# Forums for vegan - Community Ecology Package

My Monitored ForumsForum | Description | Threads | Posts | Last Post | Moderation Level |
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open-discussion | General Discussion | 16 | 41 | 2015-12-23 19:49 | No Moderation |

help | Get Public Help | 117 | 365 | 2016-09-24 08:28 | No Moderation |

developers | Project Developer Discussion | 2 | 2 | 2008-05-06 11:59 | No Moderation |

vegan-1.8-8-goes-cran | vegan 1.8-8 is a minor bug fix for R 2.6.0. It only contains backported bug fixes from R-Forge. The proper R-Forge pkg tree is still much too much "under construction" to be at CRAN. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.11-0-on-cran | New release version of vegan is now available on CRAN. It seems that CRAN has had a facelift, and the vegan frontpage sports with a link to vegan NEWS and ChangeLog files which give a more detailed description of new features. Some of the major new functions include marginal ("Type III") permutation tests for terms in constrained ordination (in anova.cca), analysis of homogeneity of multivariate dispersions (betadisper), arrow biplot for unconstrained RDA (biplot.rda), numerically robust version of canonical correlations (CCorA), analysis of nestedness of communities (oecosimu and associates), residual plots for constrained ordination (ordiresids), editable Tcl/Tk graphics for ordination (orditkplot), Lattice graphics for ordination (ordixyplot), and first version of restricted permutation schemes for vegan functions. In addition, there are numerous minor bug fixes and enhancements in other functions | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.11-2-on-cran | A minor bug fix release of vegan was made, and can be expected in CRAN within a couple of days (but there is a holiday weekend coming all over Europe, and the package must pass CRAN tests to be accepted). The fixes concern bstick.princomp (which works now) and some special cases in permuted.index2. In addition, there are some updates and additions in FAQ-vegan and diversity-vegan documents. No new features or functions from the main development branch were included with this release, but you still must use R-Forge versions to get those. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.11-3-on-cran | A new version of vegan was submitted to CRAN today. This is a minor bugfix release that cures some rare cases. The major bug fixes are: - varpart4() failed if called directly instead of being called via varpart(). Most users do not call varpart4() so that this error probably does not hit many people. However, it hit Guillaume Blanchet who reported the bug. Thanks! - plot.cca, text.cca, points.cca, plot.envfit failed in automatic scaling of arrows if axes were reversed (like xlim = c(1, -1)), or the origin of the bunch of arrows was shifted (like at = c(1,1)) in plot.envfit. I guess most people did not know that you can revert axes and therefore this may be unnoticed for a long time. - plot.procrustes could fail if two compared configurations were identical! A more major change is that permuted.index2 and associates were upgraded to the current development version. This brought along a couple of fixes in rare cases (like only rows in a grid), and function allPerms for complete enumeration of all possible permutations when this is feasible. The code is still experimental and only used in permDisper, but we plan to make all permutations to use this code in the future, and user comments are welcome. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan_1.11-4-on-cran--adonis-fix | New vegan version was submitted to CRAN today, much earlier than scheduled. The only real change is a fix in adonis permutation tests. This is a critical change, and all adonis users should upgrade vegan and re-analyse adonis models. The problem only concerns models with several explanatory variables: single-variable models are OK. THe problem was that permutation tests used different statistics than was reported. Therefore the tests were inconsistent, and much too high P-values were reported to variables after the first one. In addition, this corrects two minor problems: the degrees of freedom did not take into account aliased variables in rank-deficit models, and unused factor levels were not dropped. The fixes are also included in the devel version 1.12-11 and later in R-Forge. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.13-0-in-cran | Version 1.13-0 of vegan is available in CRAN. This is a major version update that includes most features in R-Forge. Mitchell-Olds & Shaw test of R-Forge was excluded, however, since it was not yet quite mature for prime time. The main NEWS for this version are: 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. | 1 | 1 | 2008-06-10 15:19 | No Moderation |

