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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