[Vegan-commits] r501 - pkg/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 24 20:23:28 CEST 2008
Author: jarioksa
Date: 2008-09-24 20:23:28 +0200 (Wed, 24 Sep 2008)
New Revision: 501
Modified:
pkg/inst/NEWS
Log:
NEWS for 1.15-0 release _in spe_
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2008-09-16 19:49:09 UTC (rev 500)
+++ pkg/inst/NEWS 2008-09-24 18:23:28 UTC (rev 501)
@@ -1,27 +1,194 @@
+
-*-Text-*-
- VEGAN DEVELOPMENT VERSIONS
- ==========================
+ VEGAN RELEASE VERSIONS
+ ======================
+ CHANGES IN VEGAN 1.15-0
+
+NEW FUNCTIONS
+
+ - add1.cca and drop1.cca: functions to implement permutation tests
+ in with argument test = "permutation". Function drop1.cca uses
+ anova.cca(by = "margin") and add1.cca implements a new type of
+ analysis for single term additions.
+
+ - ordilabel: new alternative for cluttered ordination plots. Text
+ labels are written on opaque background tag. The texts still
+ cover each other, but at least the uppermost are readable, and
+ the ordering can be controlled by 'priority' argument. Similar
+ to 's.label' in ade4 pacakge.
+
+ - ordipointlabel: new alternative for cluttered ordination plots.
+ Points are in fixed positions, but their text labels are located
+ to avoid overplotting. The optimization uses simulated annealing
+ of 'optim' function. Returns an "orditkplot" so that the results
+ can be edited with 'orditkplot'. Similar to 'pointLabel'
+ function in maptools package.
+ FIXME: INTERFACE WITH orditkplot NEEDS A FINISHING TOUCH.
+
+ - permatfull, permatswap: functions to permute quantitative count
+ data.
+
+ - treedive: estimation of functional diversity defined as the
+ height of dendrogram of species properties for a site (Petchey &
+ Gaston, Ecology Letters 9, 741-758; 2006). With a helper
+ function 'treeheight' to find the height of a 'hclust'
+ dendrogram.
+ FIXME: check matching names in dendrogram and community data.
+
+ - tsallis: Tsallis entropy family as an alternative to 'renyi'.
+
+ - wcmdscale: weighted metric scaling a.k.a. weighted principal
+ coordinates analysis; only uses row weights.
+ FIXME: Update documentation to know wcmdscale.
+
+NEW FEATURES AND FIXES
+
+ - anova.cca: default permutation model changed from "direct" to
+ "reduced" after Pierre Legendre's demonstrated tha model
+ "reduced" was superior in term of Type I error.
+
+ - anova.cca: handles smoothly models where constrained or
+ unconstrained models are NULL and the tests are impossible (used
+ to stop with error).
+
+ - anova.cca(..., by = "margin") was handling wrongly 'x' in
+ '~Condition(x) + x + z', or model formulae where same variables
+ where used both as conditions and (aliased constraints).
+
+ - cca/rda/capscale: improved robustness in the formula
+ interface. Partial handling of "cca" objects produced by
+ ade4:::cca.
+
+ - commsimulator: swap, trial swap and quasiswap written in C and
+ *much* faster (100x in some tests).
+
+ - oecosimu: accepts now a vector of statistics and plain
+ statistics, and the user can give the name of the statistic in
+ the function call.
+
+ - ordiplot: did not use partial matching for "sites" and
+ "species".
+
+ - orditkplot: Improved user interface. Allows zooming into
+ graphs. Imitates R plotting characters ('pch'). Label family,
+ size and font can be vectors.
+ FIXME: SHOULD BE ABLE TO EDIT ALL ordipointlabel RESULTS.
+
+ - permuted.index2 and associated functions allow for restricted
+ permutations of strata (i.e., restricted shuffling of blocks).
+
+ - specaccum: removes missing (all zero) species which gave sd = NA
+ with method = "exact".
+
+ CHANGES IN VEGAN 1.13-2
+
+ - anova.cca (and permutest.cca) now calculate the residual df as
+ (number of rows) - (rank of constraints and conditions) - 1
+ instead of using the rank of the residual ordination. With
+ single response variable in 'rda' the degrees of freedom and
+ F-values are now identical to those in 'lm' (linear
+ model). However, the change does not influence significances
+ (P-values), because these have been always found by permutation,
+ and this change does not influence the order statistic used in
+ permutations.
+
+ - oecosimu: always estimates the original statistic with binary
+ data even when the user supplies quantitative data.
+
+ - orditkplot: no superfluous pointer lines when moving labels.
+
+ - procrustes plot failed if two configurations were exactly
+ identical.
