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roblanf / concordance.R
Last active August 8, 2023 16:38
library(viridis)
library(ggplot2)
library(dplyr)
library(ggrepel)
library(GGally)
library(entropy)
# read the data
d = read.delim("concord.cf.stat", header = T, comment.char=‘#')
@roblanf
roblanf / commit-message-guidelines.md
Created July 20, 2023 04:06 — forked from robertpainsi/commit-message-guidelines.md
Commit message guidelines

Commit Message Guidelines

Short (72 chars or less) summary

More detailed explanatory text. Wrap it to 72 characters. The blank
line separating the summary from the body is critical (unless you omit
the body entirely).

Write your commit message in the imperative: "Fix bug" and not "Fixed
bug" or "Fixes bug." This convention matches up with commit messages
@roblanf
roblanf / mre_for_monophy.rmd
Created September 12, 2022 02:04
What is happening with is.monophyletic()
``` r
library(ape)
# make 1K trees to ensure we get some that seem odd...
trees = lapply(rep(4, 1000), rtree, rooted = FALSE)
# test monophyly of all six possible pairs
m1 = unlist(lapply(trees, is.monophyletic, tips = c("t1", "t2")))
m2 = unlist(lapply(trees, is.monophyletic, tips = c("t1", "t3")))
m3 = unlist(lapply(trees, is.monophyletic, tips = c("t1", "t4")))
@roblanf
roblanf / gist:6929493
Last active October 7, 2021 05:32
Setting up Python 2.7 on Windows

Below is a method to install Python 2.7 on Windows, using the Python distribution from python.org. Please note that THERE ARE EASIER WAYS THAN THIS. E.g. you can use the Anaconda distribution, which is one click, and has a nice windows installer. To do that, ignore everything below and just click here:

http://www.continuum.io/downloads

If for some reason you want to do it the slightly harder way:

  1. Install Python ================= Download the Python installer from here: http://www.python.org/getit/. Make sure you download version 2.7. The instructions that follow assume you have installed python in its default folder, which is c:\Python27.
@roblanf
roblanf / gender.r
Last active January 24, 2021 08:57
code to make two basic plots showing gender balance in an institution. An example dataset is here: https://gist.github.com/roblanf/f0f9e331adc5aae84fb1. Full description here: www.robertlanfear.com/blog/files/visualising_gender_balance_R.html
library(ggplot2)
library(reshape2)
library(plyr)
all = read.csv("genderdata.csv")
######################## Plot 1 ###############################################
# The raw data: number of men and women in each role, by year
# we need to do a bit of work so we can plot roles in the right order
@roblanf
roblanf / code.R
Last active January 3, 2020 10:58
A look at gene- and site-concordance factors. See also https://www.biorxiv.org/content/early/2018/12/05/487801
library(viridis)
library(ggplot2)
library(dplyr)
library(ggrepel)
library(GGally)
library(entropy)
# read the data
d = read.delim("concord.cf.stat", header = T, skip = 15)
@roblanf
roblanf / tables.txt
Created December 14, 2018 05:36
ID gCF gDF1 gDF2 gN sCF sDF1 sDF2 sN bootstrap branchlength
327 1.15 3.45 0 87 37.34 29.98 32.68 350.19 100 0.00304084
ID gCF gDF1 gDF2 gN sCF sDF1 sDF2 sN bootstrap branchlength gEF_p sEF_p
14 249 78.57 5.36 5.36 56 56.14 17.86 26.00 383.86 100 0.02134550 1.000000000 1.605600e-02
33 268 62.07 8.62 13.79 58 39.02 27.36 33.62 624.87 100 0.02370450 0.405380556 4.506223e-02
34 269 87.50 0.00 0.00 56 69.10 13.40 17.50 771.13 100 0.10990200 1.000000000 4.051930e-02
36 271 67.35 0.00 8.16 49 46.61 25.97 27.42 426.92 100 0.02632530 0.045500264 6.818018e-01
39 274 34.33 17.91 17.91 67 39.51 23.62 36.87 258.95 100 0.00694057 1.000000000 6.116524e-03
@roblanf
roblanf / iqtree.sh
Created December 14, 2018 02:44
# infer the concatentated tree with 1000 ultrafast bootstraps and an edge-linked fully-partitioned model (-p is the same as -spp from version 1.7 onwards)
iqtree -s alignment.nex -p alignment.nex --prefix concat -bb 1000 -nt AUTO
# infer the 88 single-locus trees
iqtree -s alignment.nex -S alignment.nex --prefix loci -nt 50
# calculate concordance factors
iqtree -t concat.treefile --gcf loci.treefile -s alignment.nex --scf 100 --prefix concord
@roblanf
roblanf / alignment.nex
Created December 14, 2018 01:00
This file has been truncated, but you can view the full file.
#NEXUS
begin DATA;
dimensions ntax=235 nchar=137324;
format datatype=nucleotide missing=? gap=-;
matrix
Acanthisitta_chloris_genome NNCTCTCAGGATCCAGACTTCACACAGGTT--AGAAACTACT-C-T-GCCTTCTGGATCC-T-TGCT----------------TT-ATGCCC---T-GTCCTG-TTTTATTGTGACAGTTGCCTG--------------TTTTT-CACAGAA--------------AC-TAAG-----------GCCTAGTGA---------CTCCTTATCCTTTGG--TTCGGGCA--ACACAGCTGTC-TTATCTTAAGGCCCAGTGGAATGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-TCAGCTGGCTC-CTCAGGTGTGA--------AAAC------------TTGGG-CATAG------GTATAGATATGCTCT-TAATTGACCTC-TAGCTG------------GTG--
@roblanf
roblanf / clunky_timelapse.sh
Created October 29, 2018 18:59
echo "copying source pics"
mkdir source_pics
cp ~/pikrellcam/media/timelapse/* source_pics
cd source_pics
echo "renaming"
mkdir renamed
counter=1
ls -1tr *.jpg | while read filename; do cp $filename renamed/$(printf %05d $counter)_$filename; ((cou\
nter++)); done