[Analogue-commits] r305 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2013-03-18 03:42:26 +0100 (Mon, 18 Mar 2013)
New Revision: 305

Modified:
   pkg/R/gradientDist.R
   pkg/man/gradientDist.Rd
Log:
fix a silly bug in prcurve method, removes 'order' argument

Modified: pkg/R/gradientDist.R
===================================================================
--- pkg/R/gradientDist.R	2013-03-18 02:41:22 UTC (rev 304)
+++ pkg/R/gradientDist.R	2013-03-18 02:42:26 UTC (rev 305)
@@ -6,11 +6,8 @@
     UseMethod("gradientDist")
 }
 
-gradientDist.default <- function(object, order, na.rm = TRUE, ...) {
+gradientDist.default <- function(object, na.rm = TRUE, ...) {
     object <- as.vector(object)
-    if(missing(order))
-        order <- seq_along(object)
-    object <- object[order]
     minD <- min(object, na.rm = na.rm)
     k <- if(any(object < 0, na.rm = na.rm)) {
         minD
@@ -30,6 +27,7 @@
                              scaling = 0, ...) {
     if(length(axis) > 1L) {
         axis <- axis[1L]
+        warning("Only the first element of `axis` used.")
     }
     scrs <- as.vector(scores(object, choices = axis, scaling = scaling,
                              display = "sites", ...))
@@ -37,7 +35,6 @@
 }
 
 gradientDist.prcurve <- function(object, na.rm = TRUE, ...) {
-    order <- object$tag
-    scrs <- object$lambda
-    gradientDist.default(scrs, order, na.rm = na.rm, ...)
+    scrs <- scores(object)
+    gradientDist.default(scrs, na.rm = na.rm, ...)
 }

Modified: pkg/man/gradientDist.Rd
===================================================================
--- pkg/man/gradientDist.Rd	2013-03-18 02:41:22 UTC (rev 304)
+++ pkg/man/gradientDist.Rd	2013-03-18 02:42:26 UTC (rev 305)
@@ -16,7 +16,7 @@
 \usage{
 gradientDist(object, \dots)
 
-\method{gradientDist}{default}(object, order, na.rm = TRUE, \dots)
+\method{gradientDist}{default}(object, na.rm = TRUE, \dots)
 
 \method{gradientDist}{cca}(object, na.rm = TRUE, axis = 1L,
              scaling = 0, \dots)
@@ -27,8 +27,6 @@
 \arguments{
   \item{object}{an R object of an appropriate type. For the default
     method, any R object that can be coerced to a vector.}
-  \item{order}{numeric vector indicating the ordering of points along
-    the gradient.}
   \item{na.rm}{logical; should missing values be removed?}
   \item{axis}{numeric, length 1; the ordination axis to take as the
     gradient.}