[Vegan-commits] r1092 - pkg/vegan/inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 4 10:18:27 CET 2010
Author: jarioksa
Date: 2010-01-04 10:18:26 +0100 (Mon, 04 Jan 2010)
New Revision: 1092
Removed:
pkg/vegan/inst/NEWS
Log:
devel branch needs no NEWS
Deleted: pkg/vegan/inst/NEWS
===================================================================
--- pkg/vegan/inst/NEWS 2010-01-04 09:17:08 UTC (rev 1091)
+++ pkg/vegan/inst/NEWS 2010-01-04 09:18:26 UTC (rev 1092)
@@ -1,1587 +0,0 @@
--*-Text-*-
-
- VEGAN RELEASE VERSIONS
- ======================
-
- CHANGES IN VEGAN 1.15-0
-
-GENERAL
-
- - Peter Solymos joined the vegan development team.
-
-NEW FUNCTIONS
-
- - add1.cca and drop1.cca: functions to implement permutation tests
- 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
- is written on opaque label. 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
- relocated to avoid overplotting. The optimization uses simulated
- annealing of 'optim' function. Returns an "orditkplot" object so
- that the results can be edited with 'orditkplot'. Similar to
- 'pointLabel' function in maptools package.
-
- - permatfull, permatswap: functions to permute quantitative count
- data.
-
- - treedive: estimation of functional diversity defined as the
- height of dendrogram of species properties (Petchey & Gaston,
- Ecology Letters 9, 741-758; 2006). With a helper function
- 'treeheight' to find the height of a 'hclust' dendrogram.
-
- - tsallis: Tsallis entropy family as an alternative to 'renyi'.
-
- - wcmdscale: weighted metric scaling a.k.a. weighted principal
- coordinates analysis; only uses row weights.
-
-NEW FEATURES AND FIXES
-
- - anova.cca: default permutation model changed from "direct" to
- "reduced" after Pierre Legendre demonstrated that 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 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. Improved zooming into
- graphs. Imitates R plotting characters ('pch'). Label family,
- size and font can be vectors.
-
- - 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
-
- - 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.
-
- - 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
- Wagner.
-
- - nestedtemp: matrix temperature method for oecosimu following
- Rodriguez-Girones & Santamaria (J. Biogeogr. 33, 924-935; 2006),
- but still without iterative optimization of row and column
- ordering.
-
- - TukeyHSD.betadisper: pairwise comparisons for betadisper.
-
-NEW FEATURES AND FIXES
-
- - adonis: returns both species and site scores.
-
- - betadisper: was not calculating distance to centroid correctly
- for observations where the imaginary distance to centroid was
- greater than the real distance. Now takes the absolute value of
- the combined distance before taking the square root. This is
- in-line with Marti Anderson's PERMDISP2.
-
- - BCI: example has spatial coordinates of plots.
-
- - biplot.rda: argument for arrow col.
-
- - capscale: accepts other distance functions than vegdist, and can
- use metaMDSdist for extended dissimilarites & "metaPCoA".
-
- - 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 into plot.
-
- - permDisper: renamed to permutest.betadisper.
-
- - permutest: now a generic function, currently with methods
- 'cca' and 'permDisper'.
-
- - rarefy: accepts vectors of sample sizes.
-
- - rgl.isomap: dynamic rgl plots for isomap.
-
- - screeplot.cca etc: return invisibly xycoords.
-
- - specaccum: returns numbers of individuals with method = "rarefaction".
-
- - summary.cca: returns more statistics on "variance explained by axes".
-
- - zzz: vegan got startup message.
-
-
- CHANGES IN VEGAN VERSION 1.11-4
-
- - A critical bug fix in adonis: there was a critical bug in adonis
- code, and inconsistent statistics were used in permutations so
- that P-values were grossly wrong in multi-variables models
- (single variable models were OK). In addition, df were wrong in
- deficit rank models, and unused factor levels were not dropped.
- All adonis users should upgrade and rerun their analyses.
-
- CHANGES IN VEGAN VERSION 1.11-3
-
-GENERAL
-
- - Bug fixes from Rev. 305 on http://r-forge.r-project.org/.
-
-FIXES
-
- - anova.cca: number of permutations could exceed perm.max.
-
- - permuted.index2: updated to the version in devel branch. This
- means bugfixes in permCheck, numPerms and permuted.index2. It
- also adds allPerms to get all possible permutations when
- complete enumeration is feasible. In addition, there is now a
- function permuplot to graphically show the current permutation
- scheme.
