similar to: Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical subscript too long

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 NMDS ordination gap_flor_NMDS_chord <- metaMDS(gaps_flor,

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, I thought it might be

Hello R experts, I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so 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

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

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 and the

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:

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

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 would like to rearrange them. Is there a

Thanks, Vedant. Yes, we have done a lot of testing of Clang/LLVM (and GCC) in the past several years (more details at https://people.inf.ethz.ch/suz/emi/index.html): [GCC/LLVM bugs: *1,602* (total) / *1,007* (fixed)] [Reports: GCC (link1 <http://tinyurl.com/ojzdt78>, link2 <http://tinyurl.com/oxlkmjc>, link3 <http://tinyurl.com/jd3jnl3>, link4

Hi guys, It would be great if you could help me with this one... I'm looking to create a script to convert a matrix of species abundance e.g: <http://r.789695.n4.nabble.com/file/n4643978/species_matrix.jpg> into two vectors e.g: <http://r.789695.n4.nabble.com/file/n4643978/communitylist.jpg> ---------------- If you feel there is no easy answer to this and that it would be

Dear list, I have to look examine hourly time - series and would like to plot variable section of them using plot.zoo. Hourly time series data which looks like this: YYYY MM DD HH P-uk P-kor P-SME EPOT EREA RO R1 R2 RGES S-SNO SI SSM SUZ SLZ 2003 1 1 1 0.385 0.456 0.021 0.000 0.000 0.000 0.013 0.223 0.235 0.01 0.38

You may also be interested in the following resources on compilers correctness (articles, software, and talks -- from the general topics to the ones specifically focused on testing, validation, and verification): https://github.com/MattPD/cpplinks/blob/master/compilers.correctness.md Best regards, Matt P. Dziubinski On 12/7/2018 20:19, Philip Reames via llvm-dev wrote: > There's also

Hello, I am using vegan to do an NMDS plot and I would like to suppress the labels for the loading vectors. Is this possible? Alternatively, how 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.,

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

Hello happy Samba People, I use the following trick for mounting my Samba Maps at start-up at my WIN NT Workstation 4.0 (hate this beast). I use the logon Scripts that could be used by WIN NT. (See Directory : \system32\repl\import\scripts). You should give the file a "good" name (I use my Login Name for that (SVEN.BAT)). Then I use the "net use" in the Script for ex. :

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

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. Sya -- View

Hello everyone! We are working on writing a paper about testing the reliability of C compilers by using Csmith (a random C99 program generator). A previous testing effort, using Csmith, found 202 LLVM bugs, which represented 2% of all reported bugs at that time (PDF: https://www.flux.utah.edu/download?uid=114 <https://www.flux.utah.edu/download?uid=114>): . However, after this paper was

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

Dear vegan team, Vegan development happens now completely in github. R-Forge repository is no more in sync with github. I tried to commit all github changes to R-Forge, but a week ago I got a conflict in file and I haven't had time to resolve that conflict. You can follow vegan development and vegan discussion also without signing to github. The system seems to be completely open and does not