Hi:

I'm kind of wondering why Area and Plot are nested within Day.  Are  you
measuring different areas and different plots on different days?

Dennis

On Fri, Aug 27, 2010 at 12:43 AM, Pablo R <riulp@hotmail.com> wrote:

>
> Hi,
>
> I need a help. I am new in R and I need to run a nested anova with fixed
> and
> random factors (Mixed Model). I have a design with three factors: Day, Area
> and Plot and the dependent variable is density. The factors Day and Area
> are
> fixed while Plot is random, factor Area is nested in factor Day, and factor
> Plot is nested in Area.
>
> I can do it using aov by:
>
> mod1<-aov(density~ day + day%in%area + day%in%area%in%plot)
> symmary(mod1)
>
> Getting this result:
>
> Analysis of Variance Table
>
> Response: total
>               Df Sum Sq Mean Sq F value  Pr(>F)
> day             2 1789.8  894.91 55.5576 < 2e-16 ***
> day:area       15 4658.8  310.59 19.2818 < 2e-16 ***
> day:area:plot  72 1715.7   23.83  1.4793 0.01145 *
> Residuals     360 5798.8   16.11
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> But I'm afraind the factor plot is not beeing calculated as random.
>
> The other way would be using the lme from nlme as below (if I had only
> factors area and plot, once I don't know how to include day and keep plot
> as
> random) just as an exemple I found in the list files:
>
> > mod2 <-  lme(density ~ area + plot, random = ~ 1 | area / plot, data =
> > data)
> > summary(mod2)
>
> Linear mixed-effects model fit by REML
>  Data: data
>       AIC      BIC    logLik
>  1422.403 1475.532 -698.2017
>
> Random effects:
>  Formula: ~1 | area
>        (Intercept)
> StdDev:    0.347117
>
>  Formula: ~1 | plot %in% area
>         (Intercept) Residual
> StdDev: 6.431067e-05 1.127295
>
> Fixed effects: density~ area + plot
>                 Value Std.Error  DF   t-value p-value
> (Intercept)  2.6131608 0.3856554 420  6.775895  0.0000
> areaarea10  -1.2073539 0.5242788   0 -2.302885     NaN
> areaarea2   -0.3062031 0.5242788   0 -0.584046     NaN
> areaarea4   -0.6109334 0.5242788   0 -1.165283     NaN
> areaarea6   -0.9808034 0.5242788   0 -1.870767     NaN
> areaarea8   -1.3437982 0.5242788   0 -2.563136     NaN
> plotb       -0.0899366 0.1680473  20 -0.535187  0.5984
> plotc        0.0257024 0.1680473  20  0.152947  0.8800
> plotd        0.0420734 0.1680473  20  0.250366  0.8049
> plote       -0.2375628 0.1680473  20 -1.413666  0.1728
>  Correlation:
>           (Intr) arer10 arear2 arear4 arear6 arear8 plotb  plotc  plotd
> areaarea10 -0.680
> areaarea2  -0.680  0.500
> areaarea4  -0.680  0.500  0.500
> areaarea6  -0.680  0.500  0.500  0.500
> areaarea8  -0.680  0.500  0.500  0.500  0.500
> plotb      -0.218  0.000  0.000  0.000  0.000  0.000
> plotc      -0.218  0.000  0.000  0.000  0.000  0.000  0.500
> plotd      -0.218  0.000  0.000  0.000  0.000  0.000  0.500  0.500
> plote      -0.218  0.000  0.000  0.000  0.000  0.000  0.500  0.500  0.500
>
> Standardized Within-Group Residuals:
>       Min         Q1        Med         Q3        Max
> -2.3554021 -0.8985867  0.1031298  0.8008967  2.6488795
>
> Number of Observations: 450
> Number of Groups:
>          area plot %in% area
>             6             30
> Warning message:
> In pt(q, df, lower.tail, log.p) : NaNs produzidos
>
> But, in addition to the lack of the factor day, I am sure its not right
> because of these "NaN" produced and because of the area beeing assigned as
> Random in the output.
>
> I would appreciate any help and thanks for your attention in advance,
>
> Pablo
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Nestad-ANOVA-with-random-Factors-tp2340725p2340725.html
> Sent from the R help mailing list archive at Nabble.com.
>
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