Nicholas J. Matzke nmatzke
nmatzke
/ sourceall_git.R
Last active
September 28, 2015 09:34
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| # Source ALL of the R files in a particular R/ directory | |
| # (so we don't have to have a fully-functioning package) | |
| # Author: Nick Matzke, nmatzke | |
| # License: GPL-3 | |
| sourceall_git <- function(repo) | |
| { | |
| library(httr) # for GET | |
| library(devtools) # for source_url |
nmatzke
/ _genericR_v1.R
Created
January 20, 2016 04:01
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| # ============================================= | |
| # genericR_v1.R: many useful utility functions | |
| # for R | |
| # | |
| # by Nick Matzke | |
| # Copyright 2011-infinity | |
| # matzkeATberkeley.edu | |
| # January 2011 | |
| # | |
| # Please link/cite if you use this, email me if you have |
nmatzke
/ num_unobservable_patterns_v2.R
Last active
February 2, 2016 14:03
Calculating the number of unobservable site patterns for the Mk-parsimony-informative ascertainment bias correction
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| ####################################################### | |
| # Calculating the number of unobservable site patterns | |
| # for the Mk-parsimony-informative ascertainment bias | |
| # correction | |
| # | |
| # by Nick Matzke, 2015-2016 | |
| # | |
| # Free to re-use; we are preparing an ms on this issue, | |
| # please email nick.matzke@anu.edu.au if interested. | |
| # |
nmatzke
/ Nicks_packages
Created
April 23, 2016 06:14
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| # Install optimx | |
| install.packages("optimx", dependencies=TRUE, repos="http://cran.rstudio.com") | |
| # Install BioGeoBEARS from CRAN 0-cloud: | |
| #install.packages("BioGeoBEARS", dependencies=TRUE, repos="http://cran.rstudio.com") | |
| # If default install for BioGeoBEARS doesn't work, install dependencies in this order, | |
| # then install BioGeoBEARS from source: | |
| install.packages("Rcpp", dependencies=TRUE) | |
| install.packages("RcppArmadillo", dependencies=TRUE) |
nmatzke
/ birthdeath_example
Created
July 23, 2016 06:38
Converting between birth rate, death rate (speciation and extinction) and r (diversification rate) and epsilon (relative death rate)
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| # Example converting between | |
| # birth rate, death rate (speciation and extinction) | |
| # and | |
| # r (diversification rate) and epsilon (relative death rate) | |
| library(ape) | |
| library(BioGeoBEARS) | |
| # Load the Psychotria tree | |
| trfn = np(paste(addslash(extdata_dir), "Psychotria_5.2.newick", sep="")) |
nmatzke
/ data_frame_utilities_v1.R
Created
December 22, 2016 04:45
Utilities to manage annoying features of R data frames (list, factor issues)
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| ####################################################### | |
| # These functions are some utilitys for dealing with | |
| # annoying features of R's use of data.frames, e.g. | |
| # the tendency for some functions to have something that | |
| # looks like a data.frame, but is actually a series of lists. | |
| # | |
| # Also, dfnums_to_numeric semi-intelligently converts | |
| # columns with numeric data to numeric (rather than | |
| # factor or character). | |
| ####################################################### |
nmatzke
/ Beast2_GeneralSubstitutionModel_v1.R
Created
December 22, 2016 04:58
Figuring out the Beast2 GeneralSubstitutionModel
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| ####################################################### | |
| # Figuring out the Beast2 GeneralSubstitutionModel | |
| ####################################################### | |
| # The Beast2 documentation says: | |
| # | |
| # file:///Applications/BEAST_2.4.3/Beast2_XML_as_HTML_help/beast.evolution.substitutionmodel.GeneralSubstitutionModel.html |
nmatzke
/ phylo_vs_cladogram.R
Created
March 2, 2017 03:28
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| # Simple setup of a human/chimp/etc. phylogeny | |
| # by Nick Matzke | |
| ####################################################### | |
| # Phylogeny versus cladogram | |
| ####################################################### | |
| # Tree specification | |
| newick_string = "((((human:6,chimp:6):1,gorilla:7):6,orang:13):5,gibbon:18);" | |
| tr = read.tree(file="",text=string) |
nmatzke
/ R package installs
Last active
March 29, 2018 03:18
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| install.packages("devtools") | |
| library(devtools) | |
| install_github("nmatzke/rexpokit") | |
| install.packages("phytools") | |
| library(phytools) | |
| install.packages("geomorph") | |
| install.packages("BioGeoBEARS") | |
| install.packages("plot3D") |
nmatzke
/ _ex_Eulers_WORKS.jl
Created
April 18, 2019 02:31
Revising Chris Rackauckas's "exp_euler_test.jl" from Julia 0.6 so it works in Julia 1.1
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| ######################################################## | |
| # Revising Chris Rackauckas's "exp_euler_test.jl" from | |
| # Julia 0.6 so it works in Julia 1.1 | |
| ######################################################## | |
| # | |
| # Original 0.6 code from: | |
| # | |
| # ChrisRackauckas/exp_euler_test.jl | |
| # https://gist.github.com/ChrisRackauckas/cf91f4575b0587a45c72620384612b82 |
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