[R] glht after lmer with "$S4class-" and "missing model.matrix-" errors with DATA
Anna Radtke
annaradtke2309 at googlemail.com
Fri Jul 25 11:34:17 CEST 2008
maybe it's in the data? So here it comes.
> sv.growth
Grouped Data: length ~ meas | box_id
meas spec comp water box_id sprouts leaves length
long.sprout
1 1 Sv control moist 1 8.800000 37.80 211.2000
60.6
2 1 Sv xfull moist 2 7.000000 8.00 174.8000
62.8
3 1 Sv control moist 3 9.000000 42.00 255.2000
66.0
4 1 Sv root moist 4 7.800000 35.00 225.8000
78.2
5 1 Sv root moist 5 7.800000 31.40 182.6000
59.4
6 1 Sv shoot moist 6 8.800000 50.80 247.6000
53.4
7 1 Sv root moist 7 7.000000 26.20 169.2000
63.0
8 1 Sv xfull moist 8 4.600000 4.00 71.8000
35.8
9 1 Sv root moist 9 8.800000 40.00 246.8000
69.4
10 1 Sv shoot moist 10 8.000000 48.20 266.8000
67.6
11 1 Sv control moist 11 15.000000 71.80 380.2000
53.6
12 1 Sv shoot moist 12 10.400000 41.20 271.8000
58.6
13 1 Sv shoot moist 13 8.200000 44.00 243.8000
53.4
14 1 Sv xfull moist 14 6.200000 10.00 171.6000
67.2
15 1 Sv root moist 15 9.600000 42.20 187.6000
57.8
16 1 Sv xfull moist 16 6.200000 7.80 164.0000
63.6
17 1 Sv control moist 17 11.000000 53.40 262.4000
59.6
18 1 Sv control moist 18 8.800000 45.00 245.4000
63.8
19 1 Sv xfull moist 19 6.200000 7.40 161.0000
61.6
20 1 Sv shoot moist 20 9.400000 38.40 209.0000
74.8
21 1 Sv root awater-logged 21 8.600000 42.00 252.0000
75.2
22 1 Sv shoot awater-logged 22 7.800000 34.80 238.8000
80.8
23 1 Sv control awater-logged 23 9.750000 37.25 182.2500
55.5
24 1 Sv control awater-logged 24 8.200000 51.00 287.2000
77.8
25 1 Sv control awater-logged 25 8.500000 45.25 290.5000
85.0
26 1 Sv xfull awater-logged 26 8.800000 11.60 204.4000
58.8
27 1 Sv shoot awater-logged 27 6.600000 22.00 138.6000
68.6
28 1 Sv shoot awater-logged 28 10.400000 34.40 225.2000
70.0
29 1 Sv root awater-logged 29 5.000000 22.40 113.4000
60.2
30 1 Sv control awater-logged 30 7.400000 38.00 220.4000
73.8
31 1 Sv xfull awater-logged 31 7.600000 5.00 143.8000
54.8
32 1 Sv xfull awater-logged 32 3.600000 10.20 124.6000
74.2
33 1 Sv xfull awater-logged 33 7.200000 6.00 162.6000
60.8
34 1 Sv shoot awater-logged 34 7.400000 26.40 210.4000
86.2
35 1 Sv root awater-logged 35 8.600000 34.80 257.6000
81.6
36 1 Sv root awater-logged 36 9.400000 31.00 196.2000
70.4
37 1 Sv root awater-logged 37 6.800000 34.20 204.4000
85.4
38 1 Sv xfull awater-logged 38 7.200000 6.60 151.6000
66.0
39 1 Sv shoot awater-logged 39 7.600000 39.60 227.4000
63.8
40 1 Sv control awater-logged 40 8.400000 51.60 257.6000
78.6
41 2 Sv control moist 1 5.400000 100.80 1104.4000
392.6
42 2 Sv xfull moist 2 5.200000 33.60 404.4000
182.4
43 2 Sv control moist 3 6.400000 108.60 1060.0000
364.2
44 2 Sv root moist 4 5.000000 91.40 1017.6000
394.4
45 2 Sv root moist 5 5.200000 78.40 772.4000
312.4
46 2 Sv shoot moist 6 5.600000 77.60 775.6000
318.0
47 2 Sv root moist 7 4.600000 73.20 730.2000
