Hello.
I am new to R. And, I want to perform a multiple nested anova on a large
datasets (with 9448 observations). Under the helps from R-Sig-ecology
mailing list, I have gained many progresses. But I still have some
confusions. I want to ask for some helps here.
my dataset("SeedL.txt") was not attached. Data are not sorted by factors.
In this dataset, "SpecN" "PopN" "TreeN" "ConeN" "SeedN" were 5 factors (as
Explanatory), with "PopN" nested within "SpecN"; "TreeN" nested within
"PopN"; "ConeN" nested within "TreeN" and "SeedN" nested within "ConeN".
These are categories.
"SeedL" is a dependent variate (as Response).
I have performed a successful mutinested anova using function lme()
(library(nlme)).But I still do not know how to get a anova result table
(sth. like SAS output).
The model I have used and output in R is as following:
> f1 <- lme(SeedL~1, data=seedL, random=~1|SpecN/PopN/TreeN,
na.action=na.omit)
> f1
Linear mixed-effects model fit by REML
Data: seedL
Log-restricted-likelihood: 14369.45
Fixed: SeedL ~ 1
(Intercept)
0.6153105
Random effects:
Formula: ~1 | SpecN
(Intercept)
StdDev: 0.08008076
Formula: ~1 | PopN %in% SpecN
(Intercept)
StdDev: 0.05413198
Formula: ~1 | TreeN %in% PopN %in% SpecN
(Intercept) Residual
StdDev: 0.04566776 0.04790476
Number of Observations: 9447
Number of Groups:
SpecN PopN %in% SpecN TreeN %in% PopN %in%
SpecN
3 47
731
> anova(f1)
numDF denDF F-value p-value
(Intercept) 1 8716 169.2052 <.0001
I appreciate any advice.
Mao J-F
State Key Lab of Systematics and Evolutionary Botany
Institute of Botany
Chinese Academy of Sciences
Beijing, China
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