In particular, look at the vegan Vignette, "Introduction to Ordination in vegan", particularly section 4 on constrained ordination which describes three approaches that seem relevant to your problem.
http://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf David Carlson -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Friendly Sent: Thursday, July 10, 2014 3:22 AM To: Maria Judith Carmona H Cc: r-help@r-project.org; John Fox Subject: Re: [R] Cansisc: Error in eigen(eHe, symmetric = TRUE) Maria The variables Araceae,Begoniaceae,Bromeliaceae,Clusiaceae,Cyclanthaceae,Ericaceae,Gesneriaceae, Melastomataceae,Orchidaceae,Piperaceae,Pteridophyta are frequencies (abundances?) of which most are 0 and this is not appropriate as multivariate normal data. There is probably a version of canonical analysis that takes such variables into account, but I don't know specifically. Have you looked at the vegan package and its references? HTH -Michael On 10/07/2014 12:54 AM, Maria Judith Carmona H wrote: > Dear John, > > I am including abundance values in my data set so obviously I have > zero abundances. > The problem is that if plot only the factors (biomasa, altdosel, > altsoto, cobertura, riqarb, elevacion, temperatura, precipitacion) I > get the graphic, the same happen when I included only the families, > but I want to see the effect of all these factors+families on this > plot . In fact I included only certain families: > > prueba4 <- > lm(cbind(biomasa,altdosel,altsoto,cobertura,riqarb,elevacion,temperatura,precipitacion, > Araceae,Begoniaceae,Bromeliaceae,Clusiaceae,Cyclanthaceae,Ericaceae,Gesneriaceae, > Melastomataceae,Orchidaceae,Piperaceae,Pteridophyta) ~ sitio, > data=bosques.p) > canprueba2 <- candisc(prueba2, term="sitio", data=bosques.p, ndim=1) > Error in eigen (EHD, symmetric = TRUE): infinite or missing values > in 'x' > In addition: Warning message: > In sqrt (wmd): NaNs produced > > You see I get the same error. > > Best regards, > Judith > > > On Wed, Jul 9, 2014 at 5:30 PM, John Fox <j...@mcmaster.ca > <mailto:j...@mcmaster.ca>> wrote: > > Dear Maria Judith Carmona Higuita, > > Since you didn't include enough information (such as your access > to your data) to reproduce the error, one can only guess. My > guess: you have fewer observations in your data set than response > variables on the LHS of the multivariate linear model. > > I hope this helps, > John > > ------------------------------------------------ > John Fox, Professor > McMaster University > Hamilton, Ontario, Canada > http://socserv.mcmaster.ca/jfox/ > > On Wed, 9 Jul 2014 11:36:35 -0500 > Maria Judith Carmona H <juditycarm...@gmail.com > <mailto:juditycarm...@gmail.com>> wrote: > > Hi, > > > > I have a problem using the function Candisc from Candisc Package. > > > > bosques1<-read.csv("bosques1.csv",header=TRUE,encoding="latin1") > > bosques1<-na.exclude(bosques1) > > attach(bosques1) > > > > #Modelo de regresión > > mod <- > > > > lm(cbind(biomasa,altdosel,altsoto,cobertura,riqarb,elevacion,temperatura,precipitacion, > > Acanthaceae, Apocinaceae, Araceae, Araliaceae, > Arecaceae, > > Aspleniaceae, Begoniaceae, > > Blechnaceae, Bromeliaceae, Clusiaceae, > Cyclanthaceae, > > Davalliaceae, Denstaedtiaceae, > > Dryopteridaceae, Ericaceae, Gesneriaceae, > Hymenophyllaceae, > > indet., Lauraceae, Lomariopsidaceae, Lycopodiaceae, Melastomataceae, > > Moraceae, Myrsinaceae, Ophioglossaceae, > > Orchidaceae, Peperomia, Piperaceae, Poaceae, > Polypodiaceae, > > Primulaceae, Pteridaceae, > > Pteridophyta.taxa, Rubiaceae, Vittariaceae) ~ sitio, > > data=bosques1) > > summary(mod) > > > > #Gráfico 1 > > can <- candisc(mod, term="sitio",data=bosques1,ndim=1,eig=T) > > ### The error happens here, so I can not run the plot. > > plot(can,titles.1d = c("Puntuación canónica", "Estructura")) > > summary(can, means = FALSE, scores = TRUE, coef = c("std"), > digits = 2) > > > > The error is: > > Error in eigen(eHe, symmetric = TRUE) : infinite or missing > values in 'x' > > In addition: Warning message: > > In sqrt(wmd) : NaNs produced > > > > Please help! > > > > -- > > Maria Judith Carmona Higuita. > > Estudiante de Biología - Universidad de Antioquia > > Medellín - Colombia > > > > "La felicidad ocurre cuando encajas en tu vida, cuando encajas > > tan armónicamente que cualquier cosa que hagas es una alegría > para ti. De > > repente lo sabrás y la meditación te seguirá. Si amas el trabajo > que haces, > > si amas la manera como vives, entonces ya estás meditando y nada > puede > > distraerte." Osho > > > > [[alternative HTML version deleted]] > > > > > > > > > > -- > Maria Judith Carmona Higuita. > Estudiante de Biología - Universidad de Antioquia > Medellín - Colombia > > "La felicidad ocurre cuando encajas en tu vida, cuando encajas > tan armónicamente que cualquier cosa que hagas es una alegría para ti. > De repente lo sabrás y la meditación te seguirá. Si amas el trabajo > que haces, si amas la manera como vives, entonces ya estás meditando y > nada puede distraerte." Osho > -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. & Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
