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added RStoolbox dependency for ggRGB due to CRAN revisison comments

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16EAGLE committed Nov 3, 2017
1 parent e105def commit 0733057c32c553b7dda30eddf98625975bbf75d7
Showing with 5 additions and 277 deletions.
  1. +2 −1 DESCRIPTION
  2. +1 −0 NAMESPACE
  3. +2 −149 R/animate_move.R
  4. +0 −127 R/moveVis-internal.R
View
@@ -31,4 +31,5 @@ Imports:
zoo,
lubridate,
parallel,
pbapply
pbapply,
RStoolbox
View
@@ -8,6 +8,7 @@ export(get_imconvert)
export(get_libraries)
import(ggplot2)
importFrom(RCurl,getURL)
importFrom(RStoolbox,ggRGB)
importFrom(dismo,gmap)
importFrom(geosphere,distGeo)
importFrom(grDevices,colorRampPalette)
View
@@ -178,6 +178,7 @@
#' @importFrom lubridate seconds_to_period hour minute second
#' @importFrom parallel detectCores makeCluster stopCluster
#' @importFrom pbapply timerProgressBar getTimerProgressBar setTimerProgressBar closepb
#' @importFrom RStoolbox ggRGB
#'
#' @export
@@ -269,155 +270,7 @@ animate_move <- function(m, out_dir, conv_dir = "",
}
}
#RGB plotting originally forked from RStoolbox::ggRGB based on raster:plotRGB
#author: Benjamin Leutner, Robert J. Hijmans
#license: GPL-3
#code taken from the ggRGB function due to dependency issues
#partly based on functions in the pixmap package by Friedrich Leisch
ggRGB <- function(img, r = 3, g = 2, b = 1, scale, maxpixels = 500000, stretch = "none", ext = NULL, limits = NULL,
clipValues = "limits", quantiles = c(0.02,0.98), ggObj = TRUE, ggLayer = FALSE,
alpha = 1, coord_equal = TRUE, geom_raster = FALSE, nullValue = 0) {
verbose <- getOption("RStoolbox.verbose")
annotation <- !geom_raster
## Subsample raster
rgb <- unlist(.numBand(raster=img,r,g,b))
nComps <- length(rgb)
if(inherits(img, "RasterLayer")) img <- brick(img)
rr <- sampleRegular(img[[rgb]], maxpixels, ext=ext, asRaster=TRUE)
RGB <- getValues(rr)
if(!is.matrix(RGB)) RGB <- as.matrix(RGB)
## Clip to limits
if (!is.null(limits)) {
## Tidy limits
if (!is.matrix(limits)) {
limits <- matrix(limits, ncol = 2, nrow = nComps, byrow = TRUE)
}
## Tidy clip values
if(!is.matrix(clipValues)){
if(!anyNA(clipValues) && clipValues[1] == "limits") {
clipValues <- limits
} else {
clipValues <- matrix(clipValues, ncol = 2, nrow = nComps, byrow = TRUE)
}
}
## Do clipping
for (i in 1:nComps) {
if(verbose){
message("Number of pixels clipped in ", c("red", "green", "blue")[i], " band:\n",
"below limit: ", sum(RGB[,i] < limits[i,1], na.rm = TRUE), " | above limit: ", sum(RGB[,i] > limits[i,2], na.rm = TRUE))
}
RGB[RGB[,i] < limits[i,1], i] <- clipValues[i,1]
RGB[RGB[,i] > limits[i,2], i] <- clipValues[i,2]
}
}
rangeRGB <- range(RGB, na.rm = TRUE)
if(missing('scale')){ scale <- rangeRGB[2] }
if(rangeRGB[1] < 0){
RGB <- RGB - rangeRGB[1]
scale <- scale - rangeRGB[1]
rangeRGB <- rangeRGB - rangeRGB[1]
}
if(scale < rangeRGB[2]) {
warning("Scale < max value. Resetting scale to max.", call.=FALSE)
scale <- rangeRGB[2]
}
RGB <- na.omit(RGB)
## Perform data stretch
if (stretch != "none") {
stretch <- tolower(stretch)
for(i in seq_along(rgb)){
RGB[,i] <- .stretch(RGB[,i], method = stretch, quantiles=quantiles)
}
scale <- 1
}
## Assemble colors
naind <- as.vector( attr(RGB, "na.action") )
nullbands <- sapply(list(r,g,b), is.null)
if(any(nullbands)) {
RGBm <- matrix(nullValue, ncol = 3, nrow = NROW(RGB))
RGBm[,!nullbands] <- RGB
RGB <- RGBm
}
if (!is.null(naind)) {
z <- rep( NA, times=ncell(rr))
z[-naind] <- rgb(RGB[,1], RGB[,2], RGB[,3], max = scale, alpha = alpha*scale)
} else {
z <- rgb(RGB[,1], RGB[,2], RGB[,3], max = scale, alpha = alpha*scale)
}
df_raster <- data.frame(coordinates(rr), fill = z, stringsAsFactors = FALSE)
x <- y <- fill <- NULL ## workaround for a R CMD check 'note' about non-visible global variable in call to ggplot (variables are column names created earlier within 'data' and hence not visible to check). This does not in any way affect ggRGB,
if(ggObj){
## We need to set up ggplot with at least the minimum aestetics x and y
exe <- as.vector(extent(rr))
df <- data.frame(x=exe[1:2],y=exe[3:4])
## Set-up plot
## I prefer annotate_raster instead of geom_raster or tile to keep the fill scale free for additional rasters
if(annotation) {
dz <- matrix(z, nrow=nrow(rr), ncol=ncol(rr), byrow = TRUE)
p <- annotation_raster(raster = dz, xmin = exe[1], xmax = exe[2], ymin = exe[3], ymax = exe[4], interpolate = FALSE)
if(!ggLayer) {
p <- ggplot() + p + geom_blank(data = df, aes(x = x,y = y))
}
} else {
p <- geom_raster(data = df_raster, aes(x = x, y = y, fill = fill), alpha = alpha)
if(!ggLayer) {
p <- ggplot() + p + scale_fill_identity()
}
}
if(coord_equal & !ggLayer) p <- p + coord_equal()
return(p)
} else {
return(df_raster)
}
}
## Perform histogram, sqrt log and 98% linear stretching
.stretch <- function (x, method = "lin", quantiles = c(0.02,0.98)) {
if(!method %in% c("lin", "hist", "log", "sqrt")) stop("Stretch method must be 'lin', 'hist', 'sqrt' or 'log'", call. = FALSE)
if(method == "lin"){
if(length(quantiles) == 1) quantiles <- c(0,1) + c(quantiles, -quantiles)/100
v <- quantile(x, quantiles, na.rm = TRUE)
temp <- (x - v[1])/(v[2] - v[1])
temp[temp < 0] <- 0
temp[temp > 1] <- 1
return(temp)
}
if(method == "hist"){
ecdfun <- ecdf(x)
return(ecdfun(x))
}
if(method == "log"){
x <- log(x + 1)
x <- x - min(x)
return(x / max(x))
}
if(method == "sqrt"){
x <- sqrt(x)
x <- x - min(x)
return(x /max(x))
}
}
.numBand <- function(raster, ...){
bands <- list(...)
lapply(bands, function(band) if(is.character(band)) which(names(raster) == band) else band )
}
#+++++++++++++++++++++++++++++++++++++++ MAIN ++++++++++++++++++++++++++++++++++++++++++++++
## PREREQUISITES
View
@@ -1,130 +1,3 @@
.Random.seed <-
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#Suppress messages and warnings
quiet <- function(expr){
return(suppressWarnings(suppressMessages(expr)))

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