$Date: 2008-04-20 18:44:59 +0300 (Sun, 20 Apr 2008) $ VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/ Version 1.11-4 (Opened April 10, 2008) * adonis: merged Rev 312 (not dropping unused factor levels), Rev 315 (wrong df in deficit rank models), Rev 320 (wrong statistics in permutations: a critical bug). Version 1.11-3 (April 8, 2008) * ordiArrowMul & associates: merged Rev 302 (scaling of arrows). * varpart4: merged Rev 289 (wrong sum of squares). * anova.cca: merged Rev 288 (no. perms could exceed perm.max) * plot.procrustes: merged Rev 278 (fails with two identical configs). * diversity.Rnw: merged Rev 301 (portable spelling R\'{e}nyi). * permuted.index2 & associates: merged Rev 274 (allPerms support functions), Rev 283 (numPerms fix), Rev 292 (permuted.index2 fix), Rev. 295 (permControl fix), Rev 298 (added permuplot), and Rev 308 (allPerms fix and permCheck.Rd update). Version 1.11-2 (March 20, 2008) * numPerms: bugfix revision 265 * permuted.index2: bugfix revision 266 * Docs: merged fixes from the main branches for FAQ-vegan.texi (r262) and diversity-vegan.Rnw (r263, but not r264). Edited FAQ-vegan.texi for the bugfix release (no rgl.isomap here). Version 1.11-1 (March 10, 2008) * diversity-vegan.Rnw: merged revision 243 and 244 * biplot.princomp: bugfix revision 247 Version 1.11-0 (Released Feb 20, 2008) * Made a realese branch (1.11-0) based on the the rev. 204, and relabelled the devel branch to 1.12-0. * Removed nestedtemp and associated functions: there was an implementation error to be fixed in the trunk. * Added a NEWS file for user visible changes, and updated vegandocs() to know abot NEWS. * Doc updates (also merged to the trunk). Version 1.10-13 (closed Feb 15, 2008) * preparing for a release and trying to close open threads. * nestedtemp: implemented smooth fill line. The kind of the fill line was not specified in the original paper, but I used parabola which is "as smooth as possible" in the sense that its second derivative is constant. Needs checking, though. Version 1.10-12 (closed Feb 12, 2008) * nestedtemp: new try with smooth fill line. * anova.cca: by = "margin" stops with informative error message if some terms are completely aliased (used to stop with an uninformative error message). Type III effects really do not make sense with aliased variables. * calibrate.cca: does correct pivoting of aliased models. * orditkplot: Set up all basic features, and added points, text, and scores methods. Features that should be added include zooming to a rectangle drawn with a mouse, and adding env variables. The latter would be trivial in a simple way, but the user should be able to move the bunch of arrows to another place, and scale the length of arrows with a mouse. Version 1.10-11 (closed Feb 3, 2008) * bgdispersal: New, more powerful test statistic (in terms of Type 1 error rate) for the McNemar test (Pierre Legendre). * CCorA: internal functions embedded in CCorA(). * orditkplot: More resilient against user errors. New output file types (bmp, xfig), jpeg uses 100% quality. more aware of operating system and capabilities. Accepts graphical par in the function call. Gains arguments xlim, ylim. Arguments col, bg, cex renamed to pcol, pb, pcex so that the do not shadow par(). * permuted.index2: fixed a bug in permutations with strata. * summary.prc: honours now argument 'axis'. Reported by Francois Gillet, Lausanne. * Documentation: added documentation for permuted.index2, permControl, permCheck and helper functions. FAQ and intro know now about orditkplot, anova.cca(..., by="margin") and permuted.index2. FAQ gained new sections on using different plotting symbols and handling congested plots in ordination graphics. Version 1.10-10 (closed Jan 27, 2008) * DESCRIPTION: suggests tcltk. * orditkplot: new function for ordination plots based on Tcl/Tk: you can edit graph by moving labels using a mouse and save the edited graph as an eps file, or export via R plot function to eps, pdf, png or jpeg, or to dump to R session for further processing. * CCorA: removed partial analysis (which needs more work and may reappear later). Version 1.10-9 (closed Jan 16, 2008) * anova.cca: new option by = "margin" to perform separate tests for each marginal effect in a model with all other terms. This is similar to Type III tests, but will only work with marginal terms, and will exclude main effects when corresponding interactions are in the model. P-value is now assessed in the true blue way as (hits+1)/(permutations+1) in all anova.cca methods. Permutations should be able to handle now rank deficit cases with pivoting in the QR decomposition (permutest.cca). * 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(). Plan to migrate vegan functions to permuted.index2() in the devel version, and will eventually replace the current