# [R] hierarchical model with heteroscedastic variances

John McKown john.archie.mckown at gmail.com
Tue Dec 2 08:42:25 CET 2014

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On Mon, Dec 1, 2014 at 7:51 PM, Rafael Moral <rafa_moral2004 at yahoo.com.br>
wrote:

> Dear useRs,I have been wondering whether it would be possible to fit a
> linear mixed model including heteroscedastic variances for a 2-level
> hierarchical study with subsampling.Suppose that I had three levels for the
> first hierarchical level and 4 for the second, with 2 subsamples, e.g.
> set.seed(2014)y <- rnorm(24, 20, 2)level1 <- gl(3, 8)level2 <- gl(4,
> 2)my.data <- data.frame(y, level1, level2)
> Then, I can easily fit a model with nested random effects, i.e.
> y_{ijk} = \mu + \alpha_i + \beta_{ij} + \epsilon_{ijk}
> with \alpha_i ~ N(0, \sigma^2_1) the random effect for level 1, \beta_{ij}
> ~ N(0, \sigma^2_2) the random effect for level 2 and \epsilon_{ijk} ~ N(0,
> sigma^2) the error,
> using the following code
> require(nlme)fit1 <- lme(y ~ 1, random=~1|level1/level2, my.data)
> # which is equivalent tofit1 <- lme(y ~ 1, random=list(level1=pdDiag(~1),
> level2=pdDiag(~1)), my.data)
> However, I would like to have different variances per each "level1" level
> (model i) and then a different model considering different variances per
> each "level1" and per each "level2" level within "level1" (model ii).So we
> would have
> Model (i):\alpha_i ~ N(0, \sigma^2_1_i), \beta_{ij} ~ N(0, \sigma^2_2) and
> \epsilon_{ijk} ~ N(0, sigma^2),
> that is, different sigma^2_1 per "level1" level
> Model (ii):\alpha_i ~ N(0, \sigma^2_1_i), \beta_{ij} ~ N(0,
> \sigma^2_2_{ij}) and \epsilon_{ijk} ~ N(0, sigma^2),
> that is, different sigma^2_1 per "level1" level and different sigma^2_2
> per "level1:level2" level combination
> I tried the following for model (i):
> fit2 <- lme(y ~ 1, random=list(level1=pdDiag(~level1)), my.data)
> and this for model (ii):
> fit3 <- lme(y ~ 1, random=list(level1=pdDiag(~level1),
> level2=pdDiag(~level1:level2)), my.data)
> This second fit also gives a warning, and I don't believe that these are
> doing what I intend to.I also tried using the weights argument, i.e., for
> model (i)
> fit2.2 <- lme(y ~ 1, random=~1|level1/level2,
> weights=varIdent(form=~1|level1), my.data)
> Perhaps this is closer to what I'm trying to do, but when it comes to
> model (ii) I can't properly work the syntax, as the "/" creates an error,
> so I tried
> fit2.3 <- lme(y ~ 1, random=~1|level1/level2,
> weights=varIdent(form=~1|level1*level2), my.data)
>
> but I'm still doubtful.
> Any suggestions on how I might be able to fit these models?
> Best wishes,Rafael.
>         [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.
>

--
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culinary vessel will not achieve 100 degrees on the Celsius scale.

Maranatha! <><
John McKown

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