[R-sig-ME] ICC for quasipoisson?

[Dr C B Stride]

Thanks Elizabeth - have downloaded rptR, got it up and running and 
tested on a few simple examples - however, in my example (I should have 
mentioned!) I am modelling a rate rather than a raw count hence I have 
an offset term - does anyone know if/how that can be incorporated into 
the rptR code? Couldn't see anything in Nakagawa & Schielzeth, and the 
rpt function only has arguments for DV, grouping var and link fn)

Likewise my data is cross-classified i.e I have multiple random effects 
hence multiple grouping vars...



Elizabeth Oliva said the following on 13/09/2011 15:18:
> I haven't tried it yet (because I have to download the most recent 
> version of R); however, it's possible to use the link in the paper to 
> download the program to calculate the ICC. I think the website for the 
> program has sample code. However, I cc'd the author of the program just 
> in case he might have some sample code.
> 
> 
> 
> On Tue, Sep 13, 2011 at 3:26 AM, Dr C B Stride 
> <c.b.stride at sheffield.ac.uk <mailto:c.b.stride at sheffield.ac.uk>> wrote:
> 
>     Hi
> 
>     Was wondering if anyone knows of a snippet of R code that will
>     perform the ICC calculations recommended in this paper?
> 
>     cheers
>     Chris
> 
>     Jarrod Hadfield said the following on 09/09/2011 16:51:
> 
>         Hi,
> 
>         You can find the relevant equations in Table 2 of:
> 
>         Repeatability for Gaussian and non-Gaussian data: a practical
>         guide for biologists. Biological reviews. 2010. Nakagawa1 &
>         Schielzeth
> 
>         Cheers,
> 
>         Jarrod
> 
>         Quoting Elizabeth Oliva <elizabeth.oliva at gmail.com
>         <mailto:elizabeth.oliva at gmail.com>> on Fri, 9 Sep 2011 08:34:50
>         -0700:
> 
>             Hi all,
> 
>             I’ve been searching at length for a way to figure out how to
>             calculate the
>             ICC for a mixed effects quasipoisson model in R from the
>             output below (i.e.,
>             intercept only model) and can't figure out the correct
>             equation to use. For
>             example, I've run mixed effects logistic regression models
>             for which I used
>             the following equation:
> 
>                           c<-a*a
> 
>                           icc<-c/(3.289868+c)
> 
>             [a being the standard deviation of the intercept]
> 
> 
> 
>             I'm not sure what the corollary type of equation is for
>             quasipoisson mixed
>             models.
> 
> 
> 
>             If you had any suggestions I would greatly appreciate it.
> 
> 
> 
>             Best,
> 
>             Elizabeth
> 
> 
> 
> 
> 
>             womentxengintonly <- glmmPQL(NewSpecOut_SUM ~ 1, random = ~1
>             |NEPEC3N,
>             family =quasipoisson, data = women)
> 
> 
> 
> 
> 
>             summary(womentxengintonly)
> 
> 
> 
>             Linear mixed-effects model fit by maximum likelihood
> 
>             Data: women
> 
>              AIC BIC logLik
> 
>               NA  NA     NA
> 
> 
> 
>             Random effects:
> 
>             Formula: ~1 | NEPEC3N
> 
>                    (Intercept) Residual
> 
>             StdDev:   0.4679934  7.26936
> 
> 
> 
>             Variance function:
> 
>             Structure: fixed weights
> 
>             Formula: ~invwt
> 
>             Fixed effects: NewSpecOut_SUM ~ 1
> 
>                           Value  Std.Error   DF  t-value p-value
> 
>             (Intercept) 3.046308 0.04805773 4960 63.38852       0
> 
> 
> 
>             Standardized Within-Group Residuals:
> 
>                   Min         Q1        Med         Q3        Max
> 
>             -1.0333625 -0.5507037 -0.3717204  0.2138915 12.4856954
> 
> 
> 
>             Number of Observations: 5099
> 
>             Number of Groups: 139
> 
>                [[alternative HTML version deleted]]
> 
> 
> 
> 
> 
>         --The University of Edinburgh is a charitable body, registered in
>         Scotland, with registration number SC005336.
> 
>         _________________________________________________
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> 
> 
> 
>     -- 
>     Dr Chris Stride, C. Stat, Statistician, Institute of Work
>     Psychology, University of Sheffield
>     Telephone: 0114 2223262
>     Fax: 0114 2727206
> 
>     “Figure It Out”
>     Statistical Consultancy and Training Service for Social Scientists
> 
>     Visit www.figureitout.org.uk <http://www.figureitout.org.uk> for
>     details of my consultancy services, and forthcoming training
>     courses, which are also available on an in-house basis:
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> 
> 


-- 
Dr Chris Stride, C. Stat, Statistician, Institute of Work Psychology, 
University of Sheffield
Telephone: 0114 2223262
Fax: 0114 2727206

“Figure It Out”
Statistical Consultancy and Training Service for Social Scientists

Visit www.figureitout.org.uk for details of my consultancy services, and 
forthcoming training courses, which are also available on an in-house basis:
- Data Management using SPSS syntax
- Multiple Regression using SPSS
- Multilevel Modelling using SPSS
- Structural Equation Modelling using MPlus