inst/extdata/examples/395lab/395_lab_setup_v1.R

In nmatzke/BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

# Install some necessary R packages from CRAN (these are precompiled,
# so easy to install on all systems)
install.packages("devtools")
install.packages("Rcpp")
install.packages("ape")
install.packages("FD")
install.packages("snow")
install.packages("rexpokit")
install.packages("cladoRcpp")

install.packages("phytools")
install.packages("phangorn")
install.packages("phylobase")
install.packages("optimx")
install.packages("GenSA")


# Install BioGeoBEARS from GitHub
# (BioGeoBEARS is pure R, so installation is easy *if* the above 
#  packages have been installed)
library(devtools)
install_github(repo="nmatzke/BioGeoBEARS", upgrade="never")

# Check that your BioGeoBEARS installation loads
library(BioGeoBEARS)


# Get the file locations for 395 lab files, inside the BioGeoBEARS installation
extdata_dir = np(system.file("extdata", package="BioGeoBEARS"))
extdata_dir
list.files(extdata_dir)

# Get the locations of the 395 lab files from GitHub install
labdir = paste(extdata_dir, "examples/395lab/", sep="/")
labpt1a = paste(extdata_dir, "examples/395lab/Psychotria_M0_equalRates/", sep="/")
labpt1b = paste(extdata_dir, "examples/395lab/Psychotria_M2_oneWayDispersal/", sep="/")
labpt1c = paste(extdata_dir, "examples/395lab/Psychotria_M4_DistanceDispersal/", sep="/")
labpt2a = paste(extdata_dir, "examples/395lab/conifer_DEC_traits_models/", sep="/")
labpt2b = paste(extdata_dir, "examples/395lab/conifer_DEC+x_traits_models/", sep="/")

labpt1a_script = paste(extdata_dir, "examples/395lab/Psychotria_M0_equalRates/Psychotria_M0_v1.R", sep="/")
labpt1b_script = paste(extdata_dir, "examples/395lab/Psychotria_M2_oneWayDispersal/Psychotria_M2_oneWayDispersal_v1.R", sep="/")
labpt1c_script = paste(extdata_dir, "examples/395lab/Psychotria_M4_DistanceDispersal/Psychotria_M4_DistanceDispersal_v1.R/", sep="/")
labpt2a_script = paste(extdata_dir, "examples/395lab/conifer_DEC_traits_models/conifer_DEC_traits_models_v3.R", sep="/")
labpt2b_script = paste(extdata_dir, "examples/395lab/conifer_DEC+x_traits_models/conifer_DEC+x_traits_models_v3.R", sep="/")


# Open an R script in R Studio
file.edit(labpt1a_script)

file.edit(labpt2a_script)