anord <andreas.nord <at> zooekol.lu.se> writes:
>
>
> Dear all,
>
> I'm trying to make multiple comparisons for an lme-object. The data is for
> an experiment on parental work load in birds, in which adults at different
> sites were induced to work at one of three levels ('treat'; H, M, L). The
> response is 'feedings', which is a quantitative measure of nest provisioning
> per parent per chick per hour. Site is included as a random effect (one
> male/female pair per site).
>
(For more complicated mixed model questions you might want
to try the r-sig-mixed-models list instead.)
It works for me:
feed.df <- read.table(textConnection("
feedings sex site treat year date
1.8877888 M 838 H 2009 81
1.9102787 M 247 H 2009 81
1.4647229 M 674 H 2010 121
1.4160590 M 7009 M 2009 144
1.3106749 M 863 M 2010 196
1.2718121 M 61 M 2009 225
1.2799263 M 729 L 2009 256
1.5829564 M 629 L 2009 256
1.4847251 M 299 L 2010 324
1.2463151 M 569 L 2010 324
2.1694169 F 838 H 2009 81
1.5966899 F 247 H 2009 81
2.4136983 F 674 H 2010 121
1.7784873 F 7009 M 2009 144
1.6681317 F 863 M 2010 196
2.3691275 F 61 M 2009 225
2.0672192 F 729 L 2009 256
1.6389902 F 629 L 2009 256
0.9307536 F 299 L 2010 324
1.6786767 F 569 L 2010 324"),
header=TRUE)
library(nlme)
m4.feed <- lme(feedings ~ treat + year + date, random = ~1|site,data=feed.df)
library(multcomp)
gg <- glht(m4.feed,linfct=mcp(treat="Tukey"))
plot(gg)
summary(gg)
It works for me (although it doesn't look like there's anything
going on there ...)
=========
Simultaneous Tests for General Linear Hypotheses
Multiple Comparisons of Means: Tukey Contrasts
Fit: lme.formula(fixed = feedings ~ treat + year + date, data = feed.df,
random = ~1 | site)
Linear Hypotheses:
Estimate Std. Error z value Pr(>|z|)
L - H == 0 -0.6452 0.7667 -0.842 0.592
M - H == 0 -0.3996 0.4276 -0.934 0.529
M - L == 0 0.2456 0.4229 0.581 0.771
(Adjusted p values reported -- single-step method)
>
sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i486-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] multcomp_1.2-4 survival_2.36-3 mvtnorm_0.9-95 nlme_3.1-97
loaded via a namespace (and not attached):
[1] grid_2.12.1 lattice_0.19-18
>
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