Nicks_packages

# 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)
install.packages("gdata", dependencies=TRUE)
install.packages("gtools", dependencies=TRUE)
install.packages("xtable", dependencies=TRUE)
install.packages("plotrix", dependencies=TRUE)
install.packages("vegan", dependencies=TRUE)
install.packages("FD", dependencies=TRUE)
install.packages("SparseM", dependencies=TRUE)
install.packages("ape", dependencies=TRUE)
install.packages("phylobase", dependencies=TRUE)
install.packages("rexpokit", dependencies=TRUE)
install.packages("cladoRcpp", dependencies=TRUE)
install.packages("BioGeoBEARS", type="source")


# Phylogenetics packages
install.packages("diversitree")
install.packages("phytools")
install.packages("phangorn")
install.packages("phyloclim")
install.packages("phylotools")
install.packages("Rphylip")
install.packages("hisse")

install.packages("TreeSim")
install.packages("TreePar")
install.packages("vegan")


install.packages("TESS")

install.packages("RPANDA")
install.packages("roxygen2")
install.packages("rgbif")
install.packages("expoTree")


install.packages("caper") # trait effect on diversity
install.packages("treebase")
install.packages("DDD")
install.packages("BAMMtools")
install.packages("markophylo")
install.packages("PBD") # protracted speciation likelihood

install.packages("paleotree")

install.packages("OutbreakTools")
install.packages("picante")

install.packages("seqinr")  # Get sequence data

# phyloch:
# http://www.christophheibl.de/Rpackages.html
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")

# Morphmetrics / continuous traits
install.packages("geomorph")
install.packages("mvMORPH")
install.packages("OUwie")

# GIS
install.packages("sp")
install.packages("geosphere")
install.packages("rgdal") # May have to be done by hand
install.packages("gdalUtils")
install.packages("spatial")

# Other
install.packages("XLConnect")
install.packages("XML")
install.packages("stringr")
install.packages("devtools")
install.packages("data.table")
install.packages("apTreeshape")
install.packages("pixiedust") # nice tables in R
install.packages("knitr") # better than Sweave
install.packages("virtualspecies")
installed.packages()
install.packages("spatstat")

install.packages("taxize")
install.packages("LearnBayes")
install.packages("evdbayes")
install.packages("geoBayes")
install.packages("geoRglm")
install.packages("glmulti")
install.packages("MultinomialCI")

# Installing latest JAGS:
# https://sourceforge.net/projects/mcmc-jags/files/latest/download?source=files

# Latest rjags:
# https://sourceforge.net/projects/mcmc-jags/files/rjags/
# Installing rjags on a Mac
# https://gist.github.com/casallas/8411082
# My version, for the default install of JAGS4.2.dmg on a Mac, which went into:
# which jags
# /usr/local/bin/jags
# This seemed to work (2016-04-23)
devtools::install_url("http://sourceforge.net/projects/mcmc-jags/files/rjags/4/rjags_4-4.tar.gz",
                      args="--configure-args='--with-jags-include=/usr/local/include/JAGS        
                                              --with-jags-lib=/usr/local/lib/JAGS'
                            "
                      )
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")

# GitHub

#LaplacesDemon
library(devtools)
install_github(repo="ecbrown/LaplacesDemon")