search for: wascores

...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 ?wascores? in package vegan and ?add.spec.scores? in package BiodiversityR. For this purpuse I have created a new species x traits table where factor traits were coded into dummy variables and all integer variables (including binary) were coerced to numeric variables. Here are the codes used and the error me...

...alysis to compare two NMDS ordinations for the same set of sites. One ordination is based on fish data, the other is based on invertebrate data. Ordinations were derived using metaMDS() from the {vegan} library as follows: fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100, wascores=TRUE, trace=TRUE, zero="add") invert.mds<-metaMDS(bugcal.a, distance="bray", k=3, trymax=100, wascores=TRUE, trace=TRUE, zero="add"), where fish.data and invert.data are site-by-abundance matrices for fish and invertebrates, respectively. I have then used protes...

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

...ariables 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, distance = "euclid", k = 2, trymax = 20, autotransform =TRUE, noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1, plot = FALSE, old.wa = FALSE, zerodist = "add") # the environmental variables to use with enfit explain1<- site[c("Tipo", "Gap.size", "Gap diameter (m)", "Size.cat", "altitud", "Slope (%)",...

...then when I plot the result, does it give me result from best solution? How do I know that. Can you plot the Stress by Iteration number? parth.mds <- metaMDS(WorldPRSenv, distance = "bray", k = 2, trymax = 100, engine = c("monoMDS", "isoMDS"), autotransform =TRUE, wascores = TRUE, expand = TRUE, trace = 2) plot(parth.mds, type = "p") Thanks in advance, Kumar -- Section of Integrative Biology University of Texas at Austin Austin, Texas 78712, USA [[alternative HTML version deleted]]

...ing this methods, I immediately get problems due to the identity between several of mycases or the presence of NA. Typical error messages are *"Error in isoMDS(DistB, k = 3) : zero or negative distance between objects 1 and 2"* or *"Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0)) { : missing value where TRUE/FALSE needed* *In addition: Warning message:* *In Ops.factor(left, right) : < not meaningful for factor"* Do you think Principal coordinate analysis on a binary distance matrix is a decent strategy? Thanks for any suggestion marco...

...of my R script is: ######################### BEGIN MDS ANALYSIS ######################### #load data data <- read.table("Ecoli33_Barry.dis", header = TRUE, row.names = 1) #perform MDS Scaling mds <- metaMDS(data, k = Dimensions, trymax = 20, autotransform =TRUE, noshare = 0.1, wascores = TRUE, expand = TRUE, trace = FALSE, plot = FALSE, old.wa = FALSE) ######################### BEGIN EM ANALYSIS ######################### #Use the points determined by MDS to perform EM clustering. #Allow only the unconstrained models. Sometimes, constrained models mess things up! EMclusters &lt...

...html latex example rankindex text html latex example varechem text html latex example vectorfit text html latex example vegdist text html latex example wascores text html latex example make[1]: Leaving directory `/cygdrive/c/R/rw1040/src/gnuwin32/help' make -C ./help RHOME=C:/R/rw1040 PKGDIR=C:/R/rw1040/src/gnuwin32 RLIB=C:/R/rw104 0/library contents-vegan make[1]: Entering directory `/cygdrive/c/R/rw1040/src/gnuwin32/h...