permuted.index(). * permCheck: New function for checking permutation schemes under permuted.index2. Uses new function numPerms() to generate the number of possible permutations. permCheck() has print, summary and print.summary methods. Version 1.10-8 (closed Dec 14 2007, at Rev. 133) * metaMDS: gains argument wascores (defaults TRUE) to suppress calculation of species scores. * wascores: return now NA for missing (all zero) species instead of failing. * ordiplot: ignore missing scores in plotting and printing. * betadisper: new functions for Marti Anderson's analysis of homogeneity of multivariate dispersions. * nestedtemp: handles now tied frequencies using ties.method = "average" in rank(). Function is still preliminary, and may be dropped from the release. * taxa2dist: issues now a warning if called with 'check = FALSE' and there are zero distances, typically meaning that basal taxa (species) were not coded. Also explained in the help. * varpart: failed if there were unused levels in factors (reported by Clément Tisseuil, Toulouse). * adonis: loses argument 'distfun'. Instead accepts now any 'dist' object as input instead of a data frame or a matrix. Version 1.10-7 (closed Nov 18, 2007 at Rev. 119) * adonis: gains argument 'distfun' (default 'vegdist') so that other standard conforming dissimilarity functions than vegdist can be used (a user request). * decorana: does not crash R when called with NULL row data such as decorana(dune[FALSE,]) (reported by Richard Tellford, Bergen, Norway), and predict(..., type="sites") works correctly with downweighted analysis (reported by Colin Beale, Aberdeen, Scotland). * isomap: checks now that input data are dissimilarities or can be changed into dissimilarities without warnings. * ordixyplot: can now display biplot arrows and factor centroids in constrained ordination or from envfit (ordisplom and ordicloud cannot display these). * ordixyplot, ordicloud and ordisplom: no longer have explicit scaling argument, but can now pass arguments to scores() as well as to the plotting functions. * oecosimu: evaluates now two-sided P-value of the statistic from simulations. Doc updates. * vignettes: use all similar style (amsart, a4paper, sidecap, date style). * FAQ: tell about docs added to R-Forge versions of vegan. Tell about predict() for having "passive" points. Version 1.10-6 (closed Oct 31, 2007 at Rev. 100) * Gavin Simpson joined the vegan team. * oecosimu: new functions for indices of nestedness of patches or islands, and simulation of null communities. * scores: cca method does now accept display = c("species", "sites"). Previous fix (1.10-5) was for rda method only. Documentation updated to reflect changes. * biplot.rda: now allows a different type to be specified for each of the species and site scores. Function now documented more completely. * ordixyplot, ordicloud and ordisplom: now have argument 'scaling'. * orditorp: now handles additional arguments passed as '...' more cleanly. Arguments can be passed to scores() or points/text. This should avoid the warning messages of previous versions. * sipoo: a new data set on the bird communities in the Sipoo (Sibbo) archipelago to demonstrate the oecosimu functions. Version 1.10-5 (closed Oct 18, 2007 at Rev. 86) * biplot.rda: new biplot function for PCA in rda() (Gavin Simpson). * scores: cca method accepts now display = c("species", "sites"), when it only used to accept c("sp","wa"). More consistent arguments in the default method. * CCorA: Pierre Legendre submitted code for permutation test of Pillai's trace. * capscale: negative scaling works now in plot() and scores(): estimates species sd() from the 'comm' if 'comm' is known. Version 1.10-4 (closed Oct 6, 2007 at Rev. 75) * anova.cca: failed in anova(object, by = "axis") when the fitted model had terms like poly(x, 2) or log(x). * ordiresids: new function for plot.lm like diagnostic plots for constrained ordination: Residuals ~ Fitted, sqrt(abs(Residuals)) ~ Fitted, and qqmath(~ Residuals) using Lattice graphics. * fitted.cca, fitted.rda: gained agument type = "working" to get the fitted values and residuals used internally in calculation (to be used in plot.lm diagnostic plots residuals ~ fitted). Version 1.10-3 (closed Oct 2, 2007 at Rev. 62) * doc: added vignettes intro-vegan on ordination methods and diversity-vegan. * Trellis graphics for ordination objects with functions ordixyplot, ordicloud and ordisplom. These functions are still unsatisfactory. In particular, I haven't found a clean way of having biplot arrows in the graphs (how do you know the coordinates and the axes used?). Contributions are welcome. * ordispantree made dysfunctional (deprecated in 1.8-1). Version 1.10-2 (closed Sep 14, 2007 at Rev. 36) * vegandocs: added FAQ-vegan, and renamed the old vegan-FAQ to decision-vegan. Only