[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]

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