vegan-1.13-1-in-cran | Vegan version 1.13-1 was released on June 11, 2008, and is now availalbe in CRAN. This is a bug fix release, and the major fixes concern handling ranks in constrained ordination and handling weights of ordination objects without weights. Vegan had used only one kind of ranks for constrained ordination: that defined by the constrianed ordination, which in effect is the same as the number of constrained axes. This works nicely with "usual" ordination problems, where constraints reduce the number of axes. However, it is possible to have a larger number of constraints than there are species (the number of rows is crucial, and that must be higher than the nubmer of constraints). Now vegan correctly handles these cases. Ordination plots and summaries show now all constraints. The change has wide side effects and may break some functions that escaped attention in testing. Please report problems to the vegan developers so that they can be fixed for the next release. See vegan NEWS for more details. Another major change was handling weights when there are no weights in ordination object. Vegan uses always weighted fitting for ordination objects in its graphical functions so that correspondence analysis can be handled correctly. Therefore vegan queries weights of ordination objects. In R 2.7.0 this gave an error with some results that do not have weights (it still worked in R 2.6.2), but now there is a workaround for this R feature, and plotting should again work like in previously. Function mso was upgraded to the latest version in vegan development branch. Function mso was added just before the release 1.13-0, and its user interface was soon changed. Most importantly, plot() gives now a standard ordination scatter diagram, and for mso output you must use msoplot function. There are small changes in several other functions: see NEWS in the package for details. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.13-2-submitted-to-cran | Vegan version 1.13-2 was submitted to CRAN on Tuesday, August 20, 2008. This is a minor release that only fixes obvious bugs and improves existing functions in the previous release. A major release (1.15-0) is tentatively scheduled for the Equinox, 2008, and it will contain most of the current package tree of vegan in R-Forge. The most important fix is that the residual degrees of freedom in anova.cca are always found from the number of rows. This should close the df transition started in 1.13-0. Other changes are detailed in the NEWS file of the package which also can be read using vegandocs() command in vegan. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan_1.15-0-in-cran | New vegan version 1.15-0 was submitted to CRAN on Spetember 30, 2008. This is major version upgrade that includes most of the new R-Forge features. The most important new features are: - model building and significance tests were improved in cca/rda/capscale. You can now invoke permutation tests in step(). Permutation tests were also improved and made more robust. The default permutation model is now "reduced". - new functions for cluttered ordination plots: ordilabel uses opaque background so that uppermost text is readable, and ordipointlabel tries to locate text labels for fixed points to avoid overwriting. - new permutation routines for general count data in addition to the Null models of presence/absence data (permatfull, permatswap). - Functions for estimating diversity from dendrogram heights like suggested for functional diversity by Petchey & Gaston (treedive and treeheight). - Tsallis diversity as an alternative to Renyi diversity family (tsallis). - Weighted metric scaling a.k.a. weighted principal coordinates analysis (wcmdscale) - swap and quasiswap routines of commsimulator were written in C and are much faster. - oecosimu handles vectors of statististics, allowing analysis of site statistics from Null models. - permuted.index2 or the new permutation routines can no permute strata. - specaccum handles empty species having only zero values. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.15-2-in-cran | Vegan version 1.15-2 was submitted to CRAN on 15 April, 2009, and is now available for all supported platforms. This is a maintenance release which also ports some stable and safe feautures from the vegan development versions (upto 1.16-17). The major new features are described in the NEWS file that is readable from the vegan front page in CRAN. After installing vegan, the NEWS file can be read from an R session with command vegandocs("NEWS") Completely new functions in this release are: 'contribdiv': Contribution diversity, 'dispindmorisita': Morisita index of dispersion, 'kendall.global': Kendall index to study signfiicance of species associations 'nestednodf': Nestedness index of overlap and decreasing fill (by Augusto Carvalho). The following functions have major enhancements or fixes: 'adonis': uses less memory and can be used for larger problems. Changed the way P-values are evaluated as order statistics. 'beals': completely rewritten by Miquel de Caceres, and does no CV smoothing plus some extras. 'mrpp': returns within-class means, and estimates Classification strength if weight.type = 3 is used. 'ordisurf': can now do bubble plot or vary point sizes by the observed values of the fitted variable. 'procrustes' got a 'text' function. 'radfit': brokenstick model ('rad.null') failed with Gamma and Gaussian errors. The 'plot' function takes now 'log' argument allowing, e.g., log-log plots where the Zipf model is a straight line. In addition, there are minor changes in 'anova.cca' with 'by = "margin"', 'summary.cca' etc, 'decostand', 'metaMDS', 'ordirgl', 'orditkplot', 'spantree' and 'mite' data, Finally, the help files do not produces warnings or errors in R parser v2 (which was the immediate reason of releasing the package just prior to the release of R 2.9.0). The next release may be in mid-June, 2009. This will probably be a minor release (1.15-3). There are still several functions that only are available in the R-Forge version of vegan (now 1.16-18). | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.15-3-released | Vegan versin 1.15-3 was submitted to CRAN on June 17, 2009. This contains some bugfixes and enhancements. The most important changes are: -anosim, mantel, mrpp, protest & envfit now have the observed statistic among permutations. Functions adonis and permutest.cca already behaved so but now they format the results clearly so. - capscale displays negative eigenvalues more prominently. There is a new component for "Imaginary" component of inertia for negative eigenvalues. The total inertia is now sum of all eigenvalues so that negative eigenvalues are subtracted from the total. The negative eigenvalues are listed after positive unconstrained ones. There is a new argument 'sqrt.dist' which avoids negative eigenvalues with Bray-Curtis and Jaccard indices and some others. The inertia and eigenvalues of indices with maximum = 1 are now smaller by a factor of sqrt(n-1). - eigenvals: new function to extract eigenvalues if such can be found from the object. The summary function displays proportions and cumulative proportions. Function summary.cca uses now summary.eigenvals. - meandist: a new sister function to 'mrpp'. Finds between and within group distances. The summary reports all three variants of the MRPP statitic plus classification strength. The plot method draws a dendrogam. - ordisurf: fits linear or quadratic trend surfaces if knots is 0, 1, or 2. - orditkplot: handels NA and NaN scores. - ordixyplot: mixed x and y axes for biplot arrows and class centroids. Failed in constrained ordination. - tsallis: new argument 'hill' to find results similar to Hill numbers of 'renyi'. - wcmdscale: removes now zero eigenvalue instead of last eigenvalue (which may be large negative). | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.15-4-in-cran | New version of vegan was released on 7 Sep 2009. This version narrows (but does not close) the gap between R-Forge version and CRAN releases. The NEWS file in the package contains more detailed information. Some new functions in the package are - indpower: the indicator power of species in beals() prediction. - mantel.correlog for multivariate Mantel correlograms. - poolaccum and estaccumR: accumulation models for extrapolated species richness. - radlattice: lattice graphics of alternative species abundance models. - rrarefy: generation of randomly rarefied communities. - RsquareAdj: adjusted R-squared for ordination methods and some standard statistical functions. Some new features in old functions include: - capscale has fitted() method and can predict() distances. - metaMDS accepts user-supplied dissimilarities (user request) - ordiellipse and ordihull return data on plotted structures, and they have a summary() method to find the centres of areas of plotted ellipses or polygons. Moreover, they can now label the ellipses or polygons. - ordixyplot has new panel function for plotting arrows. In addition there are some small bug fixes. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

