[Vegan-commits] r2466 - pkg/vegan/man

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

Author: jarioksa
Date: 2013-03-04 18:58:10 +0100 (Mon, 04 Mar 2013)
New Revision: 2466

Modified:
   pkg/vegan/man/specaccum.Rd
Log:
expand documenation of weights in specaccum

Modified: pkg/vegan/man/specaccum.Rd
===================================================================
--- pkg/vegan/man/specaccum.Rd	2013-03-04 17:19:04 UTC (rev 2465)
+++ pkg/vegan/man/specaccum.Rd	2013-03-04 17:58:10 UTC (rev 2466)
@@ -105,8 +105,28 @@
   achieves this by applying function \code{\link{rarefy}} with number of individuals
   corresponding to average number of individuals per site.
 
-  The function has a \code{plot} method. In addition, \code{method = "random"} 
-  has \code{summary} and \code{boxplot} methods. 
+  Methods \code{"random"} and \code{"collector"} can take weights
+  (\code{w}) that give the sampling effort for each site.  The weights
+  \code{w} do not influence the order the sites are accumulated, but
+  only the value of the sampling effort so that not all sites are
+  equal. The summary results are expressed against sites even when the
+  accumulation uses weights (methods \code{"random"},
+  \code{"collector"}), or is based on individuals
+  (\code{"rarefaction"}).  The actual sampling effort is given as item
+  \code{Effort} or \code{Individuals} in the printed result. For
+  weighted \code{"random"} method the effort refers to the average
+  effort per site, or sum of weights per number of sites. With
+  weighted \code{method = "random"}, the averaged species richness is
+  found from linear interpolation of single random permutations.
+  Therefore at least the first value (and often several first) have
+  \code{NA} richness, because these values cannot be interpolated in
+  all cases but should be extrapolated.  The \code{plot} function
+  defaults to display the results as scaled to sites, but this can be
+  changed selecting \code{xvar = "effort"} (weighted methods) or
+  \code{xvar = "individuals"} (with \code{method = "rarefaction"}).
+ 
+  The \code{summary} and \code{boxplot} methods are available for
+  \code{method = "random"}.
 
   Function \code{predict} can return the values corresponding to
   \code{newdata} using linear (\code{\link{approx}}) or spline
@@ -132,8 +152,13 @@
   (\code{\link{SSgompertz}}), \code{"michaelis-menten"})
   (\code{\link{SSmicmen}}), \code{"logis"} (\code{\link{SSlogis}}),
   \code{"weibull"} (\code{\link{SSweibull}}). See these functions for
-  model specification and details.
+  model specification and details. 
 
+  When weights \code{w} were used the fit is based on accumulated
+  effort and in \code{model = "rarefaction"} on accumulated number of
+  individuals.  The \code{plot} is still based on sites, unless other
+  alternative is selected with \code{xvar}.
+
   Function \code{predict} uses \code{\link{predict.nls}}, and you can
   pass all arguments to that function. In addition, \code{fitted},
   \code{residuals} and \code{coef} work on the result object.