Linux.First <- function(askCRAN = TRUE) {
###########################################
# Purpose: this is my Rprofile.site file
# This is the global file that gets called when R sets up the working environment, each time it is opened
##########################################
lib(utils)
cat("\nChanging CRAN repository away from the Revolution Analytics frozen mirror (see .../MRO/MRO-X.X.X/etc/Rprofile.site).\n\n")
options(width = 160, help_type = "html", stringsAsFactors = FALSE,
repos=c(CRAN="https://cloud.r-project.org/", CRANextra = "http://lib.stat.cmu.edu/R/CRAN/"))
switch(menu("Check for package updates?") + 1,
cat("\n"), update.packages(ask = askCRAN))
# With the 'INSTALL_opts' argument, remotes::install_github() throws a warning when the SHA number doesn't change
switch(menu("Check for GitHub updates?") + 1,
cat("\n"), { try(remotes::install_github("John-R-Wallace-NOAA/JRWToolBox")); cat("\n\n");
try(remotes::install_github("John-R-Wallace-NOAA/rgit")); cat("\n\n");
try(remotes::install_github("John-R-Wallace-NOAA/Imap")); cat("\n\n");
try(remotes::install_github("r4ss/r4ss")); cat("\n\n");
try(remotes::install_github("kaskr/TMB_contrib_R/TMBhelper")); cat("\n\n");
try(remotes::install_github("kaskr/TMB_contrib_R/TMBdebug")); cat("\n\n");
try(remotes::install_github("kaskr/TMB_contrib_R/TMBphase")); cat("\n\n");
try(remotes::install_github("mlysy/TMBtools")); cat("\n\n");
try(remotes::install_github("kaskr/adcomp/TMB")); cat("\n\n");
try(remotes::install_github("james-thorson-noaa/FishStatsUtils", INSTALL_opts="--no-multiarch --no-test-load")); cat("\n\n");
try(remotes::install_github("james-thorson/utilities")); cat("\n\n");
try(remotes::install_github("james-thorson-noaa/VAST", INSTALL_opts = "--no-multiarch --no-test-load --no-staged-install")); cat("\n\n");
try(remotes::install_github("nwfsc-assess/geostatistical_delta-GLMM")); cat("\n\n");
# try(remotes::install_github("james-thorson/MIST"))
cat("\n\n") })
# try(remotes::install_github("glmmTMB/glmmTMB",subdir="glmmTMB")); cat("\n\n")
switch(menu("Reinstall INLA?") + 1,
cat("\n"), {
try(install.packages("BiocManager")); cat("\n\n");
try(BiocManager::install(version = "3.11")); cat("\n\n");
try(BiocManager::install(c("graph", "Rgraphviz"))); cat("\n\n");
try(install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)); cat("\n\n")
})
# OLD: gives version 0.0.2: install.packages("glmmTMB", repos = "http://glmmtmb.github.io/glmmTMB/repos/") => http://glmmtmb.github.io/glmmTMB/repos/src/contrib/glmmTMB_0.0.2.tar.gz
switch(menu("Reinstall glmmTMB?") + 1,
cat("\n"), { try(install.packages("glmmTMB")); cat("\n\n") })
# switch(menu("Reinstall rstan?") + 1,
# cat("\n"), { try(install.packages('rstan', repos = 'https://cloud.r-project.org/', dependencies = TRUE)); cat("\n\n") })
switch(menu("Reinstall compiled rstan?") + 1,
cat("\n"), { try(install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)); cat("\n\n") })
switch(menu("Reinstall rstan from source?") + 1,
cat("\n"), { try({
pkgbuild::has_build_tools(debug = TRUE)
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars.win")
if (!file.exists(M)) file.create(M)
cat("\nCXX14FLAGS=-O3 -march=native", "CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y", "CXX11FLAGS=-O3 -march=corei7", file = M, sep = "\n", append = TRUE)
on.exit(file.remove(M))
Sys.setenv(MAKEFLAGS = "-j4")
install.packages("rstan", type = "source")
# lib("stan-dev/rstan", subdir = "rstan/rstan") # Failed
}); cat("\n\n") })
cat("\nDone with package updates.\n"); flush.console()
lib(datasets)
lib(stats)
lib(methods)
lib(graphics)
lib(chron)
lib(foreign)
lib(grid)
lib(grDevices)
lib(sp)
lib(rgeos)
lib(lattice)
lib(latticeExtra)
lib(akima)
lib(gdata)
lib(gplots)
lib(gstat)
lib(gtools)
# lib(stashR)
lib(gam)
# lib(Hmisc)
lib(coda)
# lib(MCMCpack)
lib(MASS)
lib(RODBC)
# lib(mvbutils)
lib(mvtnorm)
lib(numDeriv)
lib(bbmle)
lib(Matrix)
lib(devtools)
lib(data.table)
lib(TMB)
lib(TMBhelper)
lib(RhpcBLASctl)
lib(Imap)
lib(rgit)
repoList <- c("John-R-Wallace-NOAA/JRWToolBox", "John-R-Wallace-NOAA/rgit", "John-R-Wallace-NOAA/VAST_Examples_and_Scripts", "John-R-Wallace-NOAA/Length_Restricted_Catch_with_VAST")
repoPath <- repoList[1]
gitName <- "John-R-Wallace-NOAA"
gitEmail <- "John.Wallace@noaa.gov"
detach("package:JRWToolBox")
library(JRWToolBox)
# Load packages when called
# coda
autoload("mcmc", "coda")
autoload("as.mcmc", "coda")
autoload("densplot2", "coda")
cat("\nDone with lib and autoloads.\n"); flush.console()
# lattice::lattice.options(default.theme = "standard.theme")
Sys.setenv("R_HISTSIZE"=99999) # Longest possible history file
# .First on PC
if(exists(".SavedPlots")) rm(.SavedPlots, pos = 1) # if there is a plotting history, delete it
if(exists(".Traceback", 1, inherits = FALSE)) rm(.Traceback, pos = 1) # if there is an error history, delete it
# if(exists(".Random.seed")) { rm(.Random.seed, pos=1) } # deletes the random number seed if it exists
Mydata <- list(a = 1)
attach(Mydata, 2)
try(lib(Imap))
detach(pos = grep('JRWToolBox', search()))
library(JRWToolBox, pos = 3)
# try(updateTools(quiet = TRUE, force = TRUE)) # Move tools to position 2 on search path
.Last <<- function () {
###########################################
# Purpose: this is my core .Last file
# History: John Wallace Jan, 2009
###########################################
# Save backup of my session
save.image(file=paste("BACKUP ", paste(strsplit(date(), ":")[[1]],
collapse ="."), ".RData"))
# Save ASCII version of all functions
save.functions()
# Save history
# savehistory()
# Commands to clean up the working environment for next session.
rm(.SavedPlots, pos = 1) # if there is a plotting history, delete it
rm(.Traceback, pos = 1) # if there is an error history, delete it
# rm(.Random.seed,pos=1) # deletes the random number seed if it exists
rm(.Last, pos = 1) # .Last file deletes itself
}
cat("\nDone with .Rprofile.\n")
invisible()
}
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