[R] Trying to make a nested lme analysis

[Ronaldo Reis Jr.]

Thanks,

it works:))

Inte
Ronaldo


ps. rats data and others used in book is in the Crawley home page:

http://www.bio.ic.ac.uk/research/mjcraw/statcomp/welcome.htm


Em Douglas Bates, escreveu:
> Where is the rats data available?
>
> It looks as if you have an lme model with both a fixed effect for
> Treatment and a random effect for Treatment.  I would guess that you
> want to have a fixed effect for treatment and random effects for
>
>  Rat %in% Treatment
>
> and
>
>  Liver %in% Rat %in% Treatment
>
> If so you would first create a factor for Rat %in% Treatment, say rTrT
> by
>
>  rats$rTrt = getGroups(~ 1 | Treatment/Rat, data = rats, level = 2)
>
> then fit the lme model as
>
>  lme(Glycogen ~ Treatment, data = rats, random = ~ 1|rTrT/Liver)
>
> "Ronaldo Reis Jr." <chrysopa at insecta.ufv.br> writes:
> > Hi,
> >
> > I'm trying to understand the lme output and procedure.
> > I'm using the Crawley's book.
> >
> > I'm try to analyse the rats example take from Sokal and Rohlf (1995).
> > I make a nested analysis using aov following the book.
> >
> > > summary(rats)
> >
> >     Glycogen       Treatment      Rat          Liver
> >  Min.   :125.0   Min.   :1   Min.   :1.0   Min.   :1
> >  1st Qu.:135.8   1st Qu.:1   1st Qu.:1.0   1st Qu.:1
> >  Median :141.0   Median :2   Median :1.5   Median :2
> >  Mean   :142.2   Mean   :2   Mean   :1.5   Mean   :2
> >  3rd Qu.:150.0   3rd Qu.:3   3rd Qu.:2.0   3rd Qu.:3
> >  Max.   :162.0   Max.   :3   Max.   :2.0   Max.   :3
> >
> > > attach(rats)
> > > Treatment <- factor(Treatment)
> > > Rat <- factor(Rat)
> > > Liver <- factor(Liver)
> > >
> > > model <- aov(Glycogen~Treatment/Rat/Liver+Error(Treatment/Rat/Liver))
> > > summary(model)
> >
> > Error: Treatment
> >           Df  Sum Sq Mean Sq
> > Treatment  2 1557.56  778.78
> >
> > Error: Treatment:Rat
> >               Df Sum Sq Mean Sq
> > Treatment:Rat  3 797.67  265.89
> >
> > Error: Treatment:Rat:Liver
> >                     Df Sum Sq Mean Sq
> > Treatment:Rat:Liver 12  594.0    49.5
> >
> > Error: Within
> >           Df Sum Sq Mean Sq F value Pr(>F)
> > Residuals 18 381.00   21.17
> >
> >
> > OK,
> >
> > Then I try to make this analysis using lme.
> >
> > > model <- lme(Glycogen~Treatment, random=~1|Treatment/Rat/Liver)
> > > summary(model)
> >
> > Linear mixed-effects model fit by REML
> >  Data: NULL
> >        AIC      BIC    logLik
> >   233.6213 244.0968 -109.8106
> >
> > Random effects:
> >  Formula: ~1 | Treatment
> >         (Intercept)
> > StdDev:    3.541272
> >
> >  Formula: ~1 | Rat %in% Treatment
> >         (Intercept)
> > StdDev:     6.00658
> >
> >  Formula: ~1 | Liver %in% Rat %in% Treatment
> >         (Intercept) Residual
> > StdDev:    3.764883 4.600247
> >
> > Fixed effects: Glycogen ~ Treatment
> > Error in if (any(wchLv <- (as.double(levels(xtTab[, wchPval])) == 0))) {
> > : missing value where logical needed
> > In addition: Warning message:
> > NaNs produced in: pt(q, df, lower.tail, log.p)
> >
> >
> > The random effects are correct, the variance component is OK:
> >
> > In nested aov | In nested lme
> > Residual
> > 21.1666       | 21.16227
> > Liver in Rats
> > 14.16667      | 14.17434
> > Rats in Treatment
> > 36.0648       | 36.079
> >
> > But I not understand why the Fixed effects error?
> >
> > What is the problem in my formula to make this analysis using lme?
> >
> > Thanks for all
> > Inte
> > Ronaldo
> > --
> > Anger kills as surely as the other vices.
> > --
> >
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> > |
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-- 
	O muito torna-se pouco com desejar um pouco mais.
		-- Francisco de Quevedo 
--
|   // | \\   [*****************************][*******************]
|| ( õ   õ )  [Ronaldo Reis Júnior          ][PentiumIII-600     ]
|      V      [UFV/DBA-Entomologia          ][HD: 30 + 10 Gb     ]
||  /     \   [36571-000 Viçosa - MG        ][RAM: 128 Mb        ]
|  /(.''`.)\  [Fone: 31-3899-2532           ][Video: SiS620-8Mb  ]
||/(: :'  :)\ [chrysopa at insecta.ufv.br      ][Modem: Pctel-onboar]
|/ (`. `'` ) \[ICQ#: 5692561                ][Kernel: 2.4.18     ]
||  ( `-  )   [*****************************][*******************]
||| _/   \_Powered by GNU/Debian W/Sarge D+ || Lxuser#: 205366