[Vegan-commits] r2260 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2012-08-26 19:27:36 +0200 (Sun, 26 Aug 2012)
New Revision: 2260

Modified:
   pkg/vegan/R/adonis.R
   pkg/vegan/inst/ChangeLog
Log:
Streamline adonis (internal changes)

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2012-08-23 15:13:58 UTC (rev 2259)
+++ pkg/vegan/R/adonis.R	2012-08-26 17:27:36 UTC (rev 2260)
@@ -41,17 +41,18 @@
         dmat <- dist.lhs^2
     }
     n <- nrow(dmat)
-    I <- diag(n)
-    ones <- matrix(1,nrow=n)
-    A <- -(dmat)/2
-    G <- -.5 * dmat %*% (I - ones%*%t(ones)/n)
+    ## G is -dmat/2 centred by rows
+    G <- -sweep(dmat, 1, rowMeans(dmat))/2
     SS.Exp.comb <- sapply(H.s, function(hat) sum( G * t(hat)) )
     SS.Exp.each <- c(SS.Exp.comb - c(0,SS.Exp.comb[-nterms]) )
     H.snterm <- H.s[[nterms]]
+    ## t(I - H.snterm) is needed several times and we calculate it
+    ## here
+    tIH.snterm <- t(diag(n)-H.snterm)
     if (length(H.s) > 1)
         for (i in length(H.s):2)
             H.s[[i]] <- H.s[[i]] - H.s[[i-1]]
-    SS.Res <- sum( G * t(I-H.snterm))
+    SS.Res <- sum( G * tIH.snterm)
     df.Exp <- sapply(u.grps[-1], function(i) sum(grps==i) )
     df.Res <- n - qrhs$rank
     ## Get coefficients both for the species (if possible) and sites
@@ -66,8 +67,6 @@
     colnames(beta.sites) <- rownames(lhs)
     F.Mod <- (SS.Exp.each/df.Exp) / (SS.Res/df.Res)
 
-
-
     f.test <- function(tH, G, df.Exp, df.Res, tIH.snterm) {
       ## HERE I TRY CHANGING t(H)  TO tH, and
       ## t(I - H.snterm) to tIH.snterm, so that we don't have
@@ -105,7 +104,6 @@
     }
 
     tH.s <- lapply(H.s, t)
-    tIH.snterm <- t(I-H.snterm)
     ## Apply permutations for each term
     ## This is the new f.test (2011-06-15) that uses fewer arguments
     ## Set first parallel processing for all terms

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-08-23 15:13:58 UTC (rev 2259)
+++ pkg/vegan/inst/ChangeLog	2012-08-26 17:27:36 UTC (rev 2260)
@@ -4,6 +4,15 @@
 
 Version 2.1-19 (opened August 20, 2012)
 
+	* adonis: Small changes in calculations. Simplified calculations
+	of matrix G as centred distance matrix, and does not keep n x n
+	matrices that are not needed (A) or used only once (identity
+	matrix I). These can make calculations marginally faster and
+	reduce the memory usage, but probably there are no observable
+	effects in most data sets. The new centring is probably more
+	accurate than older, and therefore the last significant digits can
+	slightly change (magnitude 1e-12 in tests).
+
 	* betadisper: An effective R stats .C function was used for double
 	centring, but it was removed from the API in r60360 | ripley |
 	2012-08-22 07:59:00 UTC (Wed, 22 Aug 2012). This removal stopped