search for: trymax

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2011 Sep 23
1
Envfit, inconsistant result?
...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, 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...
2013 Sep 06
1
Fwd: calculating dissimilarity index of islands (vegan and betapart)
...pare species presence/absence between a pair of island? Should the two islands be specifically located or close to each other?) Thank you Elaine Code # NMDS library(MASS) library(vegan) island.NMDS <- metaMDS(island,k=2, distfun = betadiver, distance = "sim",trymax=100,zerodist="add") plot(island.NMDS, type = "n") #Simpson Dissimilarity Index library(betapart) island.dist<-beta.pair(island, index.family="sor") class(island.dist) [[alternative HTML version deleted]]
2010 Jan 06
1
positive log likelihood and BIC values from mCLUST analysis
...ues of BIC and log likelihood. The relevant part 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...
2008 Dec 29
0
stress value remains so high(metaMDS)
metaMDS(cm, distance = "euclidean", k = 2, trymax = 50, autotransform =TRUE, trace = 1, plot = T) (cm is a similarity matrix, in which values are positive integers or 0) I use this command to run NMDS on my matrix "cm". But the stress is very high after analysis. About 14. Actually, there is no improvment comparing with using is...