primary sources (texi, Rnw) in the source repository: derived files (.tex, .pdf) should be made when package is built. * CCorA: Pierre Legendre's functions for Canonical Correlation Analysis. These provide a more robust alternative to the standard cancor() in base R. (under work) * scores.default: handles numeric data frames. Version 1.10-1 (closed Sep 7, 2007 at Rev. 21) * taxondive: Fixed dimension checking, matching names and non-unique taxon names. Version 1.10-0 (Sep 6, 2007) * Moved vegan_1.8-7 (CRAN release) into R-Forge.R-Project.org and Subversion SCM. This ChangeLog will only contain most important news (and should be renamed to NEWS), and the real ChangeLogs are created by the SCM. The revisions will be numbered as 1.10-1 to 1.10-x, and the next release will be 1.11-0. VEGAN RELEASE VERSIONS at http://cran.r-project.org/ 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 from 1.10-3 (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 to fit the current graph if 'arrow.mul' is not given. The new behaviour is similar to the default in plot.cca and in plot.envfit. * orditorp: a new "ordination text or points" function to add text or points to an existing plot: adds text if this can be done without overwriting other text labels, and points otherwise. * linestack: a new function to draw labelled one-dimensional diagrams without overwriting the labels (a primitive one, and could easily be improved: submissions are welcome). * ordirgl, orgltext: adapted to changes in rgl package version 0.65. Workaround for older rgl packages, too. * decostand: Added Hellinger transformation. Empty columns and rows become now 0 instead of NaN in most methods, except when the input data contains negative values. Warns on input with negative entries or on output containing NaN. Has now argument 'range.global' for method 'range' based on the code supplied by Tyler Smith. * plot.radfit: puts now legend "topright" in R >= 2.1.0 (which has this keyword). * read.cep: issues a warning if vegan was compiled with gfortran, which has a bug that may corrupt the result. The bug concerns multiline input with T format modifier, and it was corrected in http://gcc.gnu.org/ml/gcc-patches/2005-09/msg00126.html, but still bugs most released versions of gcc. * vegdist: new indices 'raup' and 'binomial'. Method 'raup' implements probabilistic Raup-Crick index and is based on the code submitted by Michael Bedward. Method 'binomial' implements Millar's index, officially published as "Binomial deviance as a dissimilarity measure" (the C code has been in vegan for about two years, but now I tell about it and add the public interface). Method 'mountford' will give NA for any comparison involving an empty site. Warns about empty sites or negative entries with all methods except 'euclidean' and 'manhattan'. * Documentation: added documentation of the cca/rda/capscale result object. Dontruns used more neatly. Version 1.6-9 (April 22, 2005) * Maintenance release: 1.6-8 failed in R 2.1.0 patched and R 2.2.0 devel (works in R 2.1.0 release) due to problems in as.preston. Based on devel version 1.7-62. * as.fisher, as.preston: used table() in a way that failed in R 2.1.0 patched * calibrate.cca: new function to predict or calibrate or bioindicate the values of environmental constraints from community composition (ordination). * decostand: new argument na.rm (defaults FALSE) for ignoring missing values in row, column or matrix standardizations. * vegdist: new argument na.rm (defaults FALSE) for pairwise deletion of missing vaues in dissimilarity calculation. Version 1.6-8 (April 18, 2005) * Based on devel version 1.7-59. Adapted to R 2.1.0 beta. * DESCRIPTION: gives due credit to Roeland Kindt and Bob O'Hara as co-authors. * documentation: updates in capscale, vegdist. vegan-FAQ adapted to changes in Sweave in R 2.1.0. * several methods assumed that input is count data, but silently accepted floating point numbers and gave wrong results. Now they stop with error with non-integer input: fisherfit, prestonfit, prestondistr, rarefy, fisher.alpha, estimateR. * bioenv: uses now 'cor' instead of 'cor.test', and does not give so many superfluous warnings and is marginally faster. Changed printed output, so that gives 'call' instead of names of community and environmental data, since bioenv.formula could not handle these cleanly. * capscale: has now argument 'add' to use an additive constant to all dissimilarities so that all computed eigenvalues are non-negative. This is an argument of underlying 'cmdscale' function, which implements the "Correction method 2" of Legendre & Legendre (1998), p. 434. * decorana: checks now that there are no negative data entries. * dune: cleaner site names. * envfit: 'plot' now automatically scales arrows similarly as 'plot.cca' if 'arrow.mul' is not specified and arrows are added to an old plot. Has now a 'scores' function. * goodness.cca, predict.cca: documented separately. * goodness.metaMDS: new function to assess pointwise goodness of fit in metaMDS or isoMDS. * humpfit: user can now give starting values of parameters. 