Hello John, Michael and David, I will review Vegan Package. I am very thankful with your help.
Best, Judith On Thu, Jul 10, 2014 at 9:04 AM, David L Carlson <dcarl...@tamu.edu> wrote: > 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 ââin 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 ââ > > 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 BiologÃa - Universidad de Antioquia > > > MedellÃn - Colombia > > > > > > "La felicidad ocurre cuando encajas en tu vida, cuando encajas > > > tan armónicamente que cualquier cosa que hagas es una alegrÃa > > 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 BiologÃa - Universidad de Antioquia > > MedellÃn - Colombia > > > > "La felicidad ocurre cuando encajas en tu vida, cuando encajas > > tan armónicamente que cualquier cosa que hagas es una alegrÃa 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]] > > -- Maria Judith Carmona Higuita. Biologist - University of Antioquia MedellÃn - Colombia "Happiness happens when you fit with your life, when you fit so harmoniously that whatsoever you are doing is your joy. Then suddenly you will come to know: meditation follows you. If you love the work that you are doing, if you love the way you are living, then you are meditative". Osho [[alternative HTML version deleted]]
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