-
- - plot.cca, plot.envfit and associates: automatic scaling of
- biplot arrows and fitted vectors was wrong when axes were
- reversed (like 'xlim = c(1,-1)') or the origin was shifted in
- plot.envfit (like 'at = c(1,1)'). Added internal function
- 'ordiArrowMul'.
-
- - plot.procrustes: failed if two configurations were identical.
-
- - varpart4: sum of squares was wrong if called directly instead of
- being called via varpart(). Reported by Guillaume Blanchet.
-
- CHANGES IN VEGAN VERSION 1.11-2
-
-GENERAL
-
- - minor bug fixes and documentation updates from the devel trunk.
-
- - version 1.11-1 was made but never released to CRAN, and this is
- the first minor release of the 1.11 series.
-
-FIXES AND UPDATES
-
- - bstick.princomp: works now.
-
- - numPerms: was returning incorrect number of permutations
- when type = "strata" selected.
-
- - permuted.index2: was permuting samples within levels of strata
- as well as permuting the levels themselves if type = "strata"
- selected.
-
- - Documentation: diversity-vegan gains discussion on taxonomic
- diversity and using designdist for analysing beta diversity.
- Proof-reading and updates in diversity-vegan and FAQ-vegan.
-
-
- CHANGES IN VEGAN VERSION 1.11-0
-
-GENERAL
-
- - Based on devel version 1.10-13 (rev. 205 at R-Forge).
-
- - Gavin Simpson joined the vegan team.
-
- - Suggests now 'tcltk' (for orditkplot).
-
-NEW FUNCTIONS
-
- - anova.cca gained a new support function to analyse marginal
- effects of individual terms (which are similar to Type III
- effects). Defined with argument 'by = "margin"'.
-
- - betadisper: new functions for Marti Anderson's analysis of
- homogeneity of multivariate dispersions.
-
- - biplot.rda: biplot function for PCA run with rda. Arrows are
- used instead of points.
-
- - CCorA: Canonical correlation analysis with a robust algorithm,
- with permutation test and plot function.
-
- - oecosimu: functions to analyse nestedness of communities (such
- as on islands or patches). Function oecosimu is a general
- wrapper, and commsimulator generates null-communities of various
- types (r00, r0, r1, r2, c0, swap, trial swap, backtracking,
- quasiswap). The nestedness can be analysed with functions like
- nestedchecker (number of checkerboard units), nestedn0 (measure
- N0), nesteddisc (discrepancy), but users can supply their own
- functions or even use some standard R functions such as
- chisq.test.
-
- - ordiresids: similar diagnostic plots as in plot.lm for
- constrained ordination: Residuals ~ Fitted, sqrt(abs(Residuals))
- ~ Fitted, and qqmath(~ Residuals) using Lattice graphics.
-
- - orditkplot: interactive and editable plotting function. Function
- displays one set of points (species, sites) using both points
- and labels (text). The points are fixed, but labels can be
- dragged to better positions with mouse. The edited plots can be
- saved as EPS, exported to various graphical formats (EPS, PDF,
- PNG, JPEG, BMP, XFIG depending on the system) or dumped back to
- the R session for plotting and further processing.
-
- - ordixyplot: a set of functions for Lattice graphics of
- ordination results. Includes ordixyplot for 2D graphics,
- ordisplom for pairs plots, and ordicloud for 3D graphics. All
- can be subsetted and formatted in the usual Lattice way.
-
- - permuted.index2: New version of permuted.index() that now allows
- restricted permutations. Can produce permutations for
- time-series or line transects and for spatial grids. These can
- also be nested within 'strata'. permuted.series() and
- permuted.grid() are the relevant workhorse
- functions. Permutation options are set by new function
- permControl(). Currently used only in betadisper, but we plan to
- migrate vegan functions to permuted.index2() in the devel
- version, and will eventually replace the current
- permuted.index(). With support function permCheck for checking
- permutation schemes.
-
-NEW DATA SETS
-
- - sipoo: birds in the Sipoo archipelago (Finland, too close to
- Helsinki).
-
-NEW FEATURES AND FIXES
-
- - adonis: accepts any 'dist' object as input.
-
- - as.mlm.cca, as.mlm.rda use now correct names for variables in
- aliased models. The data were pivoted correctly in R, but the
- labels were not.
-
- - anova.cca assesses now P value as (hits+1)/(tries+1).
-
- - anova.cca: anova(..., by = "axis") failed when fitted model had
- terms like poly(x,2) or log(x).