'summary.humpfit' returns 'cov.unscaled' so that users can apply 'ellipse' function of 'ellipse' package to display approximate confidence ellipses for pairs of parameters (with Normal assumptions). * make.cepnames: No longer duplicates one component names, but 'abbreviate's them to eight characters. * metaMDS: Split to independent metaunits 'metaMDSdist' and 'metaMDSiter'. New function 'metaMDSredist' tries to reconstruct dissimilarity matrices and transformations. 'postMDS' skips halfchange scaling with too few points (with a warning) instead of stopping with an error. Prints now info about 'postMDS' operations. New 'scores' function. Improved 'plot' function with 'display' argument and labelling of axes. Argument 'shrink' to undo expansion of species scores in plot or scores functions. Workaround for a future bug in 'isoMDS' which drops names of points in R 2.1.0. Updates number of 'tries' with 'previous.best'. * ordiplot: has now 'display' argument, so that only species or sites can be plotted. * ordiplot3d: a new function for 3D static ordination diagrams. * ordirgl: new function for dynamic 3D graphics of ordination results. With support functions orglpoints, orgltext, orglsegments and orglspider to add graphical items to dynamic plots. Needs 'rgl' package. * predict.cca, predict.rda: type = "wa" with 'newdata' works now even when some species were removed from the original fit because they were all-zero (missing). Default now to 'model = "CA"' in unconstrained analysis without "CCA" component. * predict.decorana: a new function for 'decorana' results. Similar to 'predict.cca' (but refuses to give impossible results). * procrustes: obeys now 'choices' even when input is a matrix. Plots now projections of rotated axes. New argument 'scores' so that can handle other than "site" scores. * protest: passes now arguments to 'scores' so that now can handle other than "site" scores on more than two dimensions. * rda: handles now species with constant values (typically missing or all zeros). * spenvcor: new function to find the "species -- environment correlation" in contrained ordination (cca, rda, capscale). * stressplot: a new function to plot Shepard diagram for 'metaMDS' or 'isoMDS'. * summary.cca/summary.rda: print now call. * vegemite: can now 'use' 'dendrogram' objects. Version 1.6-7 (Jan 24, 2005) * Based on devel version 1.7-42. * plot.envfit did not plot vectors. Thanks to Roeland Kindt and Ron E. VanNimwegen for bug reports and fixes. * ordisurf obeys now keyword 'display', and '...' will transfer arguments to 'scores'. * ordisegments: obeys now keyword 'display'. * ordigrid: works now. * ordihull, ordiarrows, ordisegments, ordispider, ordiellipse: have a new keyword 'show.groups' to show only specified groups. With the help of this argument it is possible to use different colours and linetypes for each group. Further, it makes possible to plot results of logical comparisons (such as A1 > 4) by setting show.groups = T. Two user requests. * new diagnostic and helper functions for 'cca', 'rda' and 'capscale': 'goodness' to estimate the proportion of inertia accounted for or residuals for sites or species; 'inertcomp' to decompose species and site inertia for conditioned, contrained and residual componets; 'vif.cca' to estimate the variance inflation factors for constraints and conditions; 'fitted' and 'residuals' to approximate data by ordination scores; 'predict' to approximate data or find site or species scores, possibly with 'newdata'; 'coef' to find the regression coefficients. 'alias.cca' is now similar to 'alias.lm' (simplified version of the latter). Version 1.6-6 (Jan 7, 2005) * Based on version 1.7-34, but without still experimental functions predict, fitted, vif & goodness for cca and rda objects. * mantel: implemented partial mantel test (function 'mantel.partial'). Both 'mantel' and 'mantel.partial' should be marginally faster and not give so many superfluous warnings. * plot.envfit: should be more reliable now. A new keyword 'at' to position the bunch of arrows in other places than the origin. Thanks to Roeland Kindt for fixes. * rankindex: Default correlation now "spearman" since the older default ("kendall") was far too slow in large data sets. Should not give so many superfluous warnings. * summary.rda: Site scores were wrong with 'scaling = 3'. Influences 'plot' and 'scores' commands for 'rda' and 'capscale' results with 'scaling = 3'. * vegdist: Issues a warning if 'method = "morisita"' is used with non-integer data. Version 1.6-5 (Oct 12, 