# this is a script to perform the simulations and analyses, make all the figures
# then typset all the documents for this paper.
# NOTE: By default this will not re-do the lengthy simulations. Rather it will
# just read in stored results from the files ./simulations/out_list_01.rda and
# ./simulations/out_list_02.rda. You can change variables below to force the
# simulations to be re-done, alter that, but be warned that it will try to run things
# on 20 processors with mclapply and will take a long time...
REDO_SIMULATION_1 <- FALSE
REDO_SIMULATION_2 <- FALSE
#### Check to see if necessary packages are installed, and install if necessary ####
message("Checking that required packages are installed")
packages <- c("ggplot2", "grid", "gridExtra", "gtools", "knitr", "parallel", "reshape2", "xtable")
need_these <- setdiff(packages, rownames(installed.packages()))
if(length(need_these) > 0) {
message("We are going to attempt to install the following packages (which are not yet installed):")
message(need_these)
install.packages(need_these)
}
#### Load Packages and Check that We Are in the Right Directory ####
library(knitr)
# this script should be run from the directory that includes the directories "simulations", "supplements",
# and "manuscript"
if(!all(file.exists("simulations", "manuscript", "supplements"))) {
stop("You must run compile-analyses-and-documents.R in directory that includes: \"simulations\", \"manuscript\", \"supplements\"")
}
#### Do Simulation And Make Figures for Single Source Population Model ####
# The following line is commented out because we have the output: out_list_01.rda, already.
# If you wanted to regenerate that output, uncomment it, but plan on using a lot of cores
# to get the job done quickly.
if(REDO_SIMULATION_1 == TRUE) {
message("Starting to re-do simulation 1. This could take a while!")
source("simulations/01_simulation_1.R") # this creates the file ./simulations/out_list_01.rda
}
# these scripts place the figures and tables where they need to be relative to the LaTeX documents.
message("Making figures from results from simulation 1")
source("simulations/02_makecharts_1.R")
message("Making tables from results from simulation 1")
source("simulations/03_maketables_1.R")
#### Do Simulation And Make Figures for Mixed Fishery Model ####
# The following line is commented out because we have the output: out_list_01.rda, already.
# If you wanted to regenerate that output, uncomment it, but plan on using a lot of cores
# to get the job done quickly.
if(REDO_SIMULATION_2 == TRUE) {
message("Starting to re-do simulation 2. This could take a while!")
set.seed(10) # for reproducibility of results
source("simulations/04_simulation_2.R") # this creates the file ./simulations/out_list_02.rda
}
# this script places the figures and tables where they need to be relative to the LaTeX documents.
message("Making figures and tables from the results of simulation 2")
source("simulations/05_makecharts_tables_2.R")
#### Crop Figures As Needed ####
message("Using pdfcrop to crop PDF figures. This requires a decent LaTeX installation that has pdfcrop")
# before we start compiling up the documents, we are going to
# run pdfcrop on all of our figures
# this is a quick funtion to run pdfcrop on all the pdf files in a directory
pdfcrop_dir <- function(path = "manuscript/images/", pattern = "*.pdf", exclude = c("banner.pdf", "DAG_1.pdf", "DAG_2.pdf")) {
img <- dir(path = path, pattern = pattern)
img <- img[!(img %in% exclude)]
for(i in img) {
system(paste("pdfcrop", file.path(path, i), file.path(path, i)))
}
}
# now, do the cropping:
pdfcrop_dir()
pdfcrop_dir(path = "supplements/images", exclude = NULL)
#### Compile the Manuscript ####
message("Knitting the manuscript to PDF. This requires a decent LaTeX installation")
curdir <- getwd()
setwd("manuscript/")
knit2pdf("snp-contam-main.Rnw")
setwd(curdir)
#### Move Manuscripts and Supplements to an Output Directory ####
# not implemented yet.
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