Abarema
Abatia
Abdulmajidia
Abelia
Abeliophyllum
Abelmoschus
Abies
Abietinella
Abildgaardia
View plosone10k.txt
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000016
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000024
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000030
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000034
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000037
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000040
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000053
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000054
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000078
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000081