2004) * Based on version 1.7-27. Checked with R-1.9.1 (Linux, MacOS X) and R-2.0.0 (Linux, patched version in Windows XP). Passed other tests, but some examples in 'humpfit' failed in Windows XP, and are not run on that platfrom. General cleanup in documentation. Does not 'require(mva)' any longer. * anosim: corrected the equation in docs (function was correct). Thanks to Yong Cao for notifying this. * bioenv.formula: finds now variables from attach'ed data.frames and 'data' need not be specified. * capscale & deviance.rda: capscale was modified so that its result could be handled with step (added a terms component). Function deviance.capscale was deleted so that deviance.rda will be used. A literature reference to AIC in CCA/RDA was added to the documentation. * cca/rda/capscale: Small eigenvalues are made to zero and rank reduced accordingly. Most often influences 'capscale'. * cca/rda/capscale: Now alias constraints that are collinear with other constraints or conditions in partial analysis. New function 'alias.cca' to print aliased contrasts. NB this does not influence the proper ordination results, but only to the selection of biplot scores and centroids displayed. 'summary' no longer gives a redundant warning. * decorana: removes empty species with a warning instead of stopping with error. Still error with empty sites. The behaviour is similar to 'cca'. * envfit (vectorfit, factorfit): Has now a formula interface. Bottlenecks in permutation changed now into C functions. Much faster, in particular 'factorfit' which was 25 times faster in my tests. plot.envfit could drop names (dimensions). Now honours 'scaling' argument in cca/rda/capscale (used to 'scaling = 2' always). * envfit, ordisurf: have now weights parameter 'w'. Weights are used for the results of 'cca' and 'decorana' as default, or they can be supplied by the user. In this way, envfit gives equal results to biplot scores and centroids in 'cca', and ordisurf is consistent with envfit. Both can now access 'lc' scores of 'cca' etc. * estimateR: Abundance-based estimators of extrapolated richness, written by Bob O'Hara . * humpfit: Asesses now the dispersion parameter in non-Poisson models (summary.humpfit). Added a profile method that inherits from profile.glm, so that you can use plot.profile.glm, pairs.profile.glm and confint.profile.glm of MASS for displaying profile and finding the confidence intervals from the profile likelihood. * fisherfit: prints now standard error of the estimate. Added 'profile' and 'confint' methods. * metaMDS: A new function to collect all Peter Minchin's recommendations to run nonmetric multidimensional scaling: (1) adequate data transformation with Wisconsin double and sqrt if needed, (2) use of adequate dissimilarity measure, (3) possible stepacross if needed (this Minchin didn't have), (4) run NMDS with several random starts and stop after finding two similar solutions, (5) scale results with postMDS, and (6) add species scores with wascores. Function has print and plot methods. Function scores.default changed to understand metaMDS. * specpool: Chao is now based on unbiased equation. Standard errors now estimated for Chao, 1st-order jackknife and bootstrap richness, but SE of 2nd-order jackknife still missing. * vegdist: an option for binary indices, since some users believed these are not in vegan, although you can get them with 'decostand'. Version 1.6-4 (June 10, 2004) * Based on 1.7-12. * anova.cca: Changed defaults to beta=0.01 and perm.max=10000. * bioenv: A new function implementing the BIO-ENV procedure of Clarke & Ainsworth (Mar. Ecol. Prog. Ser. 92, 205-219; 1993). The function finds the subset of scaled environmental variables with maximum (rank) correlation with community data. * cca: added ter Braak scaling, a.k.a. Hill scaling, with negative values of `scaling'. This scaling should approximate Hill's non-linear rescaling of `decorana', but it the scaling is linear and does not rescale. The scaling is very simple: the results from corresponding positive scaling are multipiled with sqrt(1/(1-lambda)). * plot.cca: Better heuristics used for the length of biplot arrows, and they are now longer in general. Axes are drawn for biplot arrows also with `text.cca' and `points.cca' functions. * deviance.cca and extractAIC.cca: auxilliary functions which allow automatic model building with `step' or `stepAIC' (MASS) functions in cca and rda. Unfortunately, cca and rda do not have deviance or AIC, and these functions are certainly wrong and dangerous. However, with continuous candidate variables they select the variables in the same order as Canoco. * humpfit: A new family of functions to fit the no-interaction model (Oksanen, J., J. Ecol. 84, 293-295; 1996) to species richness -- biomass data. * vegdist: corrected a bug in Gower index -- range