similar to: envfit output (vegan package) - not sure what it means

I have looked all over the internet for being able to color sites differently in a plot of an MDS (metaMDS)- I would like to color the different sites in the ordination plot (plot or ordiplot). I have set the matrix up so that my site code is 1 .... 296 (first column). is there a way to make 1-23 blue, 24-40 red etc. thanks Stephen -- Let's not spend our time and resources thinking

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.,

Dear List, Some independent variable were missing in calculation using lm and glm (gaussian). (X= Y1+Y2+…..+Y16, Independent number: 16 variable) However, those variables did work well in cor(X, Y) respectively. str(dataframe) was also run to ensure that the variables were all numbers. Moreover, the missing variables were different in lm and glm. In lm, 3 factors were not taken into

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

Hi All I have a data frame in which there are 4 columns . Column 1 : name Column 2-4 : values I would like to calculate mean/Standard error of values in column 2-4 and store them in column 5,6 respectively. I have done the following but doesn't seem to work mean_N_SE <-function(x) { name <- x[1] vals <- c(x[2:4]) temp_mean <- mean(vals) SE <- sqrt(var(x)/length(x)) }

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

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 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 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

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

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) :

Hi, I've installed Dune 2000 and the 1.06 patch in Wine, and it runs very well, except that it doesn't accept keyboard input. It wasn't any better without the patch. The entry at the appdb doesn't mention anything about it. Does anybody know how to fix it? I've already tried changing all the settings on the "graphics" tab in "winecfg". Half-Life, for

hi i've been trying to get an old game (Dune 2) which i used to play through DOS to work on Linux systems, i've not used this before and am in need of an 'idiot's guide to Linux' i've gotten as far as having unpacked the file and installed it on terminal, it now to the point of running the Setup.exe however when i try to run the setup, i get the following command line

Hi Listers, This has a simple answer but it has been eluding me nonetheless. I have been building a PCA plot from scratch with the ability to plot predefined groups in different colors. This has worked fine but when I try to get a polygon drawn around each of the groups it is not recognising my colour file correctly and is only printing the first colour in the file....code is below

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't accept a

Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: > CoastNear = subset(gel_data, Habitat != "I") The resulting data.frame has three levels for Habitat, but

Hello R-user community, I am applying the function metaMDS. However, I would like to know if there is any option to export the data I got from the axis as a data frame. I have tried as.data.frame.list but is not working. Any suggestion? Thank you in advance for your help, Lineth [[alternative HTML version deleted]]

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page, from vegan package): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't

Hi! Where does samba store printer's ACL and shared driver config? Stefano