[Vegan-commits] r1342 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-11-01 17:11:58 +0100 (Mon, 01 Nov 2010)
New Revision: 1342

Modified:
   pkg/vegan/R/scores.rda.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/plot.cca.Rd
Log:
const in scores.rda can be a vector of two items: one for species, second for sites

Modified: pkg/vegan/R/scores.rda.R
===================================================================
--- pkg/vegan/R/scores.rda.R	2010-11-01 14:25:51 UTC (rev 1341)
+++ pkg/vegan/R/scores.rda.R	2010-11-01 16:11:58 UTC (rev 1342)
@@ -1,4 +1,4 @@
-"scores.rda" <-
+`scores.rda` <-
     function (x, choices = c(1, 2), display = c("sp", "wa", "cn"), 
               scaling = 2, const, ...) 
 {
@@ -25,8 +25,18 @@
         nrow(x$CA$u)
     else
         nrow(x$CCA$u)
+    ## const multiplier of scores
     if (missing(const))
         const <- sqrt(sqrt((nr-1) * sumev))
+    ## canoco 3 compatibility -- canoco 4 is incompatible
+    ##else if (pmatch(const, "canoco")) {
+    ##    const <- (sqrt(nr-1), sqrt(nr))
+    ##}
+    ##
+    ## const[1] for species, const[2] for sites and friends
+    if (length(const) == 1) {
+        const <- c(const, const)
+    }
     rnk <- x$CCA$rank
     sol <- list()
     if ("species" %in% take) {
@@ -38,7 +48,7 @@
                 v <- sweep(v, 1, x$colsum, "/")
                 v <- v * sqrt(sumev / (nr - 1))
             }
-            v <- const * v
+            v <- const[1] * v
         }
         sol$species <- v
     }
@@ -47,7 +57,7 @@
         if (scaling) {
             scal <- list(slam, 1, sqrt(slam))[[abs(scaling)]]
             wa <- sweep(wa, 2, scal, "*")
-            wa <- const * wa
+            wa <- const[2] * wa
         }
         sol$sites <- wa
     }
@@ -56,7 +66,7 @@
         if (scaling) {
             scal <- list(slam, 1, sqrt(slam))[[abs(scaling)]]
             u <- sweep(u, 2, scal, "*")
-            u <- const * u
+            u <- const[2] * u
         }
         sol$constraints <- u
     }
@@ -78,7 +88,7 @@
             if (scaling) {
                 scal <- list(slam, 1, sqrt(slam))[[abs(scaling)]]
                 cn <- sweep(cn, 2, scal, "*")
-                cn <- const * cn
+                cn <- const[2] * cn
             }
             sol$centroids <- cn
         }
@@ -93,6 +103,9 @@
     ## Only one type of scores: return a matrix instead of a list
     if (length(sol) == 1) 
         sol <- sol[[1]]
+    ## collapse const if both items identical
+    if (identical(const[1], const[2]))
+        const <- const[1]
     attr(sol, "const") <- const
     return(sol)
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-01 14:25:51 UTC (rev 1341)
+++ pkg/vegan/inst/ChangeLog	2010-11-01 16:11:58 UTC (rev 1342)
@@ -4,6 +4,15 @@
 
 Version 1.18-15 (opened November 1, 2010)
 
+	* rda: the scaling 'const' can now be a vector of two items: the
+	first is used for species and the second for sites. This allows
+	compatibility with Canoco 3.x (but Canoco 4 changed scaling): if
+	'mod' is an rda() result, and 'nr' is the number of rows in data,
+	then "scaling = -2, const = c(sqrt(nr-1), sqrt(nr))" in scores(),
+	summary() or plot() will use default scaling of Canoco 3.x. Help
+	page now points to decision decision vignette explaining scaling
+	and 'const'.
+
 	* prc: coefficients folded in a wrong way. Diagnosed, reported and
 	fixed by Cajo ter Braak.
 

Modified: pkg/vegan/man/plot.cca.Rd
===================================================================
--- pkg/vegan/man/plot.cca.Rd	2010-11-01 14:25:51 UTC (rev 1341)
+++ pkg/vegan/man/plot.cca.Rd	2010-11-01 16:11:58 UTC (rev 1342)
@@ -69,8 +69,12 @@
     vector which is \code{TRUE} for displayed items or a vector of indices
     of displayed items.}
   \item{const}{General scaling constant to \code{rda} scores. The
-    default is to use constant to give biplot scores, or scores that
-    approximate original data.}
+    default is to use a constant that tries to scale species and sites
+    similarly but to give biplot scores, or scores that approximate
+    original data (see \code{\link{vignette}}
+    \samp{decision-vegan.pdf} with \code{\link{vegandocs}} for details
+    and discussion). If \code{const} is a vector of two items, the
+    first is used for species, and the second item for site scores.}
   \item{axes}{Number of axes in summaries.}
   \item{digits}{Number of digits in output.}
   \item{n, head, tail}{Number of rows printed from the head and tail of
@@ -160,6 +164,7 @@
 text(mod, "species", col="blue", cex=0.8)
 ## Limited output of 'summary'
 head(summary(mod), tail=2)
-}
+## Read description of scaling in RDA in vegan:
+\dontrun{vegandocs("decision")}}
 \keyword{hplot}
 \keyword{aplot}