missing-values-in-cca-and-rda--please-test | Functions cca() and rda() can handle missing data in constraints or conditions (external variables) in current R-Forge version of vegan (1.16-27 and later). The functions have new argument na.action. The default is na.fail which stops the analysis if there were missing values in external variables. Other alternatives na.omit and na.exclude remove all variables with missing data in used external variables (constraints, conditions). With option na.exclude, the results for sites are padded to the same number of rows as the original data: the LC scores will be NA, but WA scores for sites are estimated even for rows with missing constraints in non-partial models. The LC scores are linear combinations of constraints and they are missing for missing data. The WA scores depend on community data, and they can be estimated even for missing constraints. In partial models with term Condition() the effect of conditions is removed from the community data, and these cannot be estimated with missing data, and therefore WA scores are not available for these. The changes was made so that the old internal structures in the cca or rda result objects were unchanged, except that the rows with missing data were removed. Therefore functions handling directly cca objects should work normally even with na.actions na.exclude or na.omit. Functions using scores() interface will be influenced by the na.action: with na.omit, the number of rows for site data does not match the original data, with na.exclude it has the same dimensions that may contain NA values. At the moment there are no open issues, and the functions are ready for testing. Please try these functions, and report problems to the vegan forums in R-Forge or directly to Jari Oksanen at Oulu.fi. Happy testing! Jari Oksanen | 2 | 2 | 2009-09-09 17:39 | No Moderation |

