search for: ordiplot

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 information is provided on their ecological preferences, and other species might not characterize well the analysis, t...

Hi! Is there a way to get biplot and identify to work togheter. Having the output of prcomp I would like to draw a biplot that. Instead of plotting the sample (row-names) names plots some "pch" symbols. (thats easy with xlabs) But now I would like to add using identify the names to only some of the points. I have noticed that both biplot.prcomp and biplot.default does a lot of

I've tried a few things both with prcomp(), and rda() and its friends in vegan (including biplot.rda and ordiplot), but can't find a solution. I'd like to associate subsets of the points in a resulting biplot ("sites" in the rda object) with different plotting colors/text styles to emphasize certain sets of points. I can't figure out how to keep the arrows (for "species" in the...

Hello, I'm trying plot points in an NMDS according to a factor with two levels: fig<-ordiplot(canod.sol, type="none",cex.axis=0.9,cex.lab=0.1,pty="m",tck=-0.01) ordisymbol(fig, y = hab, factor = "habitat", rainbow = T,col = env, legend = F) This gets me part of the way - It produces a plot with blue triangles for the first factor level and red circles fo...

...lem comes when I create a bi-plot of species and traits. As I have used a distance matrix in function ?metaMDS? there are no species scores available. This is given as a warning in R: "> NMDSgowdis<- metaMDS(SpeciesGowdis) > plot(NMDSgowdis, type = "t") Warning message:In ordiplot(x, choices = choices, type = type, display = display, :Species scores not available? I have read from internet resources that in principle I could obtain the trait ("species") scores to plot them in the ordination but my attempts have been unsuccessful. I have tried using the function...

...Species1 Species2 Species3 Site1 4 4 7 Site2 3 1 0 Site3 0 99 6 Site4 75 3 33 There are many more species than shown above this is just an example. Here are the questions. How do I read one row of data so as to load site2 into a variable called site2? Once I plot a graph using ordiplot how do I extract it from R so that I can put it into a Word for Windows document? Once I have the data in varables I hope to use designdist and Sørensen to discover diversity indices. I had a crack at this once but because I had sites as the columns it didn't work. Now that I think I have...

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 about things that are so little or so large that all they really do for us is puff us up and mak...

Hi, I have used Vegan to construct an NMDS ordination plot. I plotted sites of three forest types with the site number in it. My reviewer has asked me to use different symbols for each of the forest types. Can anyone send me how I can do this in R in simple steps. I have used the options like ordiplot, sel and pl syntaxes that are not working for the question that I asked for. Best, Sinu -- Palatty Allesh Sinu PhD FRES Fellow (Adjunct) Ashoka Trust for Research in Ecology and the Environment (ATREE) Royal Enclave Sri Rampura, Jakkur Post Bangalore 65 [[alternative HTML version deleted]]

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 easier to communic...

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 functions, and I know I am not using something already made into a distance matrix. There is missing trait data for so...

...ng 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 version deleted]]

...;, row.names=1) library(clusterSim) step2<-data.Normalization(step1,type="n10") step3<-asin(sqrt(step2))*57.3 step4<-t(step3) library(vegan) step5<-data.matrix(vegdist(step4,method="bray")) step6<-metaMDS(step5, autotransform=FALSE) plot(step5) Warning message: In ordiplot(x, choices = choices, type = type, display = display, : Species scores not available #PerMANOVA step1<-read.delim2("day20.txt", row.names=1) library(clusterSim) step2<-data.Normalization(step1,type="n10") step3<-asin(sqrt(step2))*57.3 step4<-t(step3) library(veg...

Hi, I'm a beginner with R, but I'm getting excellent results with it. Well I've got an capscale object (vegan package) and I want to made a biplot with symbols representing six groups of areas. With the plot.cca function and some par attributes (like 'labels') I was able to substitute the samples names for keyboard symbols ('x','o','#',ect), but it's

...>>> >> How do I read one row of data so as to load site2 into a variable >>called site2? > >?read.table and other read..... commands. Don't forget scan(). But Petr is right, you probably do not need to read one row at a time. >> Once I plot a graph using ordiplot how do I extract it from R so that I can >> put it into a Word for Windows document? >1. save a graph from menu Use windows metafile format for Word compatibility. >2. use ?png, ?jpeg and others to see how to output graph to files >(devices) In particular, see ?savePlot and note t...

Dear List, I am trying to plot the result of cca using matplot but failed. Pls kindly help and thanks. Elaine The error message was error in xy.coords(x, y, xlabel, ylabel, log = log) : (list) object cannot be coerced to type 'double' code rm(list=ls()) library(vegan) library(MASS) # input richness birdrich

Hi, I'm using nmds command (library vegan) to analyze some fishing data. I'd like to plot not only points, but also the names of species and stations in a specified position. I used the command text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds $points),pos=3,cex=0.5) But the labels are sometimes overlapped. Is there any way to use identify, or a similar command, to plot the

...he 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 = "red", add = TRUE, scaling = 2) Is there not a way I can tell R to plot both environmental and species scores as arrows/vectors? Thanks -- View this message in context: http://r.789695.n4.nabble.com/RDA-Triplot-tp3055474p3055474.html Sent...

Hi is there a way to plot only the loadings in a biplot (with the nice arrows), and to skip the scores? thanks christoph

Hi, I have been trying to create a function to generate a Procrustes plot, generated from package "vegan" in lattice. standard vegan code as follows library(vegan) pro=protest(P1, P8, permutations=4999,choices=1:4) plot(pro) Now, here is the code for the function that I have failed to get to work properly. panel.procrustes=function(x,y) }Pro=protest(x,y,permutations=4999,choices=1:4)