-
- - bgdispersal uses now a more powerful statistic for the McNemar
- test (in terms of Type 1 error rate).
-
- - calibrate.cca does correct pivoting in aliased models.
-
- - capscale: negative scaling in plot works similarly as in rda.
-
- - decorana does not crash R when called with NULL row data, such
- as decorana(dune[FALSE,]). Method predict(..., type="sites")
- works correctly with downweighted analysis.
-
- - fitted.cca, fitted.rda gained argument type = "working" to get
- the fitted values and residuals used internally in calculation
- (in cca() these are weigthed and Chi-square standardized
- values).
-
- - isomap checks that input data are dissimilarities or can be
- changed into dissimilarities without warnings.
-
- - metaMDS gains argument wascores (defaults TRUE) to suppress
- calculation of species scores.
-
- - orditorp now handles "..." more cleanly.
-
- - scores.cca, scores.rda accept display = c("species", "sites").
-
- - summary.prc honours argument 'axis'.
-
- - taxa2dist issues now a warning if called with 'check = FALSE'
- and some distances == 0, typically meaning that basal taxa
- (species) were not coded.
-
- - varpart failed if there were unused levels in factors.
-
- - wascores returns now NA for missing (all zero) species instead
- of failing.
-
-DOCUMENTS
-
- - new documents: FAQ, a simple introduction to ordination in
- vegan, a detailed explanation of diversity methods. New
- formatting.
-
- - Added these NEWS.
-
-
-
-
- OLDER VEGAN VERSIONS
-
-Version 1.8-8 (Oct 2, 2007)
-
- * Minor bugfix release for upcoming R-2.6.0. Based on the
- http://r-forge.r-project.org/projects/vegan/ revision 17 (= 1.8-7)
- with ported bug fix revisions (see below for revision numbers).
-
- * anova.cca: by = "term" failed in partial model. This was broken
- in 1.8-6 by introducing a test against deficit rank models (r47).
-
- * cascadeKM: Calinski index works now when the input data is a
- data.frame (r57:58).
-
- * flush.console: metaMDSiter and bioenv use now flush.console()
- so that Windows people also see the trace (r56).
-
- * ordispantree: made defunct, was deprecated in 1.8-1 (r38).
-
- * scores: handles now numeric data frames (r25).
-
- * summary.cca: failed if only one type of scores was requested
- (r50, 52).
-
- * taxondive: Fixed dim checking and matching species names in
- community data and taxonomic distance data (r21).
-
- * tweaks to pass --pedantic R CMD check, mainly in formatting
- source files, unused variables in source files and superfluous
- braces in help files (r39, r46, r62).
-
- * Updated FAQ-vegan.pdf to the current version at R-Forge.
-
-Version 1.8-7 (August 24, 2007)
-
- * Based on devel version 1.9-34.
-
- * DESCRIPTION: M. Henry H. Stevens (Miami University, Oxford,
- Ohio) joined the vegan team.
-
- * adonis: new function for nonparametric MANOVA that is
- appropriate for even extremely wide matrices sometimes associated
- with gene data and with diverse ecological communities. Author
- Hank Stevens.
-
- * taxondive: a new function for indices of taxonomic diversity and
- distinctness after Clarke & Warwick (Mar Ecol Prog Ser 216,
- 265--278, 2001 and other papers). With a helper function
- 'taxa2dist' to turn taxonomies into distances with an option for
- variable step length (Clarke & Warwick, Mar Ecol Prog Ser 184,
- 21--29, 1999), and a toy data set on the taxonomy of dune meadow
- species ('dune.taxon'). With a help, testing and pressure from
- Mike Cappo, James Cook Uni, Qld.
-
- * bgdispersal: previous version was partly garbled (by me), and
- P. Legendre provided a corrected one.
-
- * designdist: keeps 'dist' attributes even when the 'method'
- function drops them. Swapped the order to (terms, methods) in the
- default name.
-
- * metaMDS: issues a warning if data are disconnected. Passes extra
- arguments to other 'distfun' than 'vegdist' so that you can set
- 'terms' in 'designdist' etc (metaMDSdist). Can now do trymax=0 or
- skip random starts and give you enhanced 'isoMDS' result
- (metaMDSiter).
-
- * ordiplot: failed if number of species was equal to number of
- sites (and so did plot.metaMDS and plot.isomap using this).
-
- * plot.profile.fisherfit: corrected a harmless error detected by
- checkUsagePackage().
-
- * predict.rda: removed some dead (but heavy) code from type =
- "response".