vegan-1.17-1-released | Vegan version 1.17-1 is now available in CRAN. This is a quick bug fix release with some minor enhancements. There was a small inconsistency with the CCorA scores, and in the same we also added several new alternatives of biplot types. Several ordination functions and their support functions gained NA handling in the previous dot-zero release, and with these a bug sneaked into envfit which ignored weights of correspondence analysis in most analyses. We also used this opportunity to add a new function of multiplicative partitioning of gamma diversity into alpha and beta components. Smaller enhancements are that predict functions for cca/rda/capscale match 'newdata' by dimension names, and simulate.rda and simulate.cca functions gained argument 'rank' so that not all constrained axes are necessarily used in finding fitted values in constrained ordination (including rank = 0). | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.17-2 | Version 1.17-2 of vegan was released on March 8, 2010. This version was released to fix two bugs: print.permutest scrambled the ordering of P-values in paired tests (but the values were correct), and nesteddisc failed in some rare cases (and often in long chains with some null models). We also used this opportunity to have a faster (but slacker) version of nesteddisc, new 'legend' argument for screeplot.cca & friends, return an "anova" component from ordistep, and fix a warning when lattice function densityplot.oecosimu was used for non-latticed data (= single panel). | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.17-4-released | vegan_1.17-4 was released to CRAN on August 20, 2010. After this release, the R-Forge and CRAN versions are almost similar. The most long-standing difference (since May, 2008) was MOStest() or Mitchell-Olds & Shaw that ecologists use to test the location of a quadratic extreme in a given interval. The test is "generalized" so that it can be also used for the analysis for the location of optimum of the Gaussian species response model. Another new feature is that predict method for cca, rda and capscale gained argument 'newdata' for types "response" and "working". There are bug fixes in summary.meandist (correct weighting in Classificatin Strength, CS), mrpp (remove CS), vegdist (Marti Anderson variant of the Gower distance) and ordiellipse (labelling of filled polygons). | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.17-5-released | New version of vegan is now available through CRAN. This version has new function ordiR2step() for automatic model selection n rda() and capscale() based on adjusted R2 following the recommendations of Blanchet, Legendre & Borcard (Ecology 89, 2623-2632; 2008). Two functions are nearly completely rewrittedn: nestednodf() by Gustavo Carvalho and prc() by Cajo ter Braak. The printed output of constrained ordination was changed and now also shows the proportions of inertia due to different components. Handling of negative eigenvalues in capscale() and wcmdscale() was changed and now accords cmdscale() in R 2.12.1 (where this was changed). There are more improvements and new functionality in procrustes() which got a predict() method, eigenvals() which knows more objects and handles negative eigenvalues consistently with other functions, ordilabel() that git bew arguments, rankindex() than can handle other dissimilarity functions than vegdist((). The scaling of rda() and capscale() is now more flexible, and there are small improvements in treedist(), treedive() and wcmdscale(). There are small bug fixes in anova.cca(..., by = "axis"), betadisper, capscale, mantel.correlog, oecosimu, ordistep, procrustes, swan and vif.cca. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.17-6-released | Version 1.17-6 was released to CRAN soon after the previous release. The major reason for the new release was that the previous version of vegan introduced a new way of defining the total inertia in capscale (db-RDA). The old method is reinstated in this release, and new release was done quickly so that not many people have time to get confused with different results. We also use this release to improve robustness of capscale, CCorA, metaMDS and wascores. | 1 | 2 | 2011-02-15 07:51 | No Moderation |

