74 lines
2.9 KiB
R
74 lines
2.9 KiB
R
#' getSoilDataFull
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#'
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#' This function collects soil data from a given restapi, de default is soilGrid
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#'
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#' @author Roland HOLLÓS
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#' @name getSoilDataFull
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#' @importFrom glue glue
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#' @importFrom httr config with_config GET content
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getSoilDataFull <- function(lat, lon, apiURL) {
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if(missing(apiURL)){
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apiURL <- "https://81.169.232.36"
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}
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apiString <- glue("{apiURL}/query?lon={lon}&lat={lat}")
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soilREST <- #with_config(config(ssl_verifypeer=0L, ssl_verifyhost=0L),
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GET(apiString) # ) # This is temporary solution ssl_verification wont bypass
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content(soilREST)
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}
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#' createSoilFile
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#'
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#' This function collects soil data from a given restapi, de default is soilGrid
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#'
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#' @author Roland HOLLOS
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#' @name createSoilFile
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#' @importFrom glue glue
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#' @importFrom stats approx
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#' @importFrom magrittr '%>%'
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#' @export
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createSoilFile <- function(lat,lon,
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outputFile="recent.soi",
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method="constant",apiURL,
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template=system.file("examples/hhs/hhs.soi",package="RBBGCMuso")) {
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if(missing(apiURL)){
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apiURL <- "https://rest.soilgrids.org/soilgrids/v2.0/properties"
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}
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outFile <- suppressWarnings(readLines(template))
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outFile[1] <- sprintf("SOILPROP FILE - lat: %s, lon: %s, created in: %s",lat,lon,date())
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musoCenters <- c(1.5,6.5,20.0,45.0,75.0,105.0,135.0,175.0,300.0,700.0)
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# soilGridDepths <- c(0,5,15,30,60,100,200)
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soilGridDepths <- c(2.5, 10, 22.5, 45, 80, 150)
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Reduce(function(x,y){(y-x)/2+x},soilGridDepths,accumulate=TRUE)
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rest<- getSoilDataFull(lat,lon, apiURL)
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createMusoLayers <- function(values,depths=soilGridDepths,centers=musoCenters,intMethod=method){
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approx(x=depths,y=values, xout = centers, method=intMethod,rule=2)$y %>%
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paste(.,collapse="\t") %>% paste0(.," ")
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}
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soilDepth <- tryCatch(getMeanSoil(rest,"bdod")/100,error=function(e){stop("There is no data for the given coordinates")})
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outFile[55] <- sprintf("%s (%%) percentage of sand by volume in rock free soil",
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paste(createMusoLayers(getMeanSoil(rest,"sand")/10), collapse="\t"))
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outFile[56] <- sprintf("%s (%%) percentage of silt by volume in rock free soil",
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paste(createMusoLayers(getMeanSoil(rest,"silt")/10), collapse="\t"))
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outFile[57] <- sprintf("%s (dimless) soil PH",
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paste(createMusoLayers(getMeanSoil(rest,"phh2o")/10), collapse="\t"))
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# outFile[58] <- sprintf("%s (%%) bulk density",paste(createMusoLayers(soilDepth),collapse="\t"))
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writeLines(outFile,outputFile)
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}
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# createSoilFile(60,50)
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getMeanSoil <- function(rest, name){
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sapply(
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rest$properties$layers[sapply(rest$properties$layers,function(x){
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x$name == name
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})][[1]]$depths,
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function(s){
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s$values$mean
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}
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)
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}
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