[Vegan-commits] r801 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-04-14 11:59:59 +0200 (Tue, 14 Apr 2009)
New Revision: 801

Modified:
   pkg/vegan/R/ordisurf.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordisurf.Rd
Log:
ordisurf fits a quadratic trend surfaces with 'knots = 2', linear with 'knots = 1' or '0'

Modified: pkg/vegan/R/ordisurf.R
===================================================================
--- pkg/vegan/R/ordisurf.R	2009-04-08 12:36:27 UTC (rev 800)
+++ pkg/vegan/R/ordisurf.R	2009-04-14 09:59:59 UTC (rev 801)
@@ -16,6 +16,12 @@
     x2 <- X[, 2]
     if (knots <= 0)
         mod <- gam(y ~ x1 + x2, family = family, weights = w)
+    else if (knots == 1)
+        mod <- gam(y ~ poly(x1, 1) + poly(x2, 1),
+                   family = family, weights = w)
+    else if (knots == 2)
+        mod <- gam(y ~ poly(x1, 2) + poly(x2, 2) + poly(x1, 1):poly(x2, 1),
+                   family = family, weights = w)
     else if (thinplate) 
         mod <- gam(y ~ s(x1, x2, k = knots), family = family, 
                    weights = w)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-08 12:36:27 UTC (rev 800)
+++ pkg/vegan/inst/ChangeLog	2009-04-14 09:59:59 UTC (rev 801)
@@ -15,7 +15,7 @@
 	dissimilarities. Its summary function returns the overall averages
 	of those distances, and all three variants of MRPP A statistic,
 	and classification strength. The plot method draws a dendrogram
-	based on the mean dissimilarity matrix, with leafs hanging to
+	based on the mean dissimilarity matrix, with leaves hanging to
 	within-group dissimilarity.
 
 	* betadisper: Fix bug corrects the way distance to centroid is
@@ -33,7 +33,10 @@
 	because metaMDSdist/vegdist were passing 'trymax' to decostand()
 	while evaluating "gower" dissimilarity.
 
-	* ordisurf: will fit a linear trend surface if knots = 0.
+	* ordisurf: will fit a linear trend surface if knots = 0 or knots
+	= 1, and a quadratic trend surface if knots = 2. All these are
+	below the lowest permissible values of 'gam' smoothers and free
+	for creative reuse.
 	
 Version 1.16-16 (closed April 2, 2009)
 

Modified: pkg/vegan/man/ordisurf.Rd
===================================================================
--- pkg/vegan/man/ordisurf.Rd	2009-04-08 12:36:27 UTC (rev 800)
+++ pkg/vegan/man/ordisurf.Rd	2009-04-14 09:59:59 UTC (rev 801)
@@ -19,8 +19,10 @@
   \item{y}{ Variable to be plotted. }
   \item{choices}{Ordination axes. }
   \item{knots}{Number of initial knots in \code{\link[mgcv]{gam}} (one
-    more than degrees of freedom). If \code{knots = 0}, the function
-    will fit a linear trend surface instead of a smooth surface. }
+    more than degrees of freedom). If \code{knots = 0} or
+    \code{knots = 1}  the function will fit a linear trend surface, and
+    if \code{knots = 2} the function  will fit a quadratic trend surface
+    instead of a smooth surface. } 
   \item{family}{ Error distribution in  \code{\link[mgcv]{gam}}. }
   \item{col}{ Colour of contours. }
   \item{thinplate}{Use thinplate splines in \code{\link[mgcv]{gam}}.}