vegan-1.17-7-released | Version 1.17-7 of vegan was published in CRAN on February 16, 2011. The main reasons triggering the release were the new R policy on using compressed data files and more stringent tests on function arguments in R 2.13.0 (Under Development). Both of these changes are practically invisible to users. However, we also used this opportunity for some minor fixes and enhancements. This is the extract of the NEWS file of the release: - anova.cca: more robust when models were fitted without 'data' argument, or when 'na.action' or 'subset' was used. - capscale: implemented 'subset' in model definition. Additive constant with 'add = TRUE' is taken into account in predict() and fitted(). Implemented simulate() which returns a dissimilarity matrix with random error about predicted values. - eigenvals: can now extract eigenvalues of some ade4 and labdsv result objects. - nestednodf: did not use binary data when weighted = FALSE was used together with order = FALSE. Reported by Daniel Spitale. - prestonfit: gained option to split tied frequencies (1, 2, 4, 8, etc.) between adjacent octaves. - specaccum: implemented choice of using either "individuals" or "sites" as x-axis in plot(). Corrected a typo in the result object: now returns indeed "individuals". | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.17-8-released | Version 1.17-8 of vegan was released soon after the previous release in CRAN. The reason for the quick release was a bug in the new 'tiesplit = TRUE' option in Preston log-Normal abundance models (prestonfit, as.preston): the highest octave could be missing instead of being split. Other changes are minor: procrustes checks its input and hopefully reduces the number of queries by desperate users, and decorana is a bit more robust with artificial data sets that have zero eigenvalues. Most other changes are invisible to the users. One large change that should be invisible to the user is that vegan functions no longer use redundant return() of the results. Please report if this causes some unforeseen problems. BTW, the average release cycle of vegan seems to be ca. 75 days. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-1.17-9-released | Version 1.17-9 of vegan was released to CRAN on March 31, 2011. The proximate reason for this release was a fix to anova.cca(..., by = "axis") which failed in partial models. In addition, there are some new features: - ordisurf() gained several arguments to control gam fitting of surfaces. - new function drarefy() that gives the probabilities that species occur in a rarefied samples of given size. Related functions rrarefy, diversity and specnumber are a bit more permissive for the input they accept. - metaMDS is more flexible for the 'previous.best' configuration it accepts. Function metaMDSrotate() can now rotate also >2dim solutions so that the first axis is parallel to a fitted environmental vector. - prestonfit() defaults now to 'tiesplit = TRUE' (the argument was introduced in vegan 1.17-8 with default FALSE). This was a minor release. The next release is expected to be a major upgrade that includes Peter Minchin's fast NMDS code with options for global, local, linear and hybrid NMDS, adequate and configurable tie treatment, handling of missing data, and an option of adding new points to existing NMDS ordination. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan---r-2.13.0 | New major revision (2.13.0) was published on April 13, 2011. Changes in this release mean that vegan must change along. Currently, we are aware of two issues: 1) The output of cmdscale() changed in R 2.13.0. Function capscale() in vegan tries to sanitize the old output, but the new output is already sane, and unnecessary sanitization causes an error. The error may appear in capscale(..., add = TRUE), and because of this error, BiodiversityR package fails its test in example(multiconstrained). We released a new vegan version (1.17-10) to fix the problem, and you should upgrade to vegan_1.17-10 if you plan to use capscale() with argument add = TRUE, or use BiodiveristyR. 2) R 2.13.0 introduced a new generic function nobs() that returns the number of observations in a fitted model. We added nobs() functions for vegan model objects, but we did not include them in the latest release version, because we didn't realize that they would be in full use in R 2.13.0 already. Currently, some functions give unnecessary warnings. The issue was reported for ordiR2step() in vegan-help forum in R-Forge, but probably also ordistep() and step() are touched. This is not a severe problem and we won't release a new version only to fix this issue, but the fix will be included in the next release. If the issue is disturbing, you can either use the current development version (that had nobs() since Feb 24, 2011) or download the file nobs.R from vegan/pkg/vegan/R directory in R Forge. If the issue looks really bad, please contact us and we revise our policy and release a new version of vegan. | 2 | 2 | 2015-01-30 10:57 | No Moderation |

