[Vegan-commits] r325 - in pkg: R inst man

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

Author: jarioksa
Date: 2008-04-23 12:39:47 +0200 (Wed, 23 Apr 2008)
New Revision: 325

Modified:
   pkg/R/specaccum.R
   pkg/inst/ChangeLog
   pkg/man/specaccum.Rd
Log:
specaccum(..., method = rarefaction) returns numbers of individuals

Modified: pkg/R/specaccum.R
===================================================================
--- pkg/R/specaccum.R	2008-04-22 14:15:31 UTC (rev 324)
+++ pkg/R/specaccum.R	2008-04-23 10:39:47 UTC (rev 325)
@@ -1,6 +1,6 @@
 `specaccum` <-
-function (comm, method = "exact", permutations = 100, conditioned=TRUE,
-                        gamma="Jack.1", ...)
+    function (comm, method = "exact", permutations = 100, conditioned=TRUE,
+              gamma="Jack.1", ...)
 {
     x <- comm
     x <- as.matrix(x)
@@ -85,8 +85,9 @@
         sdaccum <- sqrt(apply(result * (1 - result), 1, sum))
     })
     out <- list(call = match.call(), method = method, sites = sites,
-        richness = specaccum, sd = sdaccum, perm = perm)
+                richness = specaccum, sd = sdaccum, perm = perm)
+    if (method == "rarefaction")
+        out$invidividuals <- ind
     class(out) <- "specaccum"
     out
 }
-

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-04-22 14:15:31 UTC (rev 324)
+++ pkg/inst/ChangeLog	2008-04-23 10:39:47 UTC (rev 325)
@@ -10,6 +10,12 @@
 	reported statitistic used SS improvement compared to the residual
 	of the complete model, but permutations used SS accumulation
 	compared to the residual after the current model.
+
+	* specaccum: returns item "individuals" or the average number of
+	accumulated individuals with method = "rarefaction". A user
+	request. 
+
+	* zzz: vegan got package startup message.
 	
 Version 1.12-10 (closed April 19, 2008)
 

Modified: pkg/man/specaccum.Rd
===================================================================
--- pkg/man/specaccum.Rd	2008-04-22 14:15:31 UTC (rev 324)
+++ pkg/man/specaccum.Rd	2008-04-23 10:39:47 UTC (rev 325)
@@ -87,8 +87,9 @@
   \item{call }{Function call.}
   \item{method}{Accumulator method.}
   \item{sites}{Number of sites.  For \code{method = "rarefaction"} this
-    is the average number of sites corresponding to a certain number of
-    individuals.}
+    is the number of sites corresponding to a certain number of
+    individuals and generally not an integer, and the average
+    number of individuals is also retunred in item \code{individuals}.} 
   \item{richness}{The number of species corresponding to number of
     sites.  With \code{method = "collector"} this is the observed
     richness, for other methods the average or expected richness.}