314.4
48 2 Sv xfull moist 8 3.600000 17.40 238.8000
136.6
49 2 Sv root moist 9 4.600000 94.20 980.4000
366.8
50 2 Sv shoot moist 10 7.750000 96.50 876.2500
327.0
51 2 Sv control moist 11 10.000000 127.20 1209.6000
327.2
52 2 Sv shoot moist 12 7.400000 83.40 818.6000
314.0
53 2 Sv shoot moist 13 6.800000 83.80 812.4000
283.6
54 2 Sv xfull moist 14 3.800000 29.80 325.0000
183.4
55 2 Sv root moist 15 4.600000 72.20 734.8000
378.0
56 2 Sv xfull moist 16 2.600000 24.40 282.0000
189.0
57 2 Sv control moist 17 8.000000 124.60 1246.8000
371.4
58 2 Sv control moist 18 4.400000 84.40 1061.4000
377.2
59 2 Sv xfull moist 19 4.200000 29.00 353.8000
193.4
60 2 Sv shoot moist 20 5.600000 74.40 743.2000
378.8
61 2 Sv root awater-logged 21 6.600000 93.60 912.4000
351.6
62 2 Sv shoot awater-logged 22 4.000000 62.00 714.8000
401.0
63 2 Sv control awater-logged 23 5.000000 82.00 881.6000
323.2
64 2 Sv control awater-logged 24 5.600000 110.80 1264.8000
424.8
65 2 Sv control awater-logged 25 5.800000 89.60 930.8000
346.2
66 2 Sv xfull awater-logged 26 4.000000 39.60 455.2000
268.8
67 2 Sv shoot awater-logged 27 3.400000 55.40 614.6000
384.2
68 2 Sv shoot awater-logged 28 5.400000 71.00 698.0000
320.6
69 2 Sv root awater-logged 29 3.000000 66.40 757.4000
427.8
70 2 Sv control awater-logged 30 4.800000 83.00 990.4000
413.4
71 2 Sv xfull awater-logged 31 3.200000 23.20 300.6000
238.8
72 2 Sv xfull awater-logged 32 1.400000 24.60 210.8000
192.8
73 2 Sv xfull awater-logged 33 3.200000 28.60 344.8000
185.8
74 2 Sv shoot awater-logged 34 3.600000 59.60 631.0000
402.0
75 2 Sv root awater-logged 35 5.200000 86.40 826.4000
289.8
76 2 Sv root awater-logged 36 7.200000 87.40 918.8000
351.0
77 2 Sv root awater-logged 37 4.200000 84.80 840.0000
422.0
78 2 Sv xfull awater-logged 38 2.400000 29.80 355.6000
239.6
79 2 Sv shoot awater-logged 39 6.200000 71.20 683.8000
282.0
80 2 Sv control awater-logged 40 5.400000 106.40 1083.6000
388.6
81 3 Sv control moist 1 5.200000 149.60 1863.8000
682.0
82 3 Sv xfull moist 2 2.500000 42.25 427.5000
344.5
83 3 Sv control moist 3 4.200000 134.00 1496.2000
572.0
84 3 Sv root moist 4 3.600000 121.00 1488.8000
706.8
85 3 Sv root moist 5 4.000000 115.00 1340.2000
587.2
86 3 Sv shoot moist 6 2.600000 80.00 976.0000
613.2
87 3 Sv root moist 7 3.600000 94.40 1187.2000
555.0
88 3 Sv xfull moist 8 3.500000 41.75 367.0000
195.5
89 3 Sv root moist 9 3.600000 120.20 1450.4000
630.6
90 3 Sv shoot moist 10 2.600000 85.00 1007.2000
586.0
91 3 Sv control moist 11 4.000000 118.80 1386.0000
626.6
92 3 Sv shoot moist 12 2.200000 72.40 942.6000
578.4
93 3 Sv shoot moist 13 2.200000 80.60 957.6000
606.0
94 3 Sv xfull moist 14 1.250000 27.00 308.0000
297.0
95 3 Sv root moist 15 2.600000 85.80 1080.2000
676.8
96 3 Sv xfull moist 16 1.666667 41.00 475.6667
374.0
97 3 Sv control moist 17 4.400000 148.00 1795.6000
681.8
98 3 Sv control moist 18 3.400000 107.80 1484.4000
