[Vegan-commits] r1323 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-10-03 14:28:45 +0200 (Sun, 03 Oct 2010)
New Revision: 1323

Added:
   pkg/vegan/R/fitspecaccum.R
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/specaccum.Rd
Log:
Add fitting specaccum models as Michaelis-Menten models (Stephen Sefick's idea)

Added: pkg/vegan/R/fitspecaccum.R
===================================================================
--- pkg/vegan/R/fitspecaccum.R	                        (rev 0)
+++ pkg/vegan/R/fitspecaccum.R	2010-10-03 12:28:45 UTC (rev 1323)
@@ -0,0 +1,23 @@
+fitspecaccum <- function(object, model = "michaelis-menten", method = "random",  ...)
+{
+    model <- match.arg(model)
+    if (!inherits(object, "specaccum")) 
+        object <- specaccum(object, method = method, ...)
+    if (is.null(object$perm))
+        SpeciesRichness <- as.matrix(object$richness)
+    else
+        SpeciesRichness <- object$perm
+    if (!is.null(object$inviduals))
+        x <- object$individuals
+    else
+        x <- object$sites
+    ## Only Michaelis-Menten implemented now: no need to switch() yet.
+    mods <- apply(SpeciesRichness, 2, function(y) nls(y ~ SSmicmen(x, Vm, K))) 
+    object$fitted <- drop(sapply(mods, fitted))
+    object$residuals <- drop(sapply(mods, residuals))
+    object$coefficients <- drop(sapply(mods, coef))
+    object$models <- mods
+    object$call <- match.call()
+    class(object) <- c("fitspecaccum", class(object))
+    object
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-10-03 12:23:53 UTC (rev 1322)
+++ pkg/vegan/inst/ChangeLog	2010-10-03 12:28:45 UTC (rev 1323)
@@ -4,6 +4,11 @@
 
 Version 1.18-13 (opened September 26, 2010)
 
+	* fitspecaccum: Stephen Sefick suggested adding Michaelis-Menten
+	fit to random species accumulation and sent his model function.
+	These ideas were used to add a new more general function. No
+	documentation yet: needs work.
+
 	* decorana: gives warning if residual is bigger than tolerance.
 	
 Version 1.18-12 (closed September 26, 2010)

Modified: pkg/vegan/man/specaccum.Rd
===================================================================
--- pkg/vegan/man/specaccum.Rd	2010-10-03 12:23:53 UTC (rev 1322)
+++ pkg/vegan/man/specaccum.Rd	2010-10-03 12:28:45 UTC (rev 1323)
@@ -4,6 +4,7 @@
 \alias{summary.specaccum}
 \alias{plot.specaccum}
 \alias{boxplot.specaccum}
+\alias{fitspecaccum}
 
 \title{Species Accumulation Curves }
 \description{