overhaul 2019

Author: rhijmans

.gitignore

@@ -4,12 +4,17 @@ _static
 # TODO: convert this to git-lfs
 /data
 
-_R/md
-_R/figures
-_R/run.Rout
-rst
+*.md
+*.html
 *.Rout
 
+source/*/figures/
+source/*/txt/
+
+source/analysis/_R/wc10/
+test.*
+cropped-landsat.*
+
 # Do no keep local data directories
 source/*/_R/data/
 

R/check_errors.R

@@ -0,0 +1,11 @@
+
+ff <- list.files("build/html", patt='\\.html$', recursive=TRUE, full=TRUE)
+for (f in ff) {
+	x <- readLines(f, warn=FALSE)
+	i <- grep("## Error", x)
+	if (length(i) > 0) {
+		print(f)
+		print(head(x[i]))
+		cat("----\n\n")
+	}
+}

R/make_site.R

@@ -0,0 +1,13 @@
+
+unlink("build")
+shell("make html")
+
+f <- list.files("source", patt='\\.md\\.txt$', recursive=TRUE, full=TRUE)
+f <- grep("/txt/", f, value=TRUE)
+g <- gsub("txt/", "", f)
+g <- gsub("source/", "", g)
+h <- file.path("build/html/_sources", g)
+x <- file.remove(h)
+y <- file.copy(f, h, overwrite=TRUE)
+
+

R/requirements.R

@@ -0,0 +1,26 @@
+
+libfun <- function(x) {
+	d <- readLines(x)
+	i <- grep('^library\\(', d)
+	j <- grep('^require\\(', d)
+	d[unique(c(i,j))]
+}
+
+f <- list.files("source", patt='\\.rmd$', recursive=TRUE, full=TRUE, ignore.case=TRUE)
+pkgs <- unique(unlist(sapply(f, libfun)))
+pkgs <- pkgs[nchar(pkgs) < 100]
+pkgs <- gsub("library\\(", "", pkgs)
+pkgs <- trimws(gsub(")", "", pkgs))
+pkgs <- sort(unique(c(pkgs, c("devtools", "animation", "deldir","dismo","fields","formatR","geosphere","gstat","jsonlite","kernlab","knitr", "latticeExtra","maptools","randomForest", "rasterVis","rgdal","rgeos","rgl", "rJava", "rpart","spatstat","spdep","spgwr", "XML", "sf"))))
+pkgs <- pkgs[!(pkgs=='rspatial')]
+
+ipkgs <- rownames(installed.packages())
+for (pk in pkgs) {
+  if (!(pk %in% ipkgs)) {
+	print(paste("installing", pk))
+    install.packages(pkgs=pk, repos="https://cran.cnr.berkeley.edu/", quiet=TRUE)
+    library(pk, character.only=TRUE)
+  }
+}
+
+

R/run.R

@@ -0,0 +1,107 @@
+#!/usr/bin/Rscript
+
+args <- commandArgs(TRUE)
+
+if (length(args) < 2) {
+	print(args)
+	stop("there must be at least two arguments")
+}
+
+cmd <- args[1]
+stopifnot(cmd %in% c("knit", "build"))
+
+chapters <- c("rosu", "intr", "spatial", "analysis", "cases", "sdm", "sphere", "rs")
+chapter <- tolower(args[2])
+if (chapter == "all") {
+# this is problematic as there is a lot of function hiding 
+	chapter <- chapters
+} else {
+	stopifnot(chapter %in% chapters)
+}
+
+option <- ifelse(length(args) > 2, args[3], "")
+
+oldpath <- getwd()
+
+
+
+do_build <- function(option) {
+	if (option=="pdf"){
+		shell("make latexpdf")
+		return()
+	} else if (option=="clean"){
+		unlink("_build", recursive=TRUE)
+	} 
+	shell("make html")
+	ff1 <- list.files("txt", pattern="md\\.txt$", full=TRUE)
+	ff2 <- paste0("_build/html/_sources/", basename(ff1))
+	file.copy(ff1, ff2, overwrite=TRUE)
+}
+
+do_knit <- function(option) {
+	if (option=="nocache"){
+		unlink("cache", recursive=TRUE)    
+	} else if (option=="nodata"){
+		unlink("cache", recursive=TRUE)
+		unlink("data", recursive=TRUE)
+	} else if (option=="clean"){
+		file.remove(list.files(pattern="\\.md"))
+		file.remove(list.files("txt", pattern="\\.md", full=TRUE))
+	}
+	ff <- list.files("_R", pattern='.Rmd$', ignore.case=TRUE, full.names=TRUE)
+	md <- list.files(".", pattern='.md')
+
+	#Do we need this check if we're using caching?
+	if (length(md) > 0 ) {
+		stime <- file.info(ff)
+		stime <- data.frame(f=raster::extension(basename(rownames(stime)), ""), stime = stime$mtime, stringsAsFactors=FALSE)
+
+		btime <- file.info(md)
+		btime <- data.frame(f=raster::extension(basename(rownames(btime)), ""), btime = btime$mtime, stringsAsFactors=FALSE)
+
+		m <- merge(stime, btime, by=1, all.x=TRUE)
+		m[is.na(m$btime), 'btime'] <- as.POSIXct(as.Date('2000-01-01'))
+
+		i <- which ( m$btime < m$stime ) 
+		ff <- ff[i]
+	}
+
+	if (length(ff) > 0) {
+		library(knitr)
+		# Check that folders for output exist
+#		dir.create('_R/figures/', recursive=TRUE, showWarnings=FALSE)
+		dir.create('figures/', showWarnings=FALSE)
+		dir.create('txt/', showWarnings=FALSE)
+		md <- raster::extension(basename(ff), '.md')
+
+		opts_chunk$set(
+			dev        = 'png',
+			fig.path   = 'figures/',
+			fig.width  = 6,
+			fig.height = 6,
+			collapse   = TRUE
+		)
+		
+		for (i in 1:length(ff)) {
+			print(paste("   ", basename(ff[i])))
+			knit(ff[i], md[i], envir = new.env(), encoding = 'UTF-8', quiet = TRUE)
+			purl(ff[i], paste0("txt/", gsub("md$", "md.txt", md[i])), quiet=TRUE)
+		}
+	} 
+}
+
+
+
+for (ch in chapter) {
+	path <- file.path(oldpath, 'source', ch)
+	setwd(path)
+	if (cmd == "build") {
+		do_build(option)
+	} else {
+		do_knit(option)
+	}
+	print(getwd())
+}
+setwd(oldpath)
+
+