[R-sig-ME] glth function with lme returns error Error in contrMat(table(mf[[nm]]), type = types[pm]) : less than two groups
Annie-Claude Letendre
annieclaude.letendre at gmail.com
Fri Mar 11 22:59:25 CET 2016
Hi,
I am trying to run a *posthoc* on a lme with the glht function and I get
this error that I can't figure out "Error in contrMat(table(mf[[nm]]), type
= types[pm]) :
less than two groups"
My experiment had 45 indivuduals (rep) each of these had 1 treatment
(treat) applied to it and then the variable (logcov) was measured twice for
each individual at week 6 and 12.
I've attached the csv I am using , thanks for any help you can offer !
Is there any other posthoc test that could work for me ?
Annie
>
spl<-read.table("C:/Users/Annie/Desktop/splcover.csv",header=T,sep=",",quote="")
> attach(spl)
> names(spl)
[1] "rep" "treat" "logcov" "week"
> rep<-factor(rep)
> treat<-factor(treat)
> week<-factor(week)
> levels(treat)
[1] "c" "f" "g" "p" "r"
> levels(week)
[1] "6" "12"
> levels(rep)
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14"
"15"
[16] "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29"
"30"
[31] "31" "32" "33" "34" "35" "36" "37" "38" "39" "40" "41" "42" "43" "44"
"45"
> library(nlme)
Warning message:
package ‘nlme’ was built under R version 3.1.3
> summary(modcover<-lme(logcov~treat*week, random= ~1|rep/week))
Linear mixed-effects model fit by REML
Data: NULL
AIC BIC logLik
-33.51971 -2.553367 29.75986
Random effects:
Formula: ~1 | rep
(Intercept)
StdDev: 0.09534288
Formula: ~1 | week %in% rep
(Intercept) Residual
StdDev: 0.1095635 0.04379889
Fixed effects: logcov ~ treat * week
Value Std.Error DF t-value p-value
(Intercept) -2.0000000 0.05056654 40 -39.55185 0.0000
treatf 1.5944444 0.07151188 40 22.29622 0.0000
treatg 0.0000000 0.07151188 40 0.00000 1.0000
treatp 1.3944444 0.07151188 40 19.49948 0.0000
treatr 1.5744444 0.07151188 40 22.01654 0.0000
week12 0.1400000 0.05562275 40 2.51696 0.0159
treatf:week12 -0.0266667 0.07866245 40 -0.33900 0.7364
treatg:week12 0.1888889 0.07866245 40 2.40126 0.0211
treatp:week12 -0.0222222 0.07866245 40 -0.28250 0.7790
treatr:week12 0.0077778 0.07866245 40 0.09888 0.9217
Correlation:
(Intr) treatf treatg treatp treatr week12 trtf:12 trtg:12
trtp:12
treatf -0.707
treatg -0.707 0.500
treatp -0.707 0.500 0.500
treatr -0.707 0.500 0.500 0.500
week12 -0.550 0.389 0.389 0.389 0.389
treatf:week12 0.389 -0.550 -0.275 -0.275 -0.275 -0.707
treatg:week12 0.389 -0.275 -0.550 -0.275 -0.275 -0.707 0.500
treatp:week12 0.389 -0.275 -0.275 -0.550 -0.275 -0.707 0.500 0.500
treatr:week12 0.389 -0.275 -0.275 -0.275 -0.550 -0.707 0.500 0.500
0.500
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-0.741681806 -0.152850434 -0.008438999 0.126023769 0.836897713
Number of Observations: 90
Number of Groups:
rep week %in% rep
45 90
> anova(modcover)
numDF denDF F-value p-value
(Intercept) 1 40 2817.8201 <.0001
treat 4 40 366.2476 <.0001
week 1 40 46.4611 <.0001
treat:week 4 40 2.6323 0.0483
> require(multcomp)
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: splines
Loading required package: TH.data
> summary(glht(modcover, linfct=mcp(treat="Tukey")))
Error in contrMat(table(mf[[nm]]), type = types[pm]) :
less than two groups
> is.factor(treat)
[1] TRUE
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] multcomp_1.3-6 TH.data_1.0-3 survival_2.37-7 mvtnorm_1.0-0
[5] nlme_3.1-125
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 ggplot2_2.0.0 grid_3.1.1 gtable_0.1.2
[5] lattice_0.20-33 munsell_0.4.2 plyr_1.8.3 Rcpp_0.12.2
[9] sandwich_2.3-2 scales_0.3.0 zoo_1.7-11
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