[Vegan-commits] r1091 - branches/1.17/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 4 10:17:09 CET 2010
Author: jarioksa
Date: 2010-01-04 10:17:08 +0100 (Mon, 04 Jan 2010)
New Revision: 1091
Modified:
branches/1.17/inst/NEWS
Log:
edited NEWS for release 1.17-0
Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS 2010-01-02 15:25:06 UTC (rev 1090)
+++ branches/1.17/inst/NEWS 2010-01-04 09:17:08 UTC (rev 1091)
@@ -5,60 +5,75 @@
CHANGES AND NEW FEATURES IN VEGAN 1.17-0
- - adipart: new function for additive partitioning of
- diversity. New function hiersimu() performs hierarchical null
- model testing for evaluating the adipart() components of alpha,
- beta and gamma diversity.
+ - New functions to partition data-set diversity (gamma) into
+ within-plot (alpha) and between-plot (beta) diversity
+ components. Function multipart performs multiplicative
+ partitioning (gamma = alpha*beta), and function adipart additive
+ partitioning (gamma = alpha + beta). Function hiersimu performs
+ hierarchical null model testing for adipart.
- - as.ts.oecosimu:
+ - Subsets and missing value handling added to constrained
+ ordination methods cca(), rda() and capscale(). The missing
+ values (NA) can be handled with setting na.action (defaults
+ na.fail). With na.action = na.omit, observations with missing
+ values are removed, and with na.action = na.exclude they are
+ kept, but scores may be NA. However, the WA scores for sites are
+ available in non-partial models with na.action = na.exclude.
+ - oecosimu: rewritten to handle a simple case of quantitative null
+ models. Gained keyword 'alternative' for "two-sided", or "less"
+ and "greater" one-sided tests. More robust with degenerate
+ solutions. The 'method' can now be a user-supplied function. New
+ support functions as.ts() and as.mcmc which transform
+ sequential models into form that can be analysed using tools for
+ time-series (as.ts()) or MCMC sequences of the 'coda' package
+ (as.mcmc).
+
- calibrate: calibrate is now a generic function with a new method
calibrate.ordisurf() in addition to the old calibrate.cca. These
find the estimates of environmental variables from ordination.
- - model.matrix.cca & model.frame.cca: new functions to reconstruct
- the model frame and model matrix of constraints used in
- ordination methods cca(), rda() and capscale().
+ - MOStest: new function for the Mithcell-Olds & Shaw test to
+ evaluate the probability that a quadratic response has its
+ extreme value (top or bottom) at the given interval.
- - MOStest: Mithcell-Olds & Shaw test to evaluate the probability
- that a quadratic response has its extreme value (top or bottom)
- at the given interval.
-
- - multipart: multiplicative partitioning of diversity into alpha,
- beta and gamma components.
-
- ordistep: stepwise selection of terms in constrained ordination
(cca, rda and capscale) using permutation tests instead of
pseudo-AIC that is used by the standard step() function.
- - pcnm: finds weighted principal coordinates of neighbour matrix
- (PCNM) from distances between points. These are typically used
- for spatial filtering in constrained ordination. The function
- does weighted analysis and can therefore produce PCNM for
- correspondence analysis in addition to PCA and RDA.
+ - pcnm: new function to find weighted principal coordinates of
+ neighbour matrix (PCNM) from distances between points. These are
+ typically used for spatial filtering in constrained
+ ordination. The function does weighted analysis and can
+ therefore produce PCNM for correspondence analysis in addition
+ to PCA and RDA.
+ - betadisper: can use spatial medians which are the recommended
+ method.
+
+ - decostand & vegdist: new transformation 'log' which implements
+ Marti Anderson's scaling log(x) + 1 for x>0 (which is not at all
+ the same as log(x+1)), and vegdist has alternative Gower
+ function that skips double zeros. Together these implement
+ the "modified Gower" distance of Anderson et al. (Ecology
+ Letters 9, 683-693; 2006).
+
+ - model.matrix.cca & model.frame.cca: new functions to reconstruct
+ the model frame and model matrix (model matrices in partial
+ models) of constraints used in ordination methods cca(), rda()
+ and capscale().
+
- simulate.cca & simulate.cca: simulate the community (response)
data from the result of cca() or rda() under alternative
hypothesis. Error is added to the fitted values from
ordination. The function uses either Gaussian error or permutes
- residuals and adds these to fitted values. Function is intended
- for advanced users.
+ residuals and adds these to fitted values.
- spandepth: a new function to find the depth of each node in the
minimum spanning tree produced by spantree().
- alias.cca: gained argument names.only.
- - betadisper: can use spatial medians which are the recommended
- method.
-
- - decostand & vegdist: new transformation 'log' which implements
- Marti Anderson's scaling log(x) + 1 for x>0 (which is not at all
- the same as log(x+1)), and vegdist has alternative Gower
- function that skips double zeros. Together these implement
- the "modified Gower" distance of Anderson et al. (Ecology
- Letters 9, 683-693; 2006).
-
- metaMDSrotate: a new function to rotate metaMDS so that first
axis is parallel to an environmental variable. (KEEP or DROP?)
@@ -68,11 +83,6 @@
value of the statistic in tied data. Slow, but fixes the
problems of the published method.
- - oecosimu: rewritten to handle a simple case of quantitative null
- models. Gained keyword 'alternative' for "two-sided", or "less"
- and "greater" one-sided tests. More robust with degenerate
- solutions. The 'method' can now be a user-supplied function.
-
- contribdiv: gained a plot method.
- rarefy: failed with one site and many sample sizes like
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