[Vegan-commits] r2632 - in pkg/vegan: . man vignettes

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

Author: jarioksa
Date: 2013-10-03 14:49:48 +0200 (Thu, 03 Oct 2013)
New Revision: 2632

Modified:
   pkg/vegan/NAMESPACE
   pkg/vegan/man/diversity.Rd
   pkg/vegan/vignettes/diversity-vegan.Rnw
Log:
clean-up after r2631 (fisherfit re-write and se removal)

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2013-10-03 07:51:01 UTC (rev 2631)
+++ pkg/vegan/NAMESPACE	2013-10-03 12:49:48 UTC (rev 2632)
@@ -132,7 +132,6 @@
 # confint: stats -- also uses MASS:::confint.glm & MASS:::profile.glm
 # does this work with namespaces??
 S3method(confint, MOStest)
-S3method(confint, fisherfit)
 # cophenetic: stats
 S3method(cophenetic, spantree)
 # density: stats
@@ -268,7 +267,6 @@
 S3method(plot, preston)
 S3method(plot, prestonfit)
 S3method(plot, procrustes)
-S3method(plot, profile.fisherfit)
 S3method(plot, rad)
 S3method(plot, radfit)
 S3method(plot, radfit.frame)
@@ -367,7 +365,6 @@
 # profile: stats
 # see note on 'confint'
 S3method(profile, MOStest)
-S3method(profile, fisherfit)
 S3method(profile, humpfit)
 # radfit: vegan
 S3method(radfit, data.frame)

Modified: pkg/vegan/man/diversity.Rd
===================================================================
--- pkg/vegan/man/diversity.Rd	2013-10-03 07:51:01 UTC (rev 2631)
+++ pkg/vegan/man/diversity.Rd	2013-10-03 12:49:48 UTC (rev 2632)
@@ -32,6 +32,7 @@
   \item{base}{ The logarithm \code{base} used in \code{shannon}.}
   \item{sample}{Subsample size for rarefying community, either a single
     value or a vector.}
+  \item{se}{Estimate standard errors.}
   \item{step}{Step size for sample sizes in rarefaction curves.}
   \item{xlab, ylab}{Axis labels in plots of rarefaction curves.}
   \item{label}{Label rarefaction curves by rownames of \code{x} (logical).}

Modified: pkg/vegan/vignettes/diversity-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/diversity-vegan.Rnw	2013-10-03 07:51:01 UTC (rev 2631)
+++ pkg/vegan/vignettes/diversity-vegan.Rnw	2013-10-03 12:49:48 UTC (rev 2632)
@@ -326,18 +326,7 @@
   (\Sexpr{k}).}
 \label{fig:fisher}
 \end{figure}
-We already saw $\alpha$ as a diversity index.  Now we also obtained
-estimate of standard error of $\alpha$ (these also are optionally
-available in \code{fisher.alpha}).  The standard errors are based on
-the second derivatives (curvature) of log-likelihood at the solution
-of $\alpha$.  The distribution of $\alpha$ is often non-normal
-and skewed, and standard errors are of not much use.  However,
-\code{fisherfit} has a \code{profile} method that can be used to
-inspect the validity of normal assumptions, and will be used in
-calculations of confidence intervals from profile deviance:
-<<>>=
-confint(fish)
-@
+We already saw $\alpha$ as a diversity index.
 
 Preston's log-normal model is the main challenger to Fisher's
 log-series \citep{Preston48}.  Instead of plotting species by