-
-Version 1.8-6 (May 9, 2007)
-
- * Based on devel version 1.9-23.
-
- * as.mlm.cca, as.mlm.rda: new functions to refit constrained
- ordination result (cca, rda, capscale) as a multiple response
- linear model. You can find influence statistics (Cook's distance,
- hat values) from the refitted model. You also can find t-values
- etc., but these have the same bias as in other software and should
- not be used.
-
- * bgdispersal: a new function for dispersal direction in
- biogeography (Legendre & Legendre 1998, section 13.3.4). Author
- Pierre Legendre.
-
- * designdist: a new function for defining your own dissimilarity
- index or for estimating beta diversity (Koleff et al.,
- J. Ecol. 72, 367-382; 2003).
-
- * isomap: a new function for isometric feature mapping of
- Tenenbaum et al. (Science 290, 2319-2323; 2000).
-
- * screeplot, bstick: new functions to draw screeplots of vegan
- ordination results with brokenstick lines, and alternative
- screeplot functions for prcomp and princomp with brokenstick.
- Author Gavin L. Simpson.
-
- * swan: a new function for the degree of absence (Swan 1970,
- Ecology 51, 89-102).
-
- * anova.cca: now refuses to do 'by = "terms"' if the rank of
- constraints is higher than the rank of the community matrix.
-
- * bioenv: gains argument 'partial' to perform partial bioenv.
-
- * cca, rda, capscale: can now handle longer expression within
- 'Condition()' (ordiParseFormula). Used to drop observations with
- missing values in unused variables (ordiGetData).
-
- * goodness.cca, goodness.rda. 'statistic = "distance"' was wrongly
- implemented. Now refuses to find "distance" in constrained
- analysis: distances of constrained and unconstrained components do
- not add up to to distances in unconstrained ordination.
-
- * metaMDS (metaMDSdist): gains argument 'distfun' to use other
- dissimilarity functions than vegdist.
-
- * renyiaccum: used a variable that was not defined as an argument.
- Added support functions persp.renyiaccum and rgl.renyiaccum
- (Roeland Kindt).
-
- * stressplot: R2's renamed to 'non-metric fit' and 'linear fit'.
-
- * Doc: Corrected reference to Hurlbert in diversity (thanks to
- Ralph Grundel). Updated references (varpart, renyiaccum). Removed
- discussion on t-values in cca from vignettes, because as.mlm.cca
- now implements those. General cleanup and better utf-8 encoding.
-
-Version 1.8-5 (January 11, 2007)
-
- * Based on devel version 1.9-12.
-
- * no.shared (manifest in metaMDS): prints thousands of lines of
- debugging info that I forgot to deactive in release. Not fatal,
- but extremely annoying.
-
- * capscale: inertia name as "unknown" if the dissimilarity object
- does not have a "method" name. Suggested by Roeland Kindt.
-
- * DESCRIPTION: license is now explicitly GPL v2 (but not later).
-
-Version 1.8-4 (January 8, 2007)
-
- * Based on devel version 1.9-10.
-
- * cascadeKM: a new function to wrap kmeans and optimality criteria
- for classification (Sebastien Durand, Pierre Legendre & Marie
- Helene Ouellette).
-
- * renyiaccum: a new function for Renyi (and Hill) accumulation
- curves (Roeland Kindt).
-
- * bioenv: bioenv.formula uses now "na.action = NULL" in
- 'model.frame', and bioenv.default passes arguments to 'cor' which
- means that you can set NA treatment in 'cor' using argument "use".
-
- * cca, rda: added "..." to formula versions to satisfy tests in
- R-DEVEL.
-
- * cca, rda, capscale: used to fail if called within other
- functions. Now data always evaluated in the environment of
- formula using new internal function ordiGetData.
-
- * anova.cca: checks that the model has both residual and
- constrained components or stops with understandable error message
- (used to stop with incomprehensible error message).
-
- * print.summary.cca, print.summary.decorana: have now arguments
- 'head' and 'tail' to print only a part of species and site
- scores. Suggested by Gavin Simpson.
-
- * metaMDS: checks now that the input data ('comm') is not a 'dist'
- object (like many users have had).
-
- * ordisurf: Does not depend on package 'akima' any longer, but
- directly finds fitted values in a regular grid using
- 'predict.gam'. Added pnpoly.c to find which of these values are
- within the convex hull defined by data. Results also look neater
- with sparse data now. Added argument 'labcex' passed to 'contour'
- for changing size of contour labels. Setting 'labcex = 0' will
- suppress drawing labels (by setting drawlabels = FALSE in
- 'contour()').
