[R] Nestad ANOVA with random Factors

[Pablo R]

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.