+
+ - rda (and capscale) use internal scaling constant so that the
+ returned site and species scores with scalings 1, 2 or 3
+ together provide a biplot approximation of the original
+ data. This scaling constant is calculated internally, but now
+ its numerical value is returned as an attribute of 'scores.rda',
+ and 'summary' displays its value. Vignette on "Design decisions
+ and implementation" in vegan explains the calculation of the
+ internal scaling constant.
+
+ - summary of capscale identical to the summary of rda.
+
+ - scores of rda and capscale with scaling = 0 really return the
+ unmodified scores without the scaling constant.
+
+ CHANGES IN VEGAN 1.13-1
+
GENERAL
- - User visible changes in the development version to be 1.13-0.
+ - Helene Wagner joined the vegan team.
+FIXES FOR HANDLING RANKS IN CONSTRAINED ORDINATION
+
+ - cca, rda and capscale had only known one kind of rank: the rank
+ of the ordination result (= number of axes). In fact there are
+ two other types of ranks: the rank of constraints after removing
+ conditions, and the rank of constraints + conditions, where
+ conditions refer to terms "partialled out". This hit those that
+ tried to use rda with single response variable instead of
+ community matrix, and also some partial models were handled
+ wrongly. The changes mainly concern cases where the rank of
+ constraints is higher than the rank of the ordination (more
+ constraints than ordination axes). The changes have visible
+ effects in following support functions:
+
+ - alias: no superfluous aliasing of terms, partial models aliased
+ correctly.
+
+ - anova: always uses rank of the constraints which also fixes
+ anova(..., by = "terms") when single response variable was used.
+
+ - calibrate.cca: identifies cases when the rank of constraints is
+ higher than the rank of ordination and refuses to analyse these.
+
+ - extractAIC: uses rank of constraints for degrees of freedom.
+
+ - predict: predict(..., type = "lc", newdata = somedata) works in
+ partial analysis.
+
+OTHER FIXES
+
+ - adonis: faster and improved documentation.
+
+ - intersetcor and inertcomp now check that input really is from
+ constrained ordination instead of giving obscure error messages.
+
+ - lines.spantree knows again graphical arguments such as 'col',
+ 'lty'.
+
+ - mite.xy: new data set on the spatial coordinates of sample sites
+ of Oribatid mites.
+
+ - mso: plot.mso replaced with msoplot, and plot function now
+ displays the ordination scatter plot. Function msoplot collapses
+ distances larger than half of the maximum distance into a single
+ distance class. Printed result shows the variogram data.
+
+ - ordicluster, ordiellipse, ordispider, orglspider, ordisurf,
+ factorfit and vectorfit could fail with non-vegan ordination
+ objects in R 2.7.0 whose weights.default function gave error if
+ object had no weights (these worked in R 2.6.2 and earlier).
+
+ - taxa2dist: has a "method" name for distances.
+
+
+ CHANGES IN VEGAN 1.13-0
+
+GENERAL
+
+ - Based on development version 1.12-15 (revision 354 at
+ http://vegan.r-forge.r-project.org)
+
NEW FUNCTIONS
- betadiver: beta diversity functions as reviewed by Patricia
Koleff et al. (J. Anim. Ecol., 72, 367-382; 2003), with a plot
function to produce triangular plots.
- - MOStest: Mitchell-Olds--Shaw test (quadratic extreme in an
- interval). The test was suggested for analysis humped species
- richness patterns, but function implements a generalized test,
- which also can be used for analysing location the Gaussian
- optimum in gradient analysis. Moreover, it also can be used to
- replace Tokeshi's test for bimodal species frequency
- patterns. The confidence limits for the location of the optimum
- can be estimated with Fieller theorem or from profile deviance.
-
- mso: Helene Wagner's multiscale ordination or spatial
partitioning of cca and rda. This is taken from the Ecological
Archives with minimal edition with the permission of Helene
@@ -51,17 +218,17 @@
- capscale: accepts other distance functions than vegdist, and can
use metaMDSdist for extended dissimilarites & "metaPCoA".
- - designdist: accepts 2x2 contingency table notation with a, b, c,
+ - designdist: knows 2x2 contingency table notation with a, b, c,
and d.
- metaMDS: transforms data like with distances for species WA.
- - orditkplot: allows editing labels and zooming.
+ - orditkplot: allows editing labels and zooming into plot.
- permDisper: renamed to permutest.betadisper.
- permutest: now a generic function, currently with methods
- 'cca' and 'permDisper'.
+ 'cca' and 'permDisper'.
- rarefy: accepts vectors of sample sizes.
@@ -76,10 +243,6 @@
- zzz: vegan got startup message.
- VEGAN RELEASE VERSIONS
- ======================
-
-
CHANGES IN VEGAN VERSION 1.11-4
- A critical bug fix in adonis: there was a critical bug in adonis
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