Skip to content

Instantly share code, notes, and snippets.

Ross Mounce rossmounce

Block or report user

Report or block rossmounce

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
@rossmounce
rossmounce / feeds.xml
Last active Oct 14, 2019
My OPML bundle of academic journal RSS feeds related to my interests (phylogenetics, palaeontology), split into 4 different thematic sections.
View 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"/>
View 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"
@rossmounce
rossmounce / OA-Nobel-with-rorcid-and-roadoi.R
Last active Jul 14, 2017
How many freely accessible works do Nobel prize winners have?
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
```{r, echo=FALSE}
knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)
```
# and now, all animals and with nested taxonomic ranks
So, a few people liked [this example](https://gist.github.com/dwinter/8d7bde0579daf7466508)
of using `rentrez` to investigate the taxonomic distribution of sequences in
Genbank. I though it might be fun to extend it a little. Specifically:
@rossmounce
rossmounce / bryprunedultra.tre
Last active Mar 16, 2017
Reproducing an error when trying to calculate Blomberg's K for a large 11499 tip tree
View bryprunedultra.tre
(((Coleochaete:212.07930099999998674,Chaetosphaeridium:212.07930099999998674):163.33424199999998905,((Nitella:73.024890999999996666,Tolypella:73.024890999999996666):16.564201000000000619,((Lamprothamnium:10.743121999999999616,Chara:10.743121999999999616):28.257583000000000339,(Lychnothamnus:14.391325999999999397,Nitellopsis:14.391325999999999397):24.609379000000000559):50.588388000000001909):285.82445000000001301):494.6687610000000177,(((((Isoetes:156.72701000000000704,Selaginella:156.72701000000000704):27.453109999999998792,((Lycopodiella:34.541863999999996793,(Diphasiastrum:10.702004000000000516,Lycopodium:10.702004000000000516):23.839860000000001605):21.710502999999999219,Huperzia:56.252366999999999564):127.92775199999999813):232.42645099999998592,(((Danaea:46.076124999999997556,(Christensenia:21.918482999999998384,(Marattia:15.249475999999999587,(Archangiopteris:4.3772560000000000358,Angiopteris:4.3772560000000000358):10.872220000000000439):6.6690069999999996853):24.157641999999999172):338.698598000000004
View checking-Wellcome-DOIs.R
#!/usr/bin/env Rscript
#install.packages("dplyr")
#install.packages("httr")
library(dplyr, warn.conflicts=FALSE)
library(httr)
uniquedois <- read.csv(file="wellcomeDOIs.txt",header=F,stringsAsFactors = F)
uniquedois <- as.data.frame(uniquedois)
vec <- vector("list",length(uniquedois$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
@rossmounce
rossmounce / latlongs.csv
Created May 24, 2016
Test lat long data for Ropensci question on making reverse geocoding more efficient/speedier
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
@rossmounce
rossmounce / Angiosperm-orders.tre
Last active Apr 22, 2016
Angiosperm-orders.tre
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);
@rossmounce
rossmounce / failbinoms
Last active Feb 11, 2016
836 genera that fail to match
View failbinoms
Abdulmajidia chaniana
Abdulmajidia maxwelliana
Abromeitiella brevifolia
Abromeitiella lorentziana
Abutilothamnus yaracuyensis
Acanthopeltis hirsuta
Acetabularia caliculus
Acetabularia ryukyuensis
Achasma triorgyale
Acmenosperma pringlei
You can’t perform that action at this time.