standardization was made to sites, but it should be done to species. Thanks to Brett Melbourne for the bug report. Version 1.6-3 (Mar 22, 2004) * Still based on 1.7-3, but ported some changes from version 1.7-7 (envfit, procrustes). This version was produced to prepare for incompatible changes in coming R-1.9.0. * vegan-FAQ: Does not show the vegan and R versions the documentations were built, because of stupid incompatible change in R-1.9.0 of the future. package.description() function was unnecessarily replaced with packageDescription, and to accomodate recent, present and future versions of R seemed to be too much hassle. * plot.envfit: Added option 'p.max' to display only environmental variables assessed to have P values less or equal to the given limit. * plot.procrustes: added option kind = 0 to draw only axes and functions points.procrustes and lines.procrustes to add points and line segments or arrows to the plot. Version 1.6-2: Based on devel version 1.7-3. * renyi: should work now (again?). * prestondistr: The truncation level was badly chosen. Now default level is set to -1, or log2(-1) = 0.5 which might be the left limit of the first octave. This is now a parameter, leaving the choice as the responsibility of the user. * cca.default: Removes missing species and issues a warning instead of stopping with error. Version 1.6-1: Based on devel version 1.7-1. * Minor maintanenance release to satisfy tests in R-devel. There was a buglet in ordisegments that caused a warning. I had introduced a trick to handle printCoefmat before it was invented to replace print.coefmat, but this failed in R-devel. * Vignettes included in this release. These were only in devel versions of my web pages previously. Version 1.6-0 (Fisher) * Based on devel version 1.5-58. Passes checks with R-1.8.0 and R-1.7.0 and compiles into a Windows binary. Many functions were contributed by Roeland Kindt (Nairobi, Kenya). * BCI: A new data set on tree counts on 1-ha plots in the Barro Colorado Island. Thanks to Roeland Kindt and Richard S. Condit. * capscale: A new function for [partial] constrained analysis of principal coordinates (CAP). * cca, rda: Can now handle cases where the number of constraints is higher than the number of species. * cca, decorana: Find now if data have empty rows or columns. * decostand: Added Chi-square transformation. * distconnected: A new function to find if vegetation data are disconnected below given threshold dissimilarity level. Utility function no.shared gives a logical dissimilarity matrix with values TRUE for cases with no shared species. * fisher.alpha: Should work with large sample sizes now (bug report thanks to Ariel Bergamini). * fisherfit, prestonfit, prestondistr: New functions to fit Fisher's logarithmic series and Preston's log-normal model. * make.cepnames: New utility function to change Latin names into 4+4 character CEP names. * ordicluster, ordispantree: New functions in the ordihull family to overlay a cluster dendrogram or a spanning tree onto an ordination. Weights are now really used with cca and decorana plots. * radfit: New function to fit Ranked Abundance Dominance or Dominance/ Diversity models with maximum likelihood: Pre-emption, log-normal, veiled log-normal, Zipf and Zipf--Mandelbrot models. * rankindex: Can now use stepacross and new dissimilarity indices of vegdist. * rarefy: Can now optionally find SE of rarefied richness. * renyi: A new function to find Rényi diversities or Hill numbers with any scale (thanks to Roeland Kindt). * scores.ordiplot: should be more robust now. * spantree: A new function to find a minimum spanning tree using only dissimilarities below a threshold or disregarding NA dissimilarities. * specaccum: A new function for species accumulation curves. Thanks to Roeland Kindt. * specnumber: A very simple utility function to find species richness. * specpool: New function for extrapolated species richness in a species pool, or for estimating the number of unseen species. * stepacross: New function for estimation of dissimilarities between sites that have no shared species. Implements both flexible shortest paths and their approximation known as extended dissimilarities. * vegdist: New dissimilarity indices Jaccard (finally), Morisita, Horn--Morisita and Mountford. Version 1.4-4 * Based on devel version 1.5-35. * decorana: Finds now eigenvalues from the final solution as ratio of biased weighted variances of site and species scores. The values returned by the legacy Fortran function are called ``decorana values''. * downweight: passes the downweighting fraction as an attribute, and decorana catches and prints the fraction. * wascores: Uses now biased variances for expading WAs and returns the shrinkage factors as an attribute "shrinkage". Shrinkage factors are equal to eigenvalues in CCA