similar to: Plots of envfit (vegan) - placing of vector labels

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 fellow R-users, I have the problem of being unable to repeatedly use a C++-function within R unless by dyn.unloading/dyn.loading it after each .C call. The C++-code (too large to attach) compiles without problem using R CMD SHLIB. It loads (using dyn.load("myfun.so")) and executes (via .C(myfun, ...) ) properly. The function returns no object, only reads files from disk,

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

I have the following problem: I measured co2 on 6 paired sites (one grubbed and one non-grubbed fence per site -> grubbing = treatment). These measurements I repeated 15 times over 2 years. So, now my problem is how to analyze these data. I tried the following model: mod1_CO2<-lme(co2~treatment+time,random=~1|site,data=CO2_t1_t15) I think with the random effect I included the paired

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

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

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 all, I have something like the following in my model(s) class Person < ActiveRecord::Base has_many :planung has_one :last_planung :class_name => "Planung", :conditions => "exist IS TRUE", :order => "date DESC" end class Planung < ActiveRecord::Base belongs_to :person end And the corresponding

Hi, R Devils, I'm running the actual R version in JGR (version 1.5-8 ). Sys.getlocale(category = "LC_ALL") yields [1] "LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252" I want to write some HTML-Code enhanced by statistical results and labels encoded in Latin-1, which I pass to a function.

Hi, I'm running the actual R version in JGR (version 1.5-8 ). Sys.getlocale(category = "LC_ALL") yields [1] "LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252" I want to write some HTML-Code enhanced by statistical results and labels encoded in Latin-1, which I pass to a function. Some

I couldn't find out how the following to solve: There is a column in a data.frame: > d[, 'Y6'] [1] 6 3 8 11 8 9 6 8 3 5 10 15 NA 9 8 3 8 16 6 6 NA 10 5 2 7 7 6 16 7 15 7 10 12 8 7 12 12 16 7 6 8 8 15 6 [45] NA 8 99 7 12 8 9 16 7 16 8 7 7 1 15 12 8 7 10 7 8 7 8 9 8 6 6 8 6 16 11 5 11 11 1 11 3 7 7 10 10 10 6 11 [89] 16 NA

Dear All, I have a set of environental maps and presence-only points for some species. How can I generate distributions models on R using these presence-only data? What packages and functions can I use to do so? Kind regards, Miltinho Brazil [[alternative HTML version deleted]]

Hello, Peter, I tried it out: iconv(names(attributes(spss[,'Y6'])[[1]][14]), "UTF-8", "LATIN1", sub='byte') yielded [1] "<c4>rzte Chirurgie" and c4 corresponds in most encodings to ?. What can I do next? I wonder whether there is a more comfortable way then to change the occurences of <..> by the adequate character. Regards, Matthias

Hello, I'm running samba 2.0.7 in a little nt-domain with security = domain. This works fine, but I don't want to manually put my nt-domain-users to local users of my linux server. So I put in my smb.conf quick and dirthy: add user script = /usr/sbin/useradd -m -s /bin/false %u This works, smbrun called useradd and the account would be successful createt and return is 0, but Samba asks

Hi R-users, I am trying to divide a vector (say X) into equal frequency bins. If one uses the hist() function, then a histogram is plotted, but with bins of equal widths, and not with bins having the same number of data points. I have then tried the histogram() function as follows: histogram(X, nint=10, breaks=NULL, equal.widths=F) This works as I want. However, I can't extract which

Dear all For a model I need to combine several netCDF files into one (which works fine). For better overview I'd like to delete/remove some of the attributes. Is there a simple way doing this? I'm using the package netcdf4, which creates an object of class(nc) = "ncdf4". It seems that for earlier versions of netcdf objects, there was the function att.delete.nc{RNetCDF}. But

Hi all, I'm trying to build a package 'Thiele', but run into problems with generic functions. I have a class "Benefit", and defined the function "print.Benefit". When I try "R CMD check Thiele" in X11, this warning came out ------- Functions/methods with usage in documentation object 'Benefit' but not in code: print ------- Do I need to write