search for: decorana

Hi After trying a simple decorana analysis (from the vegan package) on a simple data frame which contains no NA's the following error was returned: > tt_decorana(covN) Error in decorana(covN) : NA/NaN/Inf in foreign function call (arg 1) Have any vegan users come across this error and know what can be done about it? Cheers...

Dear all at the R-project help list. I have run into a problem when it comes to getting values for "total inertia" and "R-squared" for my DCA using "decorana" in the package "vegan". I have tried the "goodness" function, but the reply indicates that it does not work with "decorana" class objects. In Canoco one gets the Total inertia in the output together with 4 eigenvalues. In decorana one gets the 4 eigenvalues, but...

How do one dertermine the optimal number of rescaling cycles to use when performing DCA using the decorana function (library vegan)? Thanks for your time, Marc =================== Marc Bélisle Professeur adjoint Chaire de recherche du Canada en écologie spatiale et en écologie du paysage Département de biologie Université de Sherbrooke 2500 Boul. de l'Université Sherbrooke, Québec J1K 2R1 Canada...

Hi all, I have site data with plant species cover and am looking for trends. I'm kind of new to this, but have done lots of reading and can't find an answer. I tried decorana (I know it's been replaced by ca.) and see a trend, but I'm not sure what it means. Is there a way to get the loadings/eigenvectors of the axes (like in PCA)? Is there a way to do this with rda() too? How about with cca()? I know I can do scores() or summary() but that's not exactly th...

...put I get * installing *source* package ‘vegan’ ... ** package ‘vegan’ successfully unpacked and MD5 sums checked ** libs gfortran -g -O2 -pipe -c cepin.f -o cepin.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c data2hill.c -o data2hill.o gfortran -g -O2 -pipe -c decorana.f -o decorana.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c goffactor.c -o goffactor.o gfortran -g -O2 -pipe -c monoMDS.f -o monoMDS.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c nestedness.c -o nestedness.o gfortran -g -O2 -pipe -c or...

Dear people at the R-help-list. I have run into a problem in the package "vegan", while using the function "vegan", and would greatly appreciate any advice how to solve the problem. I have put in my data R, using the "decorana" function in the package "vegan" and received nice coordinates for the DCA of sites and species, as well as the Eigenvalues for the four axes. My problem is that I can not figure out how to get the "Total inertia", or the "R-squared" value. I thought that I could...

Dear all, I'm performing a detrended correspondence analysis on vascular plant community data (296 species), and I have a question on the species scores projected in the ordination diagram. When I run a ordiplot all species are projected in the output graph, but I'd like to restrict the number of species plotted in the final graph. Some species are so rare in the data, that no relevant

...titles of each species are plotted vertically while they are typically plotted at a 45 degree angle in other programs. Does anyone have any idea of how to rotates these titles? Below is an example plot (taken from the rioja help file) made the function. Cheers, Brendan Wiltse library(vegan) ## decorana data(RLGH) library(rioja) ## Not run: # create appropriately sized graphics window windows(width=12, height=7) # quartz() on Mac, X11 on linux ## End(Not run) # remove less abundant taxa mx <- apply(RLGH$spec, 2, max) spec <- RLGH$spec[, mx > 3] depth <- RLGH$depth$Depth #basic stratig...

Hello, I am looking for a workaround of "species empty" plots in a correspondence analysis. I tried to do a community structure analysis with a ca via decorana(), ca() and CAIV(), but none of them allow 0 only-rows. I have species (abs./pres) in columns and sites in rows sp1 sp1 sp3 ... plot1 0 1 1 plot2 0 0 0 plot3 1 0 1 ..... but on some plots no species could be found, therefore only 0 appear. I know that this isn't...

Can anyone point me in the right direction of figuring out what downweight() is doing? I am using vegan to perform CCA on diatom assemblage data. I have a lot of rare species, so I want to reduce the influence of rare species in my CCA. I have read that some authors reduce rare species by only including species with an abundance of at least 1% in at least one sample (other authors use 5% as a

...tes (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an error message saying that: Error in isoMDS(vare.dis) : zero or negative distance between objects 14 and 15 i.e. the two sites with the same fish species. I can run the decorana function with "sensible" results so the dataset seems to be ok. My next step would be to compare the results of the fish ordination with some other datasets from the same sites (i.e. through procrustes rotation) - so I wouldn?t like to remove one of the "twin" sites. Any sugg...

...e about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package. As far as i understand what i've done .... the relationships between vegetation categories and locations should be similar in all 3 analysis, although the 'arch' in locations / sites seen in the CA plot should be flatten out by the DCA - which it is!. My problem is...

...num  104.4 108.8 114.1 102.9 84.6 ...  $ CCL      : num  132 136 126 128 105 ...  $ CW       : num  89.9 87.8 89.3 84.2 72.6 ...  $ CCW      : num  137 118 133 125 112 ...  $ CH       : num  43.4 50.7 142.4 45.4 41.1 ...  $ CCH      : num  89.7 71.2 78.3 72.4 57.3 73.4 67 57 68.8 68 ... When I run decorana() on this dataset, it appears that the column "row.names" is included in the analysis, which isn't what I'm looking for.  If I go ahead and delete the column "row.names" from my data frames (i.e. removing it from turtles and turtles.env), I don't believe that the an...

Hi I'd like to know if the R can do the DCCA? Because I can't find the package about the DCCA in R. If it can not, please introduce a free software to me, which you think can easily do the work , thanks! jeff

Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on hypatia.math.ethz.ch X-Spam-Level: **** X-Spam-Status: No, hits=4.2 required=5.0 tests=MSGID_FROM_MTA_HEADER,RCVD_IN_BL_SPAMCOP_NET autolearn=no version=2.63 Dear r-help list, my question is about ordination technics:

...s is of some interest and it does raise the general point that programming literate ecologists don't seem to have yet fully embraced S-Plus or R. Having only recently found S-Plus and R myself I had rather hoped that some of the common ecological statistical tools such as CCA, Twinspan and Decorana, plus the miscellaneous tools described in Krebs (1989) might have found there way into an R package. Krebs, CJ (1989) Ecological Methodology, Harper & Row. Now as a 2nd edition 1995?) Cheers, Graham S -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help...

Dear members, I am performing multivariate analysis on marine benthic populations using R. At first glance I found ca and VEGANO packages to be the suitable for the task, but neither has incorporated Detrended Canonical Correspondence Analysis (DCCA), which is just the method I want to apply on my data. I've looked for alternative packages containing the method, but my suspicion is that

.../c/R/rw1040/src/gnuwin32/help' PERL5LIB=C:/R/rw1040/share/perl perl ../../../share/perl/build-help-windows.pl -txt -html -example -latex C:/R/rw1040/src/gnuwin32/vegan C:/R/rw1040/library >>> Building/Updating help pages for package `vegan' Formats: text html latex example decorana text html latex example decostand text html latex example diversity text html latex example initMDS text html latex example postMDS te...

Is there an R function that does canonical correspondence analysis. Can it be done using the VR function corresp()? If not, how hard it be to write R code to do it? I am a population biologist with long but patchy programming experience in C, Smalltalk, Java and other languages. Thanks, Patrick Foley patfoley at csus.edu