vegan--1.17-12-released--2.0-coming-soon | A minor maintenance release vegan_1.17-12 was released on August 17. Changes are many but most of them improve the stability in exceptional cases. The only new function is tolerance() which finds the species "tolerances" and sample heterogeneities from a CA or CCA result. There is a small bug fix in metaMDSrotate(), and new arguments were added to make.cepnames(), ordilabel() and swan(), and adonis() is faster. The maintenance release was made to clean the table for a new major release (vegan 2.0) which is expected in September. This includes several new features: - Future versions of R require packages to have NAMESPACE, and vegan 2.0 introduces a standard R NAMESPACE. A major source of disruption may be that S3 methods are not exported, and commands like anova.cca(mod) will fail because anova.cca was not exported: you should use anova(mod) instead, and let R decide which function to use. Packages or scripts using vegan may fail because of this change. The current release (1.17-12) also has a NAMESPACE, but that exports every function so that the user experience should be similar as earlier. - Vegan will start to use new more powerful permutation routines on the 'permute' package released soon. This package will have several alternatives of restricted permutation, and will replace vegan permuted.index2 routines. The shift to 'permute' package will be gradual, and first touch only betadisper(), but all vegan permutation will move to use new routines in next gradual releases. This also means that vegan will be dependent on 'permute' package. - Peter Minchin joins the vegan team, and he has written for us new NMDS function called monoMDS(). This will replace MASS::isoMDS() as the default ordination engine in metaMDS(). The major advantage of monoMDS() is that it can use 'weak ties' or split tied dissimilarities (particularly dissimilarity = 1 for nothing shared) which hugely improves ordination of heterogeneous data sets. In addition, monoMDS can perform local and hybrid NMDS. It is even faster than the old engine. Some more capabilities will be taken into use in gradual releases, such as adding new points to existing ordinations. - Another new set of functions will be fitspecaccum() that can fit some non-linear regression models to species accumulation results from specaccum(). In addition, vegan will have several new self-starting non-linear regression models that are used in fitspecaccum(), but can also be used separately. These include Arrhenius, Gleason, Gitay and Lomolino models. Most of these features are already available in the R-Forge version of vegan (1.90-0 and above). Please test the new features and report the problems to us. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-birthday--ten-years-on-cran--four-years-on-r-forge- | First CRAN release of vegan was on September 6, 2001: vegan is now ten-years-old. Vegan entered R-Forge on September 6, 2007 or four years ago. The first vegan release was made soon after R 1.3.1 was release, and in that there were only about 120 contributed extension packages on CRAN. The first release was made to run NMDS like recommended in vegetation science. NMDS was already available in the MASS package (isoMDS), but vegan added missing pieces: - data standardization prior to analysis (decostand, wisconsin) - dissimilarity measures for community ecologists (vegdist) - starting NMDS with random configurations (initMDS) - comparing solutions from random starts (procrustes) - post-standardization of NMDS results (postMDS) - adding species scores to NMDS ordination (wascores) - fitting environmental vectors to ordination (vectorfit) Many of these functions are now incorporated in other functions such metaMDS and envfit, but they are still all parts of vegan, although not very visible. The only living fossil is wisconsin() which has survived unchanged to the latest release (initMDS was changed in rev1792 on Sep 5, 2011). The other early major version on CRAN were: 1.2-0 (Nov 19, 2001) with decorana(). 1.4-0 (May 3, 2002) which added constrained ordination methods cca() and rda(). 1.6 series (from Oct 20, 2003) which added diversity analyses, capscale and metaMDS and expanded old features. 1.8 series with incremental changes and wider authorship, and finally moved to R-Forge. Thanks to all developers, users, bug reporters and testers. Happy birthday vegan! | 0 | 0 | 1970-01-01 00:00 | No Moderation |

