Update wDist, man

R/wDist.R

@@ -1,4 +1,4 @@
-wDist = function(pdR, sites){
+wDist = function(pdR, sites, maxpts = 1e5){
 
   if(class(pdR) != "RasterLayer" & class(pdR) != "RasterStack" & class(pdR) != "RasterBrick"){
     stop("input probability density map (pdR) should be one of the following class: RasterLayer, RasterStack or RasterBrick")
@@ -22,6 +22,13 @@ wDist = function(pdR, sites){
     stop("sites should be a SpatialPoints object")
   }
 
+  if(!is.numeric(maxpts)){
+    stop("maxpts must be numeric")
+  }
+  if(!(round(maxpts) == maxpts) | maxpts < 1){
+    stop("maxpts must be a positive integer")
+  }
+
   #make space
   wd = list() 
 
@@ -31,8 +38,13 @@ wDist = function(pdR, sites){
 
   for(i in seq_along(sites)){
     pdSP = rasterToPoints(pdR[[i]], spatial = TRUE)
+    if(length(pdSP) > maxpts){
+      index = sample(seq(length(pdSP)), maxpts)
+      pdSP = pdSP[index,]
+      pdSP@data[,1] = pdSP@data[,1] / sum(pdSP@data[,1])
+    }
 
-    #for safety, using projected data works on most platforms
+    #for safety; using projected data works on most platforms
     pdSP = spTransform(pdSP, "+proj=longlat +ellps=WGS84")
     sites = spTransform(sites, "+proj=longlat +ellps=WGS84")
 
@@ -280,7 +292,7 @@ plot.wDist = function(x, ..., bin = 20, pty = "both", index = c(1:5)){
       }
       for(j in seq_along(bins)){
         xy = wedge(bins[j], bins[j] + bin, vals[j])
-        c = col2rgb(index[i])
+        c = col2rgb(i)
         polygon(xy, col = rgb(c[1], c[2], c[3],
                               alpha = 200, maxColorValue = 255))
       }

man/getIsoscapes.Rd

@@ -29,10 +29,10 @@ Accepted \code{isoType} values are:
 \item{"GlobalPrecipGS"}{Global growing-season precipitation H and O isotope values}
 \item{"GlobalPrecipMA"}{Global mean-annual precipitation H and O isotope values}
 \item{"GlobalPrecipMO"}{Global monthly precipitation H and O isotope values}
-\item{"GlobalPrecipMA"}{Global mean-annual and monthly precipitation H and O isotope values}
+\item{"GlobalPrecipALL"}{Global mean-annual and monthly precipitation H and O isotope values}
 \item{"USPrecipMA"}{High-resolution contiguous USA mean-annual precipitation H and O isotope values}
 \item{"USPrecipMO"}{High-resolution contiguous USA monthly precipitation H and O isotope values}
-\item{"USPrecipMA"}{High-resolution contiguous USA mean-annual and monthly precipitation H and O isotope values}
+\item{"USPrecipALL"}{High-resolution contiguous USA mean-annual and monthly precipitation H and O isotope values}
 \item{"USSurf"}{High-resolution contiguous USA surface water H and O isotope values}
 \item{"USTap"}{High-resolution contiguous USA surface water H and O isotope values}
 \item{"USSr"}{High-resolution contiguous USA Sr isotope ratios}

man/wDist.Rd

@@ -11,22 +11,25 @@ Calculate the distance and bearing of migration for one or more samples, weighte
 }
 
 \usage{
-wDist(pdR, sites)
+wDist(pdR, sites, maxpts = 1e5)
 }
 
 \arguments{
   \item{pdR}{
-RasterStack or RasterBrick of n probability density maps, e.g., as produced by \code{pdRaster}.
-}
+  RasterStack or RasterBrick of n probability density maps, e.g., as produced by \code{pdRaster}.
+  }
   \item{sites}{
-SpatialPoints* object containing the collection locations for the n samples represented in pdR.
-}
+  SpatialPoints* object containing the collection locations for the n samples represented in \code{pdR}.
+  }
+  \item{maxpts}{
+  numeric. Maximum number of grid cells at which to calculate bearing and distance.
+  }
 }
 
 \details{
 \code{pdR} and \code{sites} must be of equal length and corresponding order. Names in the output object are taken from the names of the layers in \code{pdR}.
 
-Distances and bearings are calculated on the WGS84 geoid using functions from the \pkg{geosphere} package.
+Distances and bearings are calculated on the WGS84 geoid using functions from the \pkg{geosphere} package. These calculations can take a long time for large rasters. If \code{maxpts} is less than the number of grid cells in each \code{pdR} layer, calculations are caried out for \code{maxpts} randomly selected cells.
 
 Bearing values correspond to the initial bearing from source to collection location, and are reported on a scale of -180 to +180 degrees. The statistical metrics are rectified so that values for distributions spanning due south are reported correctly. Both weighted bearing and distance distributions are often multimodal, and it is recommended to review the distribution densities to assess the representativeness of the statistics (e.g., using \code{\link{plot.wDist}}). 
 }
@@ -35,10 +38,10 @@ Bearing values correspond to the initial bearing from source to collection locat
 Returns an object of class \dQuote{wDist}, a list of length n. Each item contains three named objects:
   \item{stats}{
 named number. Statistics for the distance (dist, meters) and bearing (bear, degrees) between source and collection locations, including the weighted mean (wMean) and quantile (wXX) values.}
-  \item{d.density}{
+  \item{d.dens}{
 density. Weighted kernel density for the distance between source and collection locations (meters). See \code{\link[stats]{density}}. 
   }
-  \item{s.density}{
+  \item{b.dens}{
 density. Weighted kernel density for the bearing between source and collection locations (degrees). See \code{\link[stats]{density}}.
   }
 }
@@ -71,6 +74,6 @@ sites = d$data[sample(seq(length(d$data)), 4),]
 wd = wDist(pp, sites)
 
 # structure of the wDist object
-str(wd[[1]])
+str(wd, 2)
 }