#' Function fit an ellipsoid model
#' @description Function fit an ellipsoid model using the shape matrix (covariance matrix)
#' of the niche variables.
#' @param data A RasterStack or RasterBrick objet of the niche varibles.
#' @param centroid A vector with the values of the centers of the ellipsoid (see \code{\link[hdm]{cov_center}}).
#' @param covar The shape matrix (covariance) of the ellipoid (see \code{\link[hdm]{cov_center}}).
#' @param level The proportion of points to be included inside the ellipsoid
#' @param threshold Threshold value for the suitabilities to be cosidered as 0,
#' by default all suiabilities <0.05 are cosidered as zeros
#' @param plot Logical If True a plot of niche will be shown.
#' @param size The size of the points of the niche plot.
#' @param xlab1 For x label for 2-dimensional histogram
#' @param ylab1 For y label for 2-dimensional histogram
#' @param zlab1 For z label for 2-dimensional histogram
#' @param ... Arguments passed to \code{\link[rgl]{plot3d}} function from rgl
#' @return Returns a list containing a data.frame with the suitability values; a suitability raster;
#' a data.frame with the mahalanobis and euclidean distances to the centroid.
#' @export
#' @examples
#' ## Load niche data
#' # d_cardon <- read.csv(system.file("extdata", "cardon_virtual.csv", package = "nichetoolbox"))
#' ## Compute the centroid and shape (covariance matrix) of the ellipsoid model.
#' # covar_centroid <- cov_center(d_cardon,mve=TRUE,level=0.99,vars=c(3,4,5))
#' ## RasterStack with the niche variables
#' # nicheStack <- stack(list.files(system.file("extdata",
#' # package = "nichetoolbox"),
#' # pattern = ".asc$",full.names = TRUE))
#' # Fitting the ellipsoid model
#' # ellipsoidMod <- ellipsoidfit(nicheStack,
#' # covar_centroid$centroid,
#' # covar_centroid$covariance,
#' # level=0.95,threshold=0.05,plot=TRUE,size=3)
#' # plot(ellipsoidMod$suitRaster)
ellipsoidfit <- function(data,centroid,covar,level=0.95,
threshold=0.05,plot=T,size,
xlab1="niche var 1",ylab1= "niche var 2",zlab1="Suitability",...){
if(class(data)=="RasterStack" || class(data)=="RasterBrick"){
resolution <- raster::res(data)
extention <- raster::extent(data)
toDF<- data.frame(raster::rasterToPoints(data))
coordinates <- toDF[,c(1,2)]
data <- toDF[,-c(1,2)]
}
else{
data <- data.frame(data)
}
suit <- function(data,medias,covMatrix){
a <- 1
expo <- exp(-0.5*mahalanobis(data,medias,cov = covMatrix))
return(a*expo)
}
# Computing the suitabilities
suits <- suit(data,medias = centroid,covMatrix = covar)
suits[suits<threshold] <- 0
if(dim(data)[2]==2 && plot==TRUE){
x <- seq(from = centroid[1]/1.5,to =centroid[1]*1.25 ,length=60)
y <- seq(from = centroid[2]/1.5,to =centroid[2]*1.25 ,length=60)
suit1 <- function(x,y) suit(cbind(x,y),medias = centroid,covMatrix = covar)
z <- outer(x,y,suit1)
p1 <- graphics::persp(x,y,z, box=T,xlab=xlab1,
ylab=ylab1,zlab="", col="blue",
theta = 55, phi = 30,r = 40,
d = 0.1, expand = 0.5,
ticktype = "detailed", nticks=5,
cex.lab=1.5, cex.axis=1.3,
cex.main=1.5, cex.sub=1.5)
ranges <- t(sapply(list(x,y,z),range))
means <- rowMeans(ranges)
## label offset distance, as a fraction of the plot width
labelspace <- 0.12 ## tweak this until you like the result
xpos <- min(x)-(diff(range(x)))*labelspace
ypos <- min(y)-(diff(range(y)))*labelspace
labelbot3d <- c(xpos,ypos,min(z))
labeltop3d <- c(xpos,ypos,max(z))
labelmid3d <- c(xpos,ypos,mean(range(z)))
trans3dfun <- function(v) { grDevices::trans3d(v[1],v[2],v[3],p1) }
labelbot2d <- trans3dfun(labelbot3d)
labelmid2d <- trans3dfun(labelmid3d)
labeltop2d <- trans3dfun(labeltop3d)
labelang <- 180/pi*atan2(labeltop2d$y-labelbot2d$y,labeltop2d$x-labelbot2d$x)
par(xpd=NA,srt=labelang) ## disable clipping and set string rotation
text(labelmid2d[1]$x,labelmid2d$y,zlab1,cex=1.5)
}
if(dim(data)[2]==3 && plot==TRUE){
data1 <- data[!is.na(suits),]
dfd <- dim(data1)[1] - 1
dfn <- dim(data1)[2] - 1
# Ellipsoid radius
#ell.radius_E <- sqrt(dfn * qf(level, dfn, dfd))
suits2 <- suits[!is.na(suits)]
ellips_E <- rgl::ellipse3d(covar,centre = centroid,level = 0.99)
if(dfd > 50000)
np <- 50000
else
np <- dim(data1)[1]
toSam <- sample(1:length(data1[,1]),np)
data1 <- data1[toSam,]
rgl::plot3d(data1,size = size,col=grDevices::hsv(suits2[toSam]*.71,.95,.9),...)
rgl::wire3d(ellips_E, col=4, lit=FALSE,alpha=.1)
}
# Calculating distance to the centroid
mahalanobis <- stats::mahalanobis(data,
center = centroid,
cov = covar)
ecucliedean <- sqrt(rowSums(centroid-data)^2)
distances <- data.frame(mahalanobis,ecucliedean)
data <- data.frame(data,ncel=1:dim(data)[1])
if(exists('coordinates')){
# Data Frame with coordinates and suitability values
sDataFrame <- data.frame(coordinates,suitability=suits)
rasterDF <- raster::raster(extention)
raster::res(rasterDF) <- resolution
cels <- raster::cellFromXY(rasterDF,sDataFrame[,1:2])
rasterDF[cels] <- sDataFrame[,3]
#crs(rasterDF) <- "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"
return(list(suits=cbind(sDataFrame,data),suitRaster=rasterDF,ncentedist=distances))
}
return(data.frame(suitability=suits,data,ncentedist=distances))
}
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