-
- * orditorp: handles now vector arguments of 'col', 'pcol', 'cex',
- and 'pch'.
-
- * rad.zipfbrot: less likely to overflow to NA coefficients during
- iteration.
-
- * renyi: added a plot function, and documented together with
- renyiaccum() instead of diversity().
-
- * scores.default: Knows now about ade4 objects. Primarily looks
- for scores scaled by eigenvalues both for sites and species.
-
- * specaccum: Added new conditioned method of Colwell et
- al. with estimated sd based on extrapolated richness (Roeland
- Kindt).
-
- * vegdist.c: More informative warnings with 'method' name (useful
- with rankindex).
-
- * DESCRIPTION: listed 'require()d' packages in the "Suggests:"
- field to satisfy more anal tests in R-DEVEL. Mention diversity
- analysis in the "Description:".
-
-Version 1.8-3 (Sept 29, 2006)
-
- * Based on devel version 1.9-2.
-
- * varespec.rda, varechem.rda: saved in binary form, because old
- ascii form gave warning in R-2.4.0-rc.
-
- * vegdist: added Chao index (of Jaccard type) that should take
- into account missing pairs of species. Checks that Binomial index
- is non-negative. Identical sites could have dissimilarity of
- magnitude 1e-17 after some standardizations, but now values <1e-15
- are zapped to zero.
-
- * estimateR: uses now standard unbiased formulation of Chao.
-
- * renyi: should work now (really!).
-
- * metaMDS: with zero = "add", zeros now replaced with
- min(dis[dis>0])/2 (used to be 1E-4) (metaMDSdist). Sets number of
- tries also when this was not set previously (metaMDSiter)
-
-Version 1.8-2 (June 13, 2006)
-
- * version 1.8-1 failed test in Windows because of a wrong encoding
- name. Explicit \enc added for non-ascii words. Kurt Hornik and
- Uwe Ligges diagnosed this and led me to see the light.
-
- * similar to devel version 1.7-97.
-
-Version 1.8-1 (June 12, 2006)
-
- * Based on devel version 1.7-96.
-
- * Pierre Legendre joined the vegan team.
-
- * beals: a new function for Beals smoothing.
-
- * bioenv: added 'trace' argument.
-
- * cca/rda/capscale: accept several 'Condition' elements in the
- formula.
-
- * capscale: capscale(y ~ ., data=...) or expansion of "." on the
- rhs works now. Documentation recognizes now db-RDA as the real
- mother method.
-
- * scores.cca, summary.cca etc: rewrite so that is cleaner and
- easier to maintain. User visible changes are scaling by species
- standard deviation (negative scaling) for 'rda', scaling=0
- (no scaling) for all methods and slightly changed output and
- improved user control in summary. These scalings actually were
- documented in 1.6-10, although I dropped them just before the
- release. predict.cca, predict.rda: work now with 'newdata' even
- when not called with formula.
-
- * anova.cca: new argument 'by' for tests of single terms or axes:
- with by = "terms" performs individual test for constraints, and
- with by = "axis" a separate sequential test for each axis. New
- argument 'first' to analyse only the first axis instead of all
- constrained variation.
-
- * intersetcor: new function for the interset correlation or the
- (weighted) correlation between individual constraints (contrasts)
- and invidual axes in cca/rda/capscale. (Not recommended.)
-
- * decostand: does not automatically convert matrix to a
- data.frame. NA handling more consistent now (thanks to Tyler Smith
- for diagnosis). Adds attribute 'decostand' giving the "method".
-
- * linestack: now really uses median as the midpoint with the odd
- number of cases, and does not give superfluous warnings with three
- or less items. New argument 'labels' to replace the default text
- in plot. The old argument 'label' renamed to 'side'. However, the
- function still works with the old syntax, but gives a warning if
- the old argument 'label' is used for 'side'. Returns invisibly the
- shifted positions of labels.
-
- * metaMDS: 'postMDS' sets now attributes similarly when called
- independently or within 'metaMDS'. 'metaMDS' forwards arguments
- to 'postMDS' except 'halfchange'. Change of phrasing in
- 'print'. Added handling of zero dissimilarities into
- 'metaMDSdist': either "fail" or "add" 1E-4 into zeros.
-
- * mrpp: new function for the multiresponse permutation procedure
- (MRPP). Code by Henry Stevens (Miami Univ, Oxford, Ohio).
