[Vegan-commits] r1362 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-11-10 20:32:52 +0100 (Wed, 10 Nov 2010)
New Revision: 1362

Added:
   pkg/vegan/R/SSgleason.R
Modified:
   pkg/vegan/R/fitspecaccum.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/SSarrhenius.Rd
Log:
add SSgleason species-area model

Added: pkg/vegan/R/SSgleason.R
===================================================================
--- pkg/vegan/R/SSgleason.R	                        (rev 0)
+++ pkg/vegan/R/SSgleason.R	2010-11-10 19:32:52 UTC (rev 1362)
@@ -0,0 +1,11 @@
+SSgleason <-
+    selfStart(~ k + slope*log(area),
+              function(mCall, data, LHS)
+{
+    ## Gleason is a linear model: starting values are final ones
+    xy <- sortedXyData(mCall[["area"]], LHS, data)
+    value <- as.vector(coef(lm(xy[,"y"] ~ log(xy[,"x"]))))
+    names(value) <- mCall[c("k","slope")]
+    value
+},
+c("k","slope"))

Modified: pkg/vegan/R/fitspecaccum.R
===================================================================
--- pkg/vegan/R/fitspecaccum.R	2010-11-10 14:03:06 UTC (rev 1361)
+++ pkg/vegan/R/fitspecaccum.R	2010-11-10 19:32:52 UTC (rev 1362)
@@ -1,8 +1,8 @@
 fitspecaccum <-
     function(object, model, method = "random",  ...)
 {
-    MODELS <- c("arrhenius", "gitay", "lomolino", "asymp",
-                "gompertz", "michaelis-menten", "logis",
+    MODELS <- c("arrhenius", "gleason", "gitay", "lomolino",
+                "asymp", "gompertz", "michaelis-menten", "logis",
                 "weibull")
     model <- match.arg(model, MODELS)
     if (!inherits(object, "specaccum")) 
@@ -18,6 +18,8 @@
     mods <- switch(model,
         "arrhenius" = apply(SpeciesRichness, 2,
              function(y) nls(y ~ SSarrhenius(x, k, z), ...)),
+        "gleason" = apply(SpeciesRichness, 2,
+             function(y) nls(y ~ SSgleason(x, k, slope), ...)),
         "gitay" = apply(SpeciesRichness, 2,
              function(y) nls(y ~ SSgitay(x, k, slope), ...)),
         "lomolino" = apply(SpeciesRichness, 2,

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-10 14:03:06 UTC (rev 1361)
+++ pkg/vegan/inst/ChangeLog	2010-11-10 19:32:52 UTC (rev 1362)
@@ -4,6 +4,8 @@
 
 Version 1.18-16 (opened November 9, 20109
 
+	* SSgleason: a new SS-species-area-model.
+
 	* SSlomolino: improved starting values for 'xmid' (and
 	'Asym'). Now fitspecaccum(..., "lomolino") works in several cases,
 	including BCI and bryceveg (but fails in <1% of cases). Now 'Asym'

Modified: pkg/vegan/man/SSarrhenius.Rd
===================================================================
--- pkg/vegan/man/SSarrhenius.Rd	2010-11-10 14:03:06 UTC (rev 1361)
+++ pkg/vegan/man/SSarrhenius.Rd	2010-11-10 19:32:52 UTC (rev 1362)
@@ -2,6 +2,7 @@
 \alias{SSarrhenius}
 \alias{SSlomolino}
 \alias{SSgitay}
+\alias{SSgleason}
 
 \title{
   Self-Starting nls Species-Area Models
@@ -17,6 +18,7 @@
 
 \usage{
 SSarrhenius(area, k, z)
+SSgleason(area, k, slope)
 SSgitay(area, k, slope)
 SSlomolino(area, Asym, xmid, slope)
 }
@@ -42,6 +44,11 @@
   is the steepness of the species-area curve, and \code{k} is the
   expected number of species in a unit area.
 
+  The Gleason model (\code{SSgleason}) is a linear expression 
+  \code{k + slope*log(area)} (Dengler 200). This is a linear model,  
+  and starting values give the final estimates; it is provided to 
+  ease comparison with other models.
+
   The Gitay model (\code{SSgitay}) is a quadratic logarithmic expression
   \code{(k + slope*log(area))^2} (Gitay et al. 1991, Dengler
   2009). Parameter \code{slope} is the steepness of the species-area
@@ -93,7 +100,8 @@
 ## Get species area data: sipoo.area gives the areas of islands
 example(sipoo)
 S <- specnumber(sipoo)
-plot(S ~ sipoo.area, xlab = "Island Area (ha)", ylab = "Number of Species")
+plot(S ~ sipoo.area, xlab = "Island Area (ha)", ylab = "Number of Species",
+    ylim = c(1, max(S)))
 ## The Arrhenius model
 marr <- nls(S ~ SSarrhenius(sipoo.area, k, z))
 marr
@@ -108,26 +116,29 @@
 mloglog
 lines(xtmp, exp(predict(mloglog, newdata=data.frame(sipoo.area=xtmp))),
    lty=2)
+## Gleason: log-linear
+mgle <- nls(S ~ SSgleason(sipoo.area, k, slope))
+lines(xtmp, predict(mgle, newdata=data.frame(sipoo.area=xtmp)),
+  lwd=2, col=2)
 ## Gitay: quadratic of log-linear
 mgit <- nls(S ~ SSgitay(sipoo.area, k, slope))
 lines(xtmp, predict(mgit, newdata=data.frame(sipoo.area=xtmp)), 
-  lwd=2, col = 2)
+  lwd=2, col = 3)
 ## Lomolino: using original names of the parameters (Lomolino 2000):
 mlom <- nls(S ~ SSlomolino(sipoo.area, Smax, A50, Hill))
 mlom
 lines(xtmp, predict(mlom, newdata=data.frame(sipoo.area=xtmp)), 
-  lwd=2, col = 3)
+  lwd=2, col = 4)
 ## One canned model of standard R:
 mmic <- nls(S ~ SSmicmen(sipoo.area, slope, Asym))
 lines(xtmp, predict(mmic, newdata = data.frame(sipoo.area=xtmp)),
-  lwd =2, col = 4)
-legend("bottomright", c("Arrhenius", "log-log linear", "Gitay", 
-  "Lomolino", "Michaelis-Menten"), col=c(1,1,2,3,4), lwd=c(2,1,2,2,2), 
-   lty=c(1,2,1,1,1))
+  lwd =2, col = 5)
+legend("bottomright", c("Arrhenius", "log-log linear", "Gleason", "Gitay", 
+  "Lomolino", "Michaelis-Menten"), col=c(1,1,2,3,4,5), lwd=c(2,1,2,2,2,2), 
+   lty=c(1,2,1,1,1,1))
 ## compare models (AIC)
-allmods <- list(Arrhenius = marr, Gitay = mgit, Lomolino = mlom, 
-   MicMen= mmic)
-sapply(allmods, AIC)
+allmods <- list(Arrhenius = marr, Gleason = mgle, Gitay = mgit, 
+   Lomolino = mlom, MicMen= mmic)
 }
 \keyword{ models }