R/fdSetup.r

In andrepazv/changeRangeR:

#============================================================
#============================================================
#' Initialize a set of directories to store summary outputs
#' @description Make a standardized set of directories
#' @param summaryBaseDir a file path
#' @param optionalSubDirs a vector of names (strings) of optional directories the user would like to include.
#' @examples
#' setupSummaryDirectories('~/tmpChangeRanger')
#' @return a list of file paths
#' @author Cory Merow <cory.merow@@gmail.com>
# @note
# @seealso
# @references
# @aliases - a list of additional topic names that will be mapped to
# this documentation when the user looks them up from the command
# line.
# @family - a family name. All functions that have the same family tag will be linked in the documentation
#' @export
setupSummaryDirectories=function(summaryBaseDir,
																 optionalSubDirs=c('funcDiv','phlyoDiv')){
	# this is a string that can be sub'd in so you can share code among computers
	myBaseDir=summaryBaseDir
	if(!file.exists(summaryBaseDir)) dir.create(summaryBaseDir)
	figDir=paste0(summaryBaseDir,'/Figures')
	if(!file.exists(figDir)) dir.create(figDir)
	attrDir=paste0(summaryBaseDir,'/AttributeTables')
	if(!file.exists(attrDir)) dir.create(attrDir)
	sparseDir=paste0(summaryBaseDir,'/SparseMatrices')
	if(!file.exists(sparseDir)) dir.create(sparseDir)
	cbsDir=paste0(sparseDir,'/CellBySpecies')
	if(!file.exists(cbsDir)) dir.create(cbsDir)
	rangeSizeDir=paste0(summaryBaseDir,'/RangeSize')
	if(!file.exists(rangeSizeDir)) dir.create(rangeSizeDir)
	richDir=paste0(summaryBaseDir,'/Richness/')
	if(!file.exists(richDir)) dir.create(richDir)
	envDir=paste0(summaryBaseDir,'/Env/')
	if(!file.exists(envDir)) dir.create(envDir)
	miscDir=paste0(summaryBaseDir,'/Misc/')
	if(!file.exists(miscDir)) dir.create(miscDir)
	optional=lapply(optionalSubDirs,function(x){
		d=paste0(summaryBaseDir,'/',x)
		if(!file.exists(d)) dir.create(d)
		d
	})
	names(optional)=paste0(optionalSubDirs,'Dir')
	#uniqueComDir=paste0(summaryBaseDir,'/uniqueCom/')
	#if(!file.exists(uniqueComDir)) dir.create(uniqueComDir)

	out=list(myBaseDir=myBaseDir,sumBaseDir=summaryBaseDir, figDir=figDir,
	         attrDir=attrDir,sparseDir=sparseDir, cbsDir=cbsDir, rangeSizeDir=rangeSizeDir,
	         richDir=richDir,envDir=envDir,miscDir=miscDir,
	         #uniqueComDir=uniqueComDir,
	         optional)
	out=.flattenlist(out)
	return(out)
}

#https://stackoverflow.com/questions/16300344/how-to-flatten-a-list-of-lists
.flattenlist <- function(x){
  morelists <- sapply(x, function(xprime) class(xprime)[1]=="list")
  out <- c(x[!morelists], unlist(x[morelists], recursive=FALSE))
  if(sum(morelists)){
    Recall(out)
  }else{
    return(out)
  }
}



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#' @title Convert directory structure to work on different paths or computers
#' @description change the `dirname` for a previously saved set of directories
#' @param sumDirs a list of directories as created by `setupSummaryDirectories`
#' @param newBaseDir a file path
#' @examples
#' sumDirs=setupSummaryDirectories('~/tmpChangeRanger')
#' convertSummaryBaseDir(sumDirs,'~/tmpChangeRanger2')
#' @return a list of file paths
#' @author Cory Merow <cory.merow@@gmail.com>
#' @export

convertSummaryBaseDir=function(sumDirs,newBaseDir){
	out=lapply(sumDirs,function(x){sub(sumDirs$myBaseDir,newBaseDir,x)})
}

#=============================================================
#=============================================================
# @title Build sparse matrices from rasters
# @description Convert a folder of species range maps to a sparse matrix
# setupSparseSpeciesMatrixStuff=function(sumDirs,
# 																			 scenario='Present',
# 																			 envGrid,
# 																			 allSpeciesMaps,
# 																			 nCellChunks=10,
# 																			 mc.cores=1,
# 																			 reprojectToEnv=FALSE,
# 																			 myTempPath=rasterOptions()$tmpdir,
# 																			 overwrite=F){
#
# 	#  for testing
# 	#  scenario='present'; nCellChunks=10; myTempPath=rasterOptions()$tmpdir; overwrite=F
# 	t1=proc.time()
# 	message(paste0('starting ', scenario))
# 	#================================================================
# 	# cell by species list
# 		# generate cell by species matrices, to make everything downstream faster
# 	# # write out cell ids for each species as an intermediate product
# 	# make a looooong table with columns of species index and cell index
# 		# make multiple in chunks and concatenate them later
#
# 	message('writing cell by species matrices; this can be slow...')
# 	out=changeRangeR:::.cellBySpeciesMatrices(outDir=sumDirs$cbsDir,
# 	                                          allSpeciesMaps=allSpeciesMaps,
# 	                                          scenario=scenario,env=env,
# 	                                          sp.ind=sp.ind,
# 	                                          cell.ind=cell.ind,
# 	                                          nCellChunks=nCellChunks,
# 	                                          removeTempFiles=FALSE,
# 	                                          mc.cores=mc.cores, verbose=F,
# 	                                          myTempPath=myTempPath,overwrite=overwrite)
#
# 	t2=proc.time()-t1
# 	message(paste0(round(t2[3],2),' s'))
# 	out
# }