search for: envfit

Hi R-experts, I am using the envfit function over an ordination of floristic data. The problem is that every time that I run it changes the results. Sometimes dramatically, selecting variables that the first time were not significant. I do not get what could be the problem or if is normal given the permutations are different. # the...

Hi R experts, I'm looking for some help with plotting vectors from envfit in vegan, onto a 3d plot using ordiplot3d. So far I have data.mds <- metaMDS(data, k=3,trace = FALSE) vect_data<-envfit(data.mds,vegdata[,3:21],choices=1:3,permu=9999) ordiplot3d(data.mds,envfit=vect_data) ordixyplot(data.mds,pch=pts,envfit=vect_data) (my data's not really called data,...

...o I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data in 3 dimensions (after using a scree plot to check for stress levels in the different dimensions). I then used envfit to correlate a predictor dataset of environmental variables with the NMDS results, using the following code. >Fish<-as.data.frame(read.csv("Fish.csv",header=TRUE, sep = ",")) >Fish.mds<-metaMDS(Fish,zerodist = "add",k=3,trymax=20) >Predictors<-as.da...

Dear r-helpers! Jan Thiele asked r-help-list in february, but I could not find an answer to his question. I have the same problem: While preparing figures of 'envfit' plots with vegan for publication, I ran into a layout problem, that I found no solution for in the literature or the help archive: The labels of the vectors that indicate correlations of environental variables sometimes overlap with each other or with other content of the figure. Hence, I wou...

I'm getting lots of grief from reviewers about figures generated with the envfit function in the Vegan package. Has anyone else struggled to effectively explain this analysis? If so, can you share any helpful tips? The most recent comment I've gotten back: "What this shows is which NMDS axis separates the communities, not the relationship between the edaphic factor an...

Hello there, I'm trying to plot vectors with p<0.1 in a NMDS ordination plot using p.max. Below the scripts I'm using. I guess I'm missing something! could you please give me a hand? species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species, dis="sites")plot(ef,p.max=0.1) Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical subscript too long Many thanks! Laura [[alternative HTML version deleted]]

Dear all, I did a RDA and when I looked to the signification of the test with permutest, the output was non-significant. But when I used the envfit function, some of the vectors are significant. All the test's conditions are respected. What it means? Is it an error in the script? Commands and output: > permutest(rda.ind, perm=999, first=TRUE) Permutation test for rda  Call: rda(formula = x ~ ARH_frs + CON_frs + PRP_frs + RUI_frs +...

I'm pretty new to R and would appreciate some help interpreting the output of a function that was recommended to me. I've used the *envfit *function in the vegan package to plot vectors of four climate variables onto a species matrix ordination. The output indicates that only a single variable (mean_temp) is significant: ***VECTORS NMDS1 NMDS2 r2 Pr(>r) precip 0.415...

Dear R folks While preparing figures of 'envfit' plots with vegan for publication, I ran into a layout problem, that I found no solution for in the literature or the help archive: The labels of the vectors that indicate correlations of environental variables sometimes overlap with each other or with other content of the figure. Hence, I...

...w can I avoid overlap? Many thanks for the help. Example code: #perform NMDS using metaMDS() function spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS", autotransform=F, trymax=1000) #calculate the loading (i.e., variable weights) on each NMDS axis vec.sp<-envfit(spe.nmds$points, data, perm=1000, choices=c(1:2)) #plot data in ordination ordiplot(spe.nmds, choices=c(1:2), type='text', display="sites", xlab="Axis 1", ylab="Axis 2") #plot loading vectors plot(vec.sp, p.max=0.05, col='blue') [[alternative HTML v...

...ure 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 the info I need. I basically want to interpret the axes. Also after doing envfit() and plotting, is there a way to label sites based on certain environmental factors? For instance, I want to highlight plots that have a certain treatment (or have different colored points for the different treatments. I don't know if it matters but I used downweight() before applying de...

Dear r-Community, Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data. Step2: Then I want to plot environmental variables over it, using function envfit. The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I kicked all releves with missing environmental variables. Both, metaMDS and envfit then work witho...

Hi Im currently trying to plot my NMDS data together with fitted variables (envfit funct) on an ordination plot. The plot function shows two displays="sites" and "sp". I was wondering how to plot it so that the sites come up as different points for different sites but the species come up as actual names? It looks a little busy at the moment with everything in....

Hi, I want to include a vector representing the sites - environmental data correlation in a PCA. I currently use prcomp (no scaling) to perform the PCA, and envfit to retrieve the coordinates of the environmental data vector. However, the vector length is different from the one obtained in CAnoco when performing a species - environmental biplot (scaling -2). How can I scale the vector in order to be in accordance with Canoco, or which other scaling options ar...

...use fancy permutation schemes, but the default is still simple permutation and this can be expressed by giving just the number of permutations on the command line. The functions using the new permutation scheme are adonis, anosim, anova.cca for CCA/RDA/dbRDA and hence also for ordistep etc., CCorA, envfit, mantel & mantel.partial, mrpp, mso, permutest.betadisper, permutest.cca, protest and simper. The change for functions is now complete, but same clean up and updating of documentation is still to be done. This is discussed in https://github.com/vegandevs/vegan/issues/31 - vegan 2.2-0 will also...

...faces on an NMDS ordination using GAMs (Wood 2000). The authors describe, that they used R? as goodness-of-fit statistic, which they compare to the R? of fitted vectors. Calculations were carried out using the package vegan (Oksanen). I know that I can fit vectors onto ordinations with the function envfit. The R? is listed in the output table. I also know that GAMs are implemented in vegan by the function ordisurf. But how can I get an R? from this function. Thanks in advance, Kim -- GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT! -- GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-F...

Hi Im using the VEGAN package to do an RDA ordination. In my plot I get my environmental scores as arrows/vectors, but my species scores as points. I would like to get the species scores as arrows as well. I tried the envfit function, and this creates arrows, but the lenght is not proportionate to the strengh of the correlation and the point is still there (so I both have point and arrow). fit <- envfit(rdawal, dat.one, perm = 999, display = "wa") ordiplot(rdawal, type = "p") plot(fit, col = &...

Hi everyone, I'd like to project two pcas onto one device window. I plot my first PCA: biplot(prcomp(t(cerebdevmat)), var.axes=FALSE, cex=c(1,.1), pc.biplot=TRUE) Now I'd like to project the features of another PCA onto this graph. Any suggestions? I know this is easily done in MatLab but haven't figured it out in R. Thanks, Tanya [[alternative HTML version deleted]]

Hi, I am working with a species-by-trait .csv file (columns=traits, rows=species) and get the following warning message when trying to plot results of both metaMDS and pcoa:  "Warning message: In ordiplot(x, choices = choices, type = type, display = display,  :   Species scores not available" I am using a Gower's transformation in both procedures within the metaMDS or pcoa

...d an environmental attributes matrix. After running metaMDS {vegan} on the community matrix, I can successfully use either of the other two matrices to draw hulls around points belonging to various classes of species attributes or environmental characteristics. I can also use either matrix to run envfit and plot vectors for different variables. But what I really want to do is just display the species ordination and color code the points by levels of a particular factor from the species attribute matrix. For example, I've got 650 species that have 5 different feeding mechanisms, so I want eac...