[Vegan-commits] r1473 - in pkg/vegan: R man

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

Author: jarioksa
Date: 2011-01-31 17:48:14 +0100 (Mon, 31 Jan 2011)
New Revision: 1473

Modified:
   pkg/vegan/R/prestondistr.R
   pkg/vegan/man/fisherfit.Rd
Log:
prestondistr() learnt tiesplit for plots (but this does not influence fit)

Modified: pkg/vegan/R/prestondistr.R
===================================================================
--- pkg/vegan/R/prestondistr.R	2011-01-30 22:09:32 UTC (rev 1472)
+++ pkg/vegan/R/prestondistr.R	2011-01-31 16:48:14 UTC (rev 1473)
@@ -1,4 +1,4 @@
-"prestondistr" <-
+`prestondistr` <-
     function (x, truncate = -1,  ...) 
 {
     fun <- function(par, x, truncate) {
@@ -14,7 +14,7 @@
     area <- pnorm(truncate, p[1], p[2], lower = FALSE)
     scale <- length(x)/sqrt(2 * pi)/p[2]/area
     p <- c(p, scale)
-    oct <- as.preston(x)
+    oct <- as.preston(x, ...)
     x <- as.numeric(names(oct))
     fit <- p[3] * exp(-(x - p[1])^2/2/p[2]^2) 
     names(p) <- c("mode", "width", "S0")

Modified: pkg/vegan/man/fisherfit.Rd
===================================================================
--- pkg/vegan/man/fisherfit.Rd	2011-01-30 22:09:32 UTC (rev 1472)
+++ pkg/vegan/man/fisherfit.Rd	2011-01-31 16:48:14 UTC (rev 1473)
@@ -34,6 +34,7 @@
 \method{lines}{prestonfit}(x, line.col = "red", lwd = 2, ...)
 veiledspec(x, ...)
 as.fisher(x, ...)
+as.preston(x, tiesplit = FALSE, ...)
 }
 
 \arguments{
@@ -54,7 +55,9 @@
   \item{bar.col}{Colour of data bars.}
   \item{line.col}{Colour of fitted line.}
   \item{lwd}{Width of fitted line.}
-  \item{\dots}{Other parameters passed to functions. }
+  \item{\dots}{Other parameters passed to functions. Ignored in 
+    \code{prestonfit} and \code{tiesplit} passed to \code{as.preston} in
+    \code{prestondistr}. }
 }
 \details{
   In Fisher's logarithmic series the expected
@@ -125,7 +128,10 @@
   The functions have common \code{print}, \code{plot} and \code{lines}
   methods. The \code{lines} function adds the fitted curve to the
   octave range with line segments showing the location of the mode and
-  the width (sd) of the response.
+  the width (sd) of the response. Function \code{as.preston}
+  transforms abundance data to octaves.  Argument \code{tiesplit} will
+  not influence the fit in \code{prestondistr}, but it will influence
+  the barplot of the octaves.
 
   The total extrapolated richness from a fitted Preston model can be
   found with function \code{veiledspec}. The function accepts results