Sorry,
Actually I gave my data in an image file (.RData) - I've just checked my send
emails.
Am I to give data in another format, such as text ? Here are they in text
(.txt).
The output are :
> summary(aov1 <- aov(Rendement ~ Error(Pollinisateur * Lignee), data = mca2)
Error: Pollinisateur
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 9 11.9729 1.3303
Error: Lignee
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 4 18.0294 4.5074
Error: Pollinisateur:Lignee
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 36 5.1726 0.1437
Error: Within
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 50 3.7950 0.0759
# F tests :
> Femp <- c(tab1[1:3, 3]/tab1[c(3,3,4), 3])
> names(Femp) <- c("Pollinisateur", "Lignee", "Interaction")
> Femp
Pollinisateur Lignee Interaction
9.258709 31.370027 1.893061
> 1 - pf(Femp, tab1[1:3,1], tab1[c(3,3,4),1])
Pollinisateur Lignee Interaction
4.230265e-07 2.773448e-11 1.841028e-02
# Standard deviation :
> variances <- c(c(tab1[1:3, 3] - tab1[c(3,3,4), 3]) / c(2*5, 2*10, 2),
tab1[4,3])
> names(variances) <- c(names(Femp), "Residuelle")
> variances
Pollinisateur Lignee Interaction Residuelle
0.11866389 0.21818333 0.03389167 0.07590000
# Using lmer :
> library(lme4)
> summary(lmer(Rendement ~ (1 |Pollinisateur) + (1 | Lignee) + (1 | Pollinisateur:Lignee),
data=mca2))
Linear mixed-effects model fit by REML
Formula: Rendement ~ (1 | Pollinisateur) + (1 | Lignee) + (1 |
Pollinisateur:Lignee)
Data: mca2
AIC BIC logLik MLdeviance REMLdeviance
105.3845 118.4104 -47.69227 94.35162 95.38453
Random effects:
Groups Name Variance Std.Dev.
Pollinisateur:Lignee (Intercept) 0.033892 0.18410
Pollinisateur (Intercept) 0.118664 0.34448
Lignee (Intercept) 0.218183 0.46710
Residual 0.075900 0.27550
# of obs: 100, groups: Pollinisateur:Lignee, 50; Pollinisateur, 10; Lignee, 5
Fixed effects:
Estimate Std. Error DF t value Pr(>|t|)
(Intercept) 12.60100 0.23862 99 52.808 < 2.2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Thanks,
Jacques VESLOT
Prof Brian Ripley a écrit :
Nothing was enclosed, nor was the output from summary.aov, so we are
left guessing.
On Thu, 27 Oct 2005, Jacques VESLOT wrote:
Dear R-users,
My question is how to get right F tests for random effects in random
effect models (I hope this question has not been answered too many
times yet - I didn't find an answer in rhelp archives).
My data are in mca2 (enc.) :
names(mca2)
[1] "Lignee" "Pollinisateur" "Rendement"
dim(mca2)
[1] 100 3
replications(Rendement ~ Lignee * Pollinisateur, data = mca2)
Lignee Pollinisateur Lignee:Pollinisateur
20 10 2
Of course, summary(aov(Rendement ~ Pollinisateur * Lignee, data =
mca2)) gives wrong tests of random effects. But, summary(aov1 <-
aov(Rendement ~ Error(Pollinisateur * Lignee), data = mca2)) gives no
test at all, and I have to do it like this :
tab1 <- matrix(unlist(summary(aov1)), nc=5, byrow=T)[,1:3]
Femp <- c(tab1[1:3, 3]/tab1[c(3,3,4), 3])
names(Femp) <- c("Pollinisateur", "Lignee", "Interaction")
1 - pf(Femp, tab1[1:3,1], tab1[c(3,3,4),1])
With "lme4" package (I did'nt succeed in writing a working formula
with lme from "nlme" package), I can "see" standard deviations of
random effects (but don't know how to find them) with :
library(lme4)
summary(lmer(Rendement ~ (1 |Pollinisateur) + (1 | Lignee) + (1 |
Pollinisateur:Lignee), data=mca2))
but I can't get F tests.
Thanks in advance.
Best regards,
Jacques VESLOT
Lignee Pollinisateur Rendement
L1 P1 13.4
L1 P1 13.3
L2 P1 12.4
L2 P1 12.6
L3 P1 12.7
L3 P1 13
L4 P1 12.6
L4 P1 12.6
L5 P1 11.9
L5 P1 11.6
L1 P2 12.6
L1 P2 12.7
L2 P2 12.1
L2 P2 11.3
L3 P2 12.4
L3 P2 11.9
L4 P2 12.2
L4 P2 12.1
L5 P2 11.3
L5 P2 11.5
L1 P3 13.3
L1 P3 13.2
L2 P3 12.9
L2 P3 12.3
L3 P3 12.1
L3 P3 12.9
L4 P3 12.8
L4 P3 13.4
L5 P3 11.7
L5 P3 11.8
L1 P4 13.5
L1 P4 14
L2 P4 13.5
L2 P4 12.7
L3 P4 13.3
L3 P4 13.5
L4 P4 13.4
L4 P4 13.4
L5 P4 13
L5 P4 13.1
L1 P5 13.7
L1 P5 13.8
L2 P5 12.5
L2 P5 13.1
L3 P5 12.8
L3 P5 12.5
L4 P5 13.7
L4 P5 13.8
L5 P5 12.2
L5 P5 12.1
L1 P6 12.8
L1 P6 13.1
L2 P6 12
L2 P6 11.8
L3 P6 12.4
L3 P6 12.2
L4 P6 13.3
L4 P6 13.5
L5 P6 12.4
L5 P6 11.5
L1 P7 13.2
L1 P7 13.2
L2 P7 12.4
L2 P7 12.2
L3 P7 12.1
L3 P7 12.1
L4 P7 12.9
L4 P7 13.3
L5 P7 12.6
L5 P7 12.2
L1 P8 13.4
L1 P8 12.8
L2 P8 12.2
L2 P8 12.4
L3 P8 12
L3 P8 12.2
L4 P8 12.7
L4 P8 13.4
L5 P8 11.8
L5 P8 11.8
L1 P9 12.6
L1 P9 13
L2 P9 11.9
L2 P9 12.3
L3 P9 12.6
L3 P9 12.5
L4 P9 13.5
L4 P9 12.9
L5 P9 11.5
L5 P9 12.1
L1 P10 12.7
L1 P10 12.5
L2 P10 11.8
L2 P10 12.1
L3 P10 12.3
L3 P10 12.1
L4 P10 12.5
L4 P10 12.7
L5 P10 12.3
L5 P10 12.1
______________________________________________
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
