#' Select best performance layers for classification with a LLOCV
#' @description uses a forward feature selection (FFS) to select the best predictors for the classification
#' @param tDat data.frame - with values of the predictors (see details)
#' @param predCol numeric - seq of columns with the predictor values. By default uses 1:(length(tDat)-1) for tDat format computed by 'IKARUS::exrct_Traindat'
#' @param classCol character - name of the column containing the class information
#' @param classLocCol character - name of the column containing the class and location information
#' @param nk - numeric - number for k in spacefolds
#' @param Cores numeric - amount of Cores to exclude from calculation, default = 1
#' @return returns a list of best performing predictors
#' @details The function is used to select best performing predictor variables for a classification. The
#' * predCol - specific predictors can be selected by setting predCol = x:y
#' * tDat - the use of IKARUS::exrct_Traindat is recommended.
#' * parallel processing - the function uses parallel processing for multicore processors. by default all cores -1 are used.
#' @note The function will compute a huge number of models. Depending on the sizes of the training data the
#' process can take long time even with multicore processing.
#' @author Andreas Schönberg
#' @examples
#'# load data
#' require(caret)
#' require(CAST)
#' require(doParallel)
#' require(raster)
#' require(IKARUS)
#' lau_Stk <- raster::stack(system.file("extdata","lau_RGB.grd",package = "IKARUS"))
#' lau_tP <-rgdal::readOGR(system.file("extdata","lau_TrainPolygon.shp",package = "IKARUS"))
#' # handle CRS string
#' crs(lau_tP) <- crs(lau_Stk)
#' ### extract values using 'exrct_Tdat' to generate training dataset
#' tDat <- exrct_Traindat_LLOCV(lau_tP,lau_Stk,classCol="class",locname="location")
#' # check for class column and predictor columns in input training dataset
#' head(tDat)
#' # FFS with all layers in the RasterStack (this example could take some minutes)
#' ffs <- BestPredFFS_LLOCV(tDat=tDat,classCol = "class",classLocCol="class_location",nk=5)
#' # some code to look at the results
#' ffs$selectedvars # show seleted variables
#' ffs$perf_all # show performance of all combinations
#' ffs$finalModel # show confusion matrix
#' @export BestPredFFS_LLOCV
#' @aliases BestPredFFS_LLOCV
BestPredFFS_LLOCV <- function(tDat,predCol="default",classCol=NULL,classLocCol="class_location",nk=NULL,Cores=1){
#check input
cat("checking inputs ",sep="\n")
## missing arguments
if(is.null(predCol)){
stop("missing argument predCol")
}
if(is.null(classCol)){
stop("missing argument classCol")
}
if(is.null(classLocCol)){
stop("missing argument classLocCol")
}
if(is.null(nk)){
stop("missing argument nk")
}
if(any(names(tDat)==classCol)==FALSE){
stop("selected column name for 'classCol' could not be found in tDat")
}
if(any(names(tDat)==classLocCol)==FALSE){
stop("selected column name for 'classLocCol' could not be found in tDat")
}
# prepare columns
classColumn <- which(names(tDat)==classCol)
# prepare predictor columns
if(any(predCol=="default")==TRUE){
predCol <- seq(1:(length(tDat)-3))
}
cat("using predictors: ")
cat(paste(names(tDat[,predCol]),collapse = ", "),sep="\n")
# prepare Cores
cl = makeCluster(detectCores()-Cores)
cat(paste("using",length(cl),"of",length(cl)+Cores,"availible Cores"),sep="\n")
#set seed
set.seed(112019)
#create Spacefolds, k= amount of unique spatial units
indices = CAST::CreateSpacetimeFolds(tDat, spacevar = classLocCol, k = nk)
#set seed
set.seed(112019)
#create trainControl for LLOCV
tC <-trainControl(method = "cv", classProbs = TRUE, index = indices$index, indexOut = indices$indexOut)
cat(" ",sep = "\n")
cat("IKARUS starting model with LLOCV",sep = "\n")
# start cores
set.seed(112019)
registerDoParallel(cl)
# start FFS
starttime <- Sys.time()
FFSmodel <- CAST::ffs(tDat[,predCol],
tDat[,classColumn],
method = "rf", withinSE = FALSE, metric= "Kappa",
importance = TRUE, trControl = tC)
#stop FFS
stopCluster(cl)
stoptime <- Sys.time()
diftim <-round(difftime(stoptime,starttime,units = "hours"),4)
cat(" ",sep = "\n")
cat(paste0("needed ",diftim," hours"))
cat(" ",sep = "\n")
cat(" ",sep = "\n")
cat("selected variables",sep = "\n")
cat(paste(FFSmodel$selectedvars,collapse = ", "))
cat(" ",sep = "\n")
cat(" ",sep = "\n")
cat("IKARUS finished",sep = "\n")
return(FFSmodel)
} # end of main function
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