Merge pull request #109 from adamlilith/horizon

Fix error in calculation of Hellinger's I as per erratum to Warren et…
adamlilith · Nov 24, 2020 · 744607f · 744607f
2 parents dea3d93 + c2204e1
commit 744607f
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Showing 5 changed files with 1 addition and 7 deletions.
diff --git a/R/compareNiches.r b/R/compareNiches.r
@@ -5,9 +5,6 @@
 #' @param x2 Numeric. Vector or matrix of predictions from another model.
 #' @param method Character vector, indicates type of metric to calculate:
 #' \itemize{
-#' \item \code{meanDiff}: Mean difference between \code{x1} and \code{x2}
-#' \item \code{meanAbsDiff}: Mean absolute difference between \code{x1} and \code{x2} (ie, \code{sum(abs(x1 - x2))})
-#' \item \code{rmsd}: Root mean squared difference.
 #' \item \code{d}: Schoener's \emph{D}
 #' \item \code{i}: Warren's \emph{I}
 #' \item \code{esp}: Godsoe's \emph{ESP}

diff --git a/R/nicheOverlap.r b/R/nicheOverlap.r
@@ -138,7 +138,7 @@ nicheOverlap <- compiler::cmpfun(function(
 	freqOcc2 <- x2dens / envDens
 
 	# calculate niche overlap statistics
-	out <- compareNiches(freqOcc1, freqOcc2)
+	out <- compareNiches(freqOcc1, freqOcc2, method=c('d', 'i', 'esp', 'rho', 'rankCor'))
 
 	if (densities) {
 		out <- list(similarity=out, environDensity=envDens, x1density=x1dens, x2density=x2dens)

diff --git a/man/compareNiches.Rd b/man/compareNiches.Rd
diff --git a/zipTarFiles/enmSdm_0.5.3.0.tar.gz b/zipTarFiles/enmSdm_0.5.3.0.tar.gz
diff --git a/zipTarFiles/enmSdm_0.5.3.0.zip b/zipTarFiles/enmSdm_0.5.3.0.zip