[R-sig-ME] Unbalanced nested design
Stephen Cole
swbcole at gmail.com
Tue Apr 21 15:32:33 CEST 2009
Hello All - I would like to run a 2 factor nested ANOVA. The design
is unbalanced as i have 6 sites in 3 regions and 3 sites in 1 other
region. Site is nested in region I am interested in the differences
in mean recruit density among 4 regions. I have used the lme function
in the nlme library and am confused about the output. I have a copy
of P/B and I quote p. 25 " The lme function does produce sensible
maximum likelihood estimates or restricted maximum likelihood
estimates from the unbalanced data." Thus, as i understand it lme can
handle this unbalanced data set that i have. However, when i compared
the lme model to an aov model, the fixed effects results are
identical. (f-ratio and p-value). How does lme handle unbalanced data
if the result is the same as aov which can not handle unbalanced data.
Thank-you for any help provided.
I have attached a subsection of my data. The total number of records
is 420, with a sample of 20 quadrat counts from each site (21 sites x
20 = 420)
Data:
adults recruits region site site2 site3
1 138 1268.3300 ANS 1 1 ANS:1
2 131 608.3300 ANS 1 1 ANS:1
3 13 696.8800 ANS 1 1 ANS:1
4 12 412.5000 ANS 1 1 ANS:1
5 2 355.5600 ANS 1 1 ANS:1
6 0 528.0000 ANS 1 1 ANS:1
7 4 421.2100 ANS 1 1 ANS:1
8 0 378.0000 ANS 1 1 ANS:1
9 92 893.3300 ANS 1 1 ANS:1
10 77 1184.3100 ANS 1 1 ANS:1
11 92 961.4200 ANS 1 1 ANS:1
12 0 1029.0000 ANS 1 1 ANS:1
13 19 1144.6800 ANS 1 1 ANS:1
Region (4 levels, fixed)
Site (6 levels and 3 levels, random)
data$site <- as.factor(data$site)
data$site3 <-factor(data$region:data$site)
mod.lme <- lme(recruits ~ region, data=data, random=~1|site3)
anova(mod)
numDF denDF F-value p-value
(Intercept) 1 399 93.58730 <.0001
region 3 17 19.21751 <.0001
mod.aov <- aov(recruits ~ region + Error(site3), data=data)
summary(mod.aov)\
Error: site3
Df Sum Sq Mean Sq F value Pr(>F)
region 3 32024226 10674742 19.218 1.057e-05 ***
Residuals 17 9442984 555470
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Error: Within
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 399 11839881 29674
Now, both F-ratios are 19.21, I am not sure what i am doing
incorrectly but I would appreciate any advice on my mistake. Thanks
very much
Stephen Cole
Graduate student
Marine Ecology Lab
Saint Francis Xavier University
More information about the R-sig-mixed-models
mailing list