software.R

## Software installation instructions
## By: T. Hengl
## http://gsif.isric.org

## These examples based on the MRO version of R ()

## Check that all packages have been installed:
list.of.packages <- c("GSIF", "plotKML", "nnet", "plyr", "ROCR", "randomForest", "plyr", "parallel", "psych", "mda", "h2o", "dismo", "grDevices", "snowfall", "hexbin", "lattice", "ranger", "xgboost", "doParallel", "caret")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

## (optional) install from R-Forge:
install.packages("GSIF", repos=c("http://R-Forge.R-project.org"), type="source", dependencies=TRUE)

## http://stackoverflow.com/questions/8229859/sourcing-an-r-script-from-github-for-global-session-use-from-within-a-wrapper
source_https <- function(url, ...) {
  # load package
  require(RCurl)
  # download:
  cat(getURL(url, followlocation = TRUE, cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")), file = basename(url))
  source(basename(url))
}
source_https("https://raw.githubusercontent.com/cran/GSIF/master/R/OCSKGM.R")
OCSKGM

## Test GSIF package:
library(GSIF)
library(sp)
library(boot)
library(aqp)
library(plyr)
library(rpart)
library(splines)
library(gstat)
library(quantregForest)
library(plotKML)
demo(meuse, echo=FALSE)
omm <- fit.gstatModel(meuse, om~dist+ffreq, meuse.grid, method="quantregForest")
om.rk <- predict(omm, meuse.grid)
plotKML(om.rk)

## SAGA GIS (https://sourceforge.net/projects/saga-gis/):
saga_cmd = "C:/Progra~1/SAGA-GIS/saga_cmd.exe"
system(paste(saga_cmd))

library(rgdal)
library(raster)
data("eberg_grid")
gridded(eberg_grid) <- ~x+y
proj4string(eberg_grid) <- CRS("+init=epsg:31467")
writeGDAL(eberg_grid["DEMSRT6"], "DEMSRT6.sdat", "SAGA")
system(paste(saga_cmd, 'ta_lighting 0 -ELEVATION "DEMSRT6.sgrd" -SHADE "hillshade.sgrd" -EXAGGERATION 2'))
plot(raster("hillshade.sdat"), col=SAGA_pal[[3]])

## GDAL (https://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries):
if(.Platform$OS.type == "windows"){
  gdal.dir <- shortPathName("C:/Program files/GDAL")
  gdal_translate <- paste0(gdal.dir, "/gdal_translate.exe")
  gdalwarp <- paste0(gdal.dir, "/gdalwarp.exe") 
} else {
  gdal_translate = "gdal_translate"
  gdalwarp = "gdalwarp"
}
system(paste(gdalwarp))
system(paste(gdalwarp, ' DEMSRT6.sdat DEMSRT6_ll.tif -t_srs \"+proj=longlat +datum=WGS84\"'))
plot(raster("DEMSRT6_ll.tif"))