-permute--an-r-package-for-restricted-permutations | Yesterday, I rolled up the first public release of the *permute* package and submitted it to CRAN. This represents the first beta release of *permute* and presages significant changes to the way permutation tests are performed, and to the sorts of permutation available, in *vegan*. *permute* allows the following permutation designs: o free permutation (randomisation) o permutation of spatial transect or time series data via cyclic wrapping o permutation of spatial grids via toroidal wrapping Each of these can be used at one or both of the block level and the within-block level. Blocks of samples are defined by the argument `strata` as has been used in *vegan* for many years. As such, *permute* allows for testing of split-plot designs. For spatial data (transect or grid), the cyclic or toroidal wrapping can be performed forwards or backwards in either spatial dimension, and the same permutation can be used for the samples in each block (for example, in the case a time series data where the samples in each block have been "exposed" to the same "time process"). The main functions in *permute* are the `shuffle()` and `shuffleSet()` functions which generate a single permutation or a set of many permutations for a stated design. Permutation designs are defined using function `permControl()`. Function `allPerms()` can be used to generate the entire set of permutations for a given design, which is useful if there are only a small number of permutations possible for the combination of permutation design and number of observations and/or complete enumeration (an exact test) is required. With the release of *permute*, the older functions in *vegan* that implemented a previous version of these restricted permutations have been made defunct. Old code that utilised these functions should be ported to use the new functions in *permute*; help is available upon request. These changes are in *vegan* from version 2.0-0, which has also been released to CRAN. The main reason for splitting the permutation code out from *vegan* was that by doing so we might make this code available to other package authors without having to depend on the entirety of *vegan*. A nascent Vignette is provided with the package which aims to document the new functions and will, by version 0.8 include a section on using *permute* within functions for package authors wishing to make use of the functionality in *permute*. If you have questions about or comments on the package, contact me or post a message in the Forums section of the R-forge website[1] for the *vegan* stable of packages/ Gavin Simpson [1] https://r-forge.r-project.org/forum/?group_id=68 | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-2.0-0-published | *Vegan* 2.0-0 was published in CRAN on September 8, 2011. This is a major release with changed dependencies, standard NAMESPACE and new functions and features. You can read more detailed news in http://cran.r-project.org/web/packages/vegan/news.html but here the main points: 1. *Vegan* depends on *permute* package. This package will provide new, strong schemes of restricted permutations. Currently only permutest() for betadisper() uses the new permutation infrastructure, but with time all vegan permutation will be transferred to use *permute*. 2. *Vegan* has a standard NAMESPACE which only exports the functions that are intended for users. In particular, S3 method functions are not exported, and you cannot any longer use commands line 'cca.default()', but you must only use 'cca()'. However, most *vegan* functions were intended to be visible for users, and are exported. This change may disrupt other packages, scripts etc that use *vegan*. If you think that some non-exported functions should be exported, please contact us. 3. There are several new functions and features. Most importantly, we have new non-metric multidimensional scaling (NMDS) function monoMDS which is the default engine in metaMDS. Function monoMDS can do local NMDS, hybrid MDS and metric MDS in addition to classical global NMDS, it handles tied dissimilarities adequately in heterogeneous data sets, it can handle zero and NA dissimilarities, and it is fast. The FORTRAN code for the function was written by Peter Minchin, who joined the *vegan* author team. For other new functions and features, see the vegan NEWS (link above). Jari Oksanen | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-2.0-1-on-cran | Version 2.0-1 of vegan was published today on CRAN. The immediate reason for the release was that R 2.14.0 will be released soon, and vegan will give a lot of annoying warnings in R 2.14.0. The sd() function will no longer accept matrix input in R 2.14.0 and vegan was adapted to this change. There are also some minor bug fixes in meandist(), metaMDS(), permatswap() and permutest() for cca() objects. The 2.0-1 release will contain two new functions: clamtest() implements a test to classify species to habitat specialists and generalists (CLAM of Chazdon et al., Ecology 92, 1332-1343; 2011), and raupcrick() implements a version of Raup-Crick dissimilarity where species co-occurrence probabilities are based on species frequencies (Chase et al. (2011) _Ecosphere_ 2:art24). | 1 | 2 | 2011-12-18 12:26 | No Moderation |

trying-github | We have tried GitHub (https://github.com/jarioksa/vegan) as an alternative development site for vegan for a couple of weeks. At the moment, R-Forge is still the official main development environment, but some of the work happens at GitHub first. The interface between GitHub and R-Forge is not completely painless and we are going to drop one of these platforms someday, but so far we try to keep R-Forge and GitHub in sync. The major advantage of R-Forge is its excellent R support and good CRAN connectivity. The major advantage of GitHub is its better collaborative environment which allows easier contribution to vegan. The final choice between these two platforms will finally depend on the productivity: the developers and contributors will choose which one they prefer. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

trying-github | We have tried GitHub (https://github.com/jarioksa/vegan) as an alternative development site for vegan for a couple of weeks. At the moment, R-Forge is still the official main development environment, but some of the work happens at GitHub first. The interface between GitHub and R-Forge is not completely painless and we are going to drop one of these platforms someday, but so far we try to keep R-Forge and GitHub in sync. The major advantage of R-Forge is its excellent R support and good CRAN connectivity. The major advantage of GitHub is its better collaborative environment which allows easier contribution to vegan. The final choice between these two platforms will finally depend on the productivity: the developers and contributors will choose which one they prefer. | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-2.0-6-in-cran | Vegan 2.0-6 was released in CRAN on Feb 11, 2013. The new version contains several small bug fixes and minor improvements of existing functions. More detailed information can be found in its NEWS file at http://vegan.r-forge.r-project.org/NEWS.html | 0 | 0 | 1970-01-01 00:00 | No Moderation |

vegan-moves-to-github-and-new-release-2.2-0 | Vegan development has moved to GitHub. The front page of vegan is https://github.com/vegandevs/vegan. We do still update R-Forge, but that is now a secondary site. All changes are first pushed to github and then mirrored to R-Forge. This also means that R-Forge is potentially out of date, and may become functional at any time without notice. We are just in process of preparing vegan release 2.2-0 to CRAN. Among other things, this will use permute package in all permutations, allow parallel processing in several functions, introduce a new and more powerful null model simulation, and remove rgl and scatterplot3d based functions to a separate package vegan3d. The release is scheduled for early October, 2014. | 0 | 0 | 1970-01-01 00:00 | No Moderation |