-
- * ordiarrows: draws arrowhead only in the last segment. New
- argument 'startmark' for marking the starting point of the arrow.
-
- * ordisurf: new arguments 'main' for the title and 'nlevels' and
- 'levels' for the number of contour or their values.
-
- * orditorp: arguments for text colour and text character expansion
- changed to standard 'col' and 'cex' from previous 'tcol' and
- 'tcex'.
-
- * procrustes: 'summary' prints now rotation matrix, translation
- and scale, and honours 'digits'.
-
- * prc: new functions for Principal Response Curves (PRC) of van
- den Brink and ter Braak (Envir. Toxicol. Chem, 18, 138-148; 1999).
- This is a special rda() model with dedicated summary and plot
- functions. New data set 'pyrifos' to demonstrate 'prc'.
-
- * radfit: added brokenstick as a null model (rad.null), removed
- rad.veil (as it was a bad idea originally), corrected minor bugs
- in rad.preempt (which did not fail gracefully). Line colours
- start from the point colour in plot.radfit.frame. 'print' uses
- "g" format for coefficients and adds 'digits' argument. Added
- 'summary.radfit.frame' that simply prints each model.
-
- * rankindex: uses now cluster:::daisy when 'grad' includes
- factors.
-
- * spantree: now a method function with 'plot', 'lines' and
- 'cophenetic' methods. 'lines' replaces 'ordispantree'. The plot
- has a weird, new way of finding configuration for a spanning tree
- from cophenetic distances (unpublished). Documented separately.
-
- * specaccum: 'plot' honours now 'ylim'.
-
- * specpool: Chao richness was wrongly defined, but now uses the
- biased formula (error introduced in 1.6-5, correct earlier).
- Failed with zero species or if there were no species that occurred
- exactly one in the 'pool' (thanks to Emmanuel Castella, Geneve CH,
- for the bug report).
-
- * varpart: new functions for unbiased partitioning of variation by
- two to four explanatory tables in RDA or linear regression. The
- author of these functions is Pierre Legendre & co (Univ
- Montreal). New data sets 'mite', 'mite.env' and 'mite.pcnm' to
- demonstrate the functions.
-
- * vegandocs: new function to display *all* pdf documentation and
- ChangeLog. This really should be in base R -- this is a kluge to
- fill the hole.
-
- * vegemite: added argument to 'select' a subset of sites. Drops
- missing species from the table. Prints number of species and
- number of sites and the used cover scale at the end of the table.
- Passes arguments (i.e., 'maxabund') to coverscale().
-
- * coverscale: added argument 'maxabund' to 'scale = "log"'.
- Returns the name of the cover scale as an attribute for vegemite()
- to print.
-
- * vegdist: now first checks input and then transforms (if
- needed). Thanks to Tyler Smith,
-
- * Internal changes: permuted.index acceptes NULL strata as an
- alternative to missing strata. ordispantreee deprecated.
- spider.cca removed.
-
- * Documentation: general cleanup in help files. New chapter on
- t-values in cca/rda/capscale in vegan-FAQ. New pdf document on
- partioning with varpart by Pierre Legendre & co. Non-latin
- characters now use UTF-8 in documentation. R manual says that you
- should not use non-latin characters in help files, but that was
- written by Englishmen. However, this seems to cause distress to
- some users of a US West Coast OS (Windows), but OK with mainstream
- OS's (Linux, MacOS). .
-
-Version 1.6-10 (September 26, 2005)
-
- * Based on devel version 1.7-77. Checked with R 2.1.1 (stable)
- and R 2.2.0 (alpha).
-
- * rda: negative scalings explicitly ignored and treated as
- corresponding positive values. Function summary.rda used to fail
- with NA centroids.
-
- * permutest.cca & anova.cca: permutation of 'cca' result now
- re-weights environmental data properly with permuted community
- weights (this breaks compliance with popular proprietary
- software). New default method 'direct' that always permutes the
- data instead of residuals. Now clearly faster basic routines, but
- re-weighting in 'cca' is costly, and permutations may even be
- slower than earlier in small data sets. The permutest.cca returns
- more data: constrained and residual total inertia, degrees of
- freedom in the input model, and .Random.seed used in iterations.
- Thanks to Pierre Legendre for pushing me to make this faster.
-
- * ordination plot functions: obey now xlim and ylim.
-
- * ordination text and points functions: a new argument 'select'
- that can be used to select a subset of items, and a new argument
- 'labels' for text used instead of the default row names.
-
- * points.cca, text.cca: biplot arrows will be scaled automatically
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1092
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