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rename shpStudyRegionFull --> shpStudyAreaLarge
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@eliotmcintire
eliotmcintire committed Oct 23, 2018
1 parent 8be89e8 commit 20d47e7
Showing 1 changed file with 27 additions and 27 deletions.
54 changes: 27 additions & 27 deletions Boreal_LBMRDataPrep.R
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ defineModule(sim, list(
expectsInput("shpStudyArea", "SpatialPolygonsDataFrame",
desc = "this shape file contains two informaton: Sub study area with fire return interval attribute",
sourceURL = NA), # i guess this is study area and fire return interval
expectsInput("shpStudyRegionFull", "SpatialPolygonsDataFrame",
expectsInput("shpStudyAreaLarge", "SpatialPolygonsDataFrame",
desc = "this shape file contains two informaton: Full study area with fire return interval attribute",
sourceURL = NA), # i guess this is study area and fire return interval
expectsInput("specieslayers", "RasterStack",
Expand Down Expand Up @@ -408,21 +408,21 @@ Save <- function(sim) {
ecodistrictAE <- basename(paste0(tools::file_path_sans_ext(ecodistrictFilename), ".", fexts))
ecozoneAE <- basename(paste0(tools::file_path_sans_ext(ecozoneFilename), ".", fexts))

if (!suppliedElsewhere("shpStudyRegionFull", sim)) {
message("'shpStudyRegionFull' was not provided by user. Using a polygon in southwestern Alberta, Canada,")
if (!suppliedElsewhere("shpStudyAreaLarge", sim)) {
message("'shpStudyAreaLarge' was not provided by user. Using a polygon in southwestern Alberta, Canada,")

polyCenter <- SpatialPoints(coords = data.frame(x = c(-1349980), y = c(6986895)),
proj4string = crsUsed)
sim$shpStudyRegionFull <- SpaDES.tools::randomPolygon(x = polyCenter, hectares = 10000)
sim$shpStudyAreaLarge <- SpaDES.tools::randomPolygon(x = polyCenter, hectares = 10000)
}

if (!suppliedElsewhere("shpStudyArea", sim)) {
message("'shpStudyArea' was not provided by user. Using the same as 'shpStudyRegionFull'")
sim$shpStudyArea <- sim$shpStudyRegionFull
message("'shpStudyArea' was not provided by user. Using the same as 'shpStudyAreaLarge'")
sim$shpStudyArea <- sim$shpStudyAreaLarge
}

if (!identical(crsUsed, crs(sim$shpStudyRegionFull))) {
sim$shpStudyRegionFull <- spTransform(sim$shpStudyRegionFull, crsUsed) #faster without Cache
if (!identical(crsUsed, crs(sim$shpStudyAreaLarge))) {
sim$shpStudyAreaLarge <- spTransform(sim$shpStudyAreaLarge, crsUsed) #faster without Cache
}

if (!identical(crsUsed, crs(sim$shpStudyArea))) {
Expand Down Expand Up @@ -469,7 +469,7 @@ Save <- function(sim) {
url = extractURL("ecoDistrict"),
alsoExtract = ecodistrictAE,
destinationPath = dPath,
studyArea = sim$shpStudyRegionFull,
studyArea = sim$shpStudyAreaLarge,
overwrite = TRUE,
useSAcrs = TRUE, # this is required to make ecoZone be in CRS of studyArea
fun = "raster::shapefile",
Expand All @@ -484,7 +484,7 @@ Save <- function(sim) {
alsoExtract = ecoregionAE,
url = extractURL("ecoRegion"),
destinationPath = dPath,
studyArea = sim$shpStudyRegionFull,
studyArea = sim$shpStudyAreaLarge,
overwrite = TRUE,
useSAcrs = TRUE, # this is required to make ecoZone be in CRS of studyArea
fun = "raster::shapefile",
Expand All @@ -499,7 +499,7 @@ Save <- function(sim) {
url = extractURL("ecoZone"),
alsoExtract = ecozoneAE,
destinationPath = dPath,
studyArea = sim$shpStudyRegionFull,
studyArea = sim$shpStudyAreaLarge,
overwrite = TRUE,
useSAcrs = TRUE, # this is required to make ecoZone be in CRS of studyArea
fun = "raster::shapefile",
Expand All @@ -516,7 +516,7 @@ Save <- function(sim) {
destinationPath = dPath,
url = extractURL("standAgeMap"),
fun = "raster::raster",
studyArea = sim$shpStudyRegionFull,
studyArea = sim$shpStudyAreaLarge,
rasterToMatch = sim$biomassMap,
method = "bilinear",
datatype = "INT2U",
Expand All @@ -537,7 +537,7 @@ Save <- function(sim) {
specieslayersList <- Cache(loadkNNSpeciesLayers,
dataPath = asPath(dPath),
rasterToMatch = sim$biomassMap,
studyArea = sim$shpStudyRegionFull,
studyArea = sim$shpStudyAreaLarge,
speciesList = sim$speciesList,
# thresh = 10,
url = extractURL("specieslayers"),
Expand Down Expand Up @@ -572,7 +572,7 @@ Save <- function(sim) {
sim$successionTimestep <- 10

