[R] Cansisc: Error in eigen(eHe, symmetric = TRUE)

[Maria Judith Carmona H]

Dear John

There is my data set.

Thanks.


On Wed, Jul 9, 2014 at 8:12 PM, John Fox <jfox at mcmaster.ca> wrote:

> Dear Judith,
>
> I take it from your reply that you have *more* observations than there are
> response variables in the multivariate linear model, but since you still
> haven't provided access to the data, it's still impossible to tell what the
> problem is.
>
> I don't follow your application, possibly because I'm ignorant of the area
> in which you work, but also possibly because there's insufficient
> information about that too. When you say that there are 0 abundances, I
> assume that this doesn't mean that some abundance values are 0 for *all*
> observations. If that's the case, then that would I believe produce a
> computational error, though not I think the one you observed. As an aside,
> if there are many 0 abundances then using the multivariate normal
> distribution for the responses likely isn't reasonable, which is what
> you're doing, but this in itself won't produce a computational error in
> candisc().
>
> So, to reiterate, without the data, there's not much more that I can say.
> Because I'm out of town and will be traveling tomorrow, I'm unlikely to be
> able to respond again for several days.
>
>  Best,
>  John
>
> On Wed, 9 Jul 2014 17:54:56 -0500
>  Maria Judith Carmona H <juditycarmona at gmail.com> 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 <jfox at 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 <juditycarmona at 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
>
> ------------------------------------------------
> John Fox, Professor
> McMaster University
> Hamilton, Ontario, Canada
> http://socserv.mcmaster.ca/jfox/
>
>
>
>


-- 
Maria Judith Carmona Higuita.
Biologist - University of Antioquia
Medellín - 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