653.6
99 3 Sv xfull moist 19 2.400000 49.80 450.6000
326.2
100 3 Sv shoot moist 20 2.800000 73.60 896.2000
663.8
101 3 Sv root awater-logged 21 4.800000 119.00 1431.6000
585.0
102 3 Sv shoot awater-logged 22 1.800000 61.20 896.8000
654.0
103 3 Sv control awater-logged 23 4.600000 123.80 1471.6000
552.0
104 3 Sv control awater-logged 24 5.000000 144.00 1906.6000
734.2
105 3 Sv control awater-logged 25 3.400000 107.80 1388.4000
639.0
106 3 Sv xfull awater-logged 26 1.800000 53.20 586.8000
439.4
107 3 Sv shoot awater-logged 27 1.800000 68.40 910.6000
704.4
108 3 Sv shoot awater-logged 28 3.400000 88.20 1092.0000
615.0
109 3 Sv root awater-logged 29 2.800000 101.20 1342.8000
740.4
110 3 Sv control awater-logged 30 4.000000 125.40 1556.6000
769.6
111 3 Sv xfull awater-logged 31 2.000000 52.20 534.8000
451.0
112 3 Sv xfull awater-logged 32 1.800000 40.40 428.6000
375.6
113 3 Sv xfull awater-logged 33 2.000000 41.20 420.6000
295.6
114 3 Sv shoot awater-logged 34 1.800000 74.60 978.8000
760.6
115 3 Sv root awater-logged 35 4.000000 110.80 1262.8000
494.4
116 3 Sv root awater-logged 36 6.400000 129.20 1518.8000
590.4
117 3 Sv root awater-logged 37 4.600000 124.60 1389.8000
746.0
118 3 Sv xfull awater-logged 38 2.000000 39.00 472.6000
398.4
119 3 Sv shoot awater-logged 39 1.600000 59.80 809.4000
576.4
120 3 Sv control awater-logged 40 4.400000 134.60 1622.6000
664.4
2008/7/25 Anna Radtke <annaradtke2309 at googlemail.com>:
>> Hello everybody.
> In my case, calculating multiple comparisons (Tukey) after lmer
> produced the following two errors:
>
> > sv.mc <- glht(model.sv,linfct=mcp(comp="Tukey"))
> Error in x$terms : $ operator not defined for this S4 class
> Error in factor_contrasts(model) :
> no 'model.matrix' method for 'model' found!
>
> What I have done before:
>
> > sv.growth <- groupedData(length~meas|box_id,outer=~comp,data=sv.growth)
> > model.sv <- lmer(length~comp+(meas|box_id),data=sv.growth)
> Warning message:
> In .local(x, ..., value) :
> Estimated variance-covariance for factor 'box_id' is singular
> > summary(model.sv)
> Linear mixed-effects model fit by REML
> Formula: length ~ comp + (meas | box_id)
> Data: sv.growth
> AIC BIC logLik MLdeviance REMLdeviance
> 1587 1606 -786.4 1605 1573
> Random effects:
> Groups Name Variance Std.Dev. Corr
> box_id (Intercept) 466698.1 683.153
> meas 230733.7 480.347 -1.000
> Residual 9138.3 95.595
> number of obs: 120, groups: box_id, 40
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 600.90 21.31 28.196
> comproot -124.84 30.14 -4.142
> compshoot -167.36 30.14 -5.553
> compxfull -375.13 30.14 -12.446
> Correlation of Fixed Effects:
> (Intr) comprt cmpsht
> comproot -0.707
> compshoot -0.707 0.500
> compxfull -0.707 0.500 0.500
>
> Thanks for youR help in advance.
> Anna
--
Anna Radtke
Hopfengarten 21
35043 Marburg
Tel.: 0162-8211685
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