if (!suppliedElsewhere(sim$studyArea)) {
sim$studyArea <- sim$shpStudyRegionFull
sim$studyArea <- sim$shpStudyAreaLarge
}

needRstSR <- FALSE
Expand All @@ -583,30 +583,30 @@ Save <- function(sim) {
needRstSR <- TRUE
}
if (needRstSR) {
message(" Rasterizing the shpStudyRegionFull polygon map")
if (!is(sim$shpStudyRegionFull, "SpatialPolygonsDataFrame")) {
dfData <- if (is.null(rownames(sim$shpStudyRegionFull))) {
polyID <- sapply(slot(sim$shpStudyRegionFull, "polygons"), function(x) slot(x, "ID"))
data.frame("field" = as.character(seq_along(length(sim$shpStudyRegionFull))), row.names = polyID)
message(" Rasterizing the shpStudyAreaLarge polygon map")
if (!is(sim$shpStudyAreaLarge, "SpatialPolygonsDataFrame")) {
dfData <- if (is.null(rownames(sim$shpStudyAreaLarge))) {
polyID <- sapply(slot(sim$shpStudyAreaLarge, "polygons"), function(x) slot(x, "ID"))
data.frame("field" = as.character(seq_along(length(sim$shpStudyAreaLarge))), row.names = polyID)
} else {
polyID <- sapply(slot(sim$shpStudyRegionFull, "polygons"), function(x) slot(x, "ID"))
data.frame("field" = rownames(sim$shpStudyRegionFull), row.names = polyID)
polyID <- sapply(slot(sim$shpStudyAreaLarge, "polygons"), function(x) slot(x, "ID"))
data.frame("field" = rownames(sim$shpStudyAreaLarge), row.names = polyID)
}
sim$shpStudyRegionFull <- SpatialPolygonsDataFrame(sim$shpStudyRegionFull, data = dfData)
sim$shpStudyAreaLarge <- SpatialPolygonsDataFrame(sim$shpStudyAreaLarge, data = dfData)
}

# Layers provided by David Andison sometimes have LTHRC, sometimes LTHFC ... chose whichever
LTHxC <- grep("(LTH.+C)",names(sim$shpStudyRegionFull), value= TRUE)
LTHxC <- grep("(LTH.+C)",names(sim$shpStudyAreaLarge), value= TRUE)
fieldName <- if (length(LTHxC)) {
LTHxC
} else {
if (length(names(sim$shpStudyRegionFull)) > 1) { ## study region may be a simple polygon
names(sim$shpStudyRegionFull)[1]
if (length(names(sim$shpStudyAreaLarge)) > 1) { ## study region may be a simple polygon
names(sim$shpStudyAreaLarge)[1]
} else NULL
}

sim$rstStudyRegion <- crop(fasterizeFromSp(sim$shpStudyRegionFull, sim$biomassMap, fieldName),
sim$shpStudyRegionFull)
sim$rstStudyRegion <- crop(fasterizeFromSp(sim$shpStudyAreaLarge, sim$biomassMap, fieldName),
sim$shpStudyAreaLarge)
sim$rstStudyRegion <- Cache(writeRaster, sim$rstStudyRegion,
filename = file.path(dataPath(sim), "rstStudyRegion.tif"),
datatype = "INT2U", overwrite = TRUE)
Expand Down

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