when only this one variable is used as constraint. Function `eigengrad' returns only these eigenvalues. * rda summary/plot bugfix: Failed with non-default scaling (1 or 3) when there were no factor constraints. Corrected a statement giving a harmless warning in plot.cca. * ordiplot knows now option type = "text". New simpleminded functions points.ordiplot and text.ordiplot for adding items in an ordiplot graph. * ordiarrows, ordisegments could drop dimensions (when will I learn!) and fail if only one arrow or one segment should be drawn. One argument was missing in a `gl' command in `ordigrid'. Version 1.4-3 (Luova) * Based on devel version 1.5-30 * `cca' and `rda' use canonical expansion of the formula and return the `terms' component. Functions like `terms', `formula' and `update' magically started to work with cca and rda (and eight lines of code would allow `step' and `stepAIC' to work magically in model building... but it's so much magic that I don't trust it). Some of the allowed things are now `mod <- cca(dune ~ . - Use, dune.env)' (all variables but `Use' in dune.env), and `update(mod, . ~ . - Manure)' (remove `Manure' from the previous). * `cca' and `rda' find centroids of factor levels with factor constraints (only with formula interface). These can be accessed with `display="cn"' in `scores', `summary' and `plot'. If `display="cn"' is requested in `plot', biplot arrows are still drawn unless there is a class centroid with the same name: continuous variables are still shown as arrows and ordered factors both as arrows as centroids. * Enhanced user control of many ordination plots. Some accept more graphical parameters (`ordiplot', `plot.procrustes'). New functions `points.cca' and `text.cca' to add these items into CCA/RDA plots (documented separately). * `identify.ordiplot' knows more alternatives, among them `plot.procrustes'. This was helped with new, very generic `scores.ordiplot'. * New functions to add graphical items in ordination diagrams: `ordihull' draws convex hulls for groups, `ordiarrows' draws arrows, `ordisegments' segments, `ordigrid' combines points in to a grid, `ordispider' combines points to their (weighted) centroids or WA scores to the corresponding LC score in cca/rda, `ordiellipse' draws dispersion or confidence ellipses for points. All these take a groups argument for selecting subsets of points. `ordispider' obsoletes `spider.cca' (introduced in the previous release). * Implemented simple ``deshrinking'' of weighted averages in `wascores'. * A new diversity function `fisher.alpha' that estimates the diversity as the alpha parameter of Fisher's log-series. Thanks to Bob O'Hara for the main code. * `summary.decorana' now in canonical form so that printing is done by `print.summary.decorana' and user can intercept and catch the result. Several users had been surprised of the earlier non-canonical behaviour. `summary' knows again the prior weights used in downweighting of rare species (these evaporated in 1.4-0). * rda summary/scores/plot bugfix: Scaling of site scores was wrong with scaling alternatives 1 and 3. * envfit (vectorfit, factorfit) bug fixes: Can now handle single vectors (labelling, permutation). Recognize now `choices' so that the user can select ordination axes. * Checked with released R-1.7.0. Version 1.4-2 Based on devel version 1.5-18 * New functions and data sets: * dune: A new data set -- the classic Dune Meadow data with the environmental data. * ordiplot, identify.ordiplot: New functions to plot "any" ordination result and identify plotted points. Intended to provide similar functionality as `plot', `plotid' and `specid' functions in `labdsv' without name clashes. Functions `plot.cca' and `plot.decorana' return (invisibly) `ordiplot' objects as well, and these can be used by `identify' to label species and sites. * rda: Redundancy Analysis, or optionally, yet another PCA. This is a spin-off from cca(), and it is documented together with cca. The only new functions are rda, rda.default, rda.formula and summary.rda. Otherwise rda uses cca methods which were changed to be aware of rda. * read.cep: A function to read Cornell Ecology Package or CEP formatted files into R. This has been in devel versions since 1.1-1, but it never made to the releases, since this worked only in Linux, but crashed R in Windows. It seemed to work in R-1.6.1 with gcc 3.2 (MinGW) in Windows, so it is included. Treat with caution. * spider.cca: A tiny function that joins each WA score to the corresponding LC score in cca/rda plots. Minor changes: * Checked with R-1.7.0 (unstable devel version, snapshot 2003-02-05) and corrected as needed. * Added symmetric scaling (=3) to alternitves in cca and rda. * Minor improvements and bug fixes in vegemite. Version 1.4-1 (Logan) Based on devel version 1.5-10. New features: * Permutation tests added to envfit (vectorfit, factorfit) and procrustes (called protest). * All permutation tests take now argument strata: If given, permutations made only within strats. Concerns anosim, anova.cca (permutest.cca), mantel, envfit (factorfit, envfit) and protest (in procrustes). * fitted.procrustes(): A new function. * rarefy(): A new function for rarefaction species richness. Other changes: * cca.default(): Handles now NULL matrices X and Z: skips them. * cca.formula(): Knows now cca(X ~ 1) and permforms unconstrained CA, and cca(X ~ ., data) and perfors CCA using all variables in `data' as constraints. Has now na.action=na.fail so that cca crashes more informatively (used to crash mysteriously). A more graceful na.action may come. Assignment "=" corrected to the true blue "<-" (used to crash in old R). * envfit (factorfit, vectorfit): Use `scores' now. Various bugfixes and should work now with single factors or vectors. * plot.envfit(): Options `choices' works now like documented. * ordisurf(): A new name to surf() to avoid name clash with labdsv. * procrustes(): added option `symmetric' for symmetric rotation and goodness of fit statistic. * plot.procrustes(): Keyword `axes' changed to `choices' to be consistent with other functions. * vegemite(): A new name to vegetab. The name was chosen because the output is so compact (and to avoid confusion with function vegtab in labdsv). Function checks now that the cover codes fit in one column and splits the output if it does not fit into used page width. Version 1.4-0 Based on devel version 1.3-19. New functions: * `anosim': Analysis of Similarities. * `cca': [Partial] [Constrained] Correspondence Analysis. This is an alternative to Dray's `CAIV' (package `CoCoAn'). Differences include formula interface, WA scores in addition to LC scores, partial CCA, residual CA after constraints, algorithm based on svd (and much faster), more standard support functions (`plot', `summary', `print'). * `anova.cca' and `permutest.cca': Permutation tests for `cca'. * `envfit': A new wrapper function which calls either `vectorfit' or new `factorfit' function, and `plot.envfit' for easier display of results in graphs. * `mantel': Mantel test for two dissimilarity matrices. * `scores': A generic function to extract scores from `cca', `decorana' or even from some common ordination methods in R. * `surf': Surface fitting for ordination, intended as an alternative to `vectorfit'. * `vegetab': Prints a compact, ordered vegetation table, together with `coverscale' to transform data into compact format. Other changes: * `downweight': directly callable instead of being embedded in `decorana'. Now it can be used with other downweighting thresholds or with other CA's than `decorana', e.g., `cca', `ca', `CAIV'. * `plot.decorana': new keyword `type', removed keyword `tol'. * `vectorfit': centres now ordination before fitting, so it will work with other ordinations than MDS. * Mainly user invisible changes in `plot.decorana', `plot.procrustes', `postMDS', `print.summary.procrustes', `vectorfit', `procrustes'. One of the main changes was that `eqscplot' of `MASS' library was replaced with `plot(..., asp=1)' of standard R (but this is not S-plus compliant). * Edited help files. More examples run from help files. * Tried to improve LabDSV compliance, see http://labdsv.nr.usu.edu/. * Checked with R-1.5.0. However, `log' in diversity not changed into `logb' (yet), although base is specified, because `logb' won't work in R pre-1.5.0. Version 1.2-1 * Checked with R-1.4-0 (frozen snapshot) tools: Documentation and method consistency corrected (summary.decorana.R, decorana.Rd), and file permissions changed. * decorana.Rd: removed dependence on package `multiv' in the example, since it is not a `recommended package' -- replaced with `decorana(..., ira=1)'. Version 1.2-0 Based on experimental version 1.1-6. Doesn't include read.cep() of the experimental version, because the function is certainly unportable to all platforms (works on Red Hat Linux 7.1, but perhaps nowhere else). Major new feature: * decorana(): R port of Mark Hill's DECORANA for Detrended correspondence analysis, with methods print(), summary() and plot(). Minor changes: * postMDS(): finds isoMDS scores and doesn't destroy list structure. * vectorfit: finds isoMDS scores and decorana row scores (which are uncentred, though). * Proof reading in documentation. Version 1.0-3 *`plot.procrustes': selection of axes plotted, improved scaling in graphics, control of axis labels. * `postMDS': added plot to demonstrate half-change scaling. * `procrustes': target can now have lower dimensionality than rotated matrix. Version 1.0-2 * Fixed bugs in documentation. * `plot.procrustes': Fixed passing `...' to graphics functions. Version 1.0-1 * The first public version.