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Anna Radtke

2010-Oct-29 16:05 UTC

[R] Tukey post hoc comparison (glht?) after 3factorial mixed model (lmer)

Hello, dear R-community.

This is a question about TukeyHSD between factor combinations of a Three-Way
ANOVA, which is - since it is a multi measure ANOVA - not a simple ANOVA but
a Generalised Linear Mixed Model (GLMM), calculated with "lmer".
> growth <-
groupedData(length~meas|box_id,outer=~spec*comp*water,data=all.spec)> model <- lmer(length~spec*comp*water+(meas|box_id),data=growth)
> summary(model)
This works fine. But now, I would like to calculate Tukey HSD among certain
factor combinations. Formerly (before version 1.0), Tukey contrasts
including all levels of interactions could be calculated with the multcomp
package more or less automatically like this:
> summary (glht (model, linfct = mcp (spec*comp*water = "Tukey")))
Now, Mr Hothorn et al. have changed the function and it is "suggestet to
the
users that they write out, manually, the set of contrasts they want". I
think that is not a bad idea, but I got problems with the syntax in my case.
And I would really grateful if anybody could help me. So far I tried:
> K <- cbind(0,diag(length(fixef(model))-1))
> rownames(K) <- names(fixef(model))[-1]
> model_glht <- glht(model,linfct=K)
> summary(model_glht)  # but actually this is not what I want
I'm rather looking for a Tukey output like this

specSt:compControl - specSt:compRoot         p that they are equal < 0.05
specSt:compControl - specSt:compShoot
specSt:compControl - specSt:compFull
specSt:compRoot - specSt:compShoot
specSt:compRoot - specSt:compFull
specSt:compShoot - specSt:compFull

and that for each of the 3 studied species, i.e. compare all-pairwise
combinations of the levels of the second factor within each level of the
first factor. We are not interested in the third factor, so data can be
averaged over that.


THANKS A LOT FOR ANY ADVICE, Sincerely

Anna Radtke



-----> model output:

Linear mixed model fit by REML
Formula: length ~ spec * comp * water + (meas | box_id)
   Data: growth
  AIC  BIC logLik deviance REMLdev
 4800 4909  -2372     4988    4744
Random effects:
 Groups   Name        Variance Std.Dev. Corr
 box_id   (Intercept)      0.0   0.000
          meas        222484.2 471.682    NaN
 Residual               9439.4  97.157
Number of obs: 360, groups: box_id, 120

Fixed effects:
                            Estimate Std. Error t value
(Intercept)                 -353.554     65.777  -5.375
specSt                      -103.111     93.023  -1.108
specSv                        -4.485     93.023  -0.048
comproot                     -41.686     93.023  -0.448
compshoot                    241.847     93.023   2.600
compxfull                    316.849     93.023   3.406
watermoist                   -48.620     93.023  -0.523
specSt:comproot               97.168    131.554   0.739
specSv:comproot               54.849    131.554   0.417
specSt:compshoot              10.416    131.554   0.079
specSv:compshoot               6.584    131.554   0.050
specSt:compxfull              90.949    131.554   0.691
specSv:compxfull              43.284    131.554   0.329
specSt:watermoist              9.222    131.554   0.070
specSv:watermoist            104.229    131.554   0.792
comproot:watermoist           15.931    131.554   0.121
compshoot:watermoist          28.999    131.554   0.220
compxfull:watermoist          39.363    131.554   0.299
specSt:comproot:watermoist    45.513    186.046   0.245
specSv:comproot:watermoist   -24.350    186.046  -0.131
specSt:compshoot:watermoist   46.027    186.046   0.247
specSv:compshoot:watermoist    1.232    186.046   0.007
specSt:compxfull:watermoist   23.749    186.046   0.128
specSv:compxfull:watermoist  -57.109    186.046  -0.307
-------------- next part --------------
"meas" "spec" "comp" "water"
"box_id" "sprouts" "leaves" "length"
"long.sprout"
"81" 1 "Sf" "xfull" "moist" 81 6.8 13.6
150.4 43.8
"82" 1 "Sf" "root" "moist" 82 6.5 18.5
104.25 25.75
"83" 1 "Sf" "control" "moist" 83 9.25 29
146 27
"84" 1 "Sf" "control" "moist" 84 6.8
31.4 163.8 46.6
"85" 1 "Sf" "shoot" "moist" 85 4.8 19.8
127.6 32.8
"86" 1 "Sf" "control" "moist" 86 8.2
30.6 144.4 31.6
"87" 1 "Sf" "root" "moist" 87 7.8 32.8
174 38.8
"88" 1 "Sf" "shoot" "moist" 88 5 8.5 54
22.25
"89" 1 "Sf" "xfull" "moist" 89 2.25 7
54.25 27
"90" 1 "Sf" "control" "moist" 90 5.6
21.2 103 30
"91" 1 "Sf" "shoot" "moist" 91 4.25 18
84.25 29.25
"92" 1 "Sf" "root" "moist" 92 5.8 26.4
133.2 33
"93" 1 "Sf" "shoot" "moist" 93 11.25
35.25 215 44.25
"94" 1 "Sf" "root" "moist" 94 6
17.33333333 90.66666667 19.33333333
"95" 1 "Sf" "root" "moist" 95
4.666666667 5.333333333 33.66666667 9.333333333
"96" 1 "Sf" "shoot" "moist" 96 6.5 11.5
88.25 25.5
"97" 1 "Sf" "xfull" "moist" 97 9.8 13
184.4 40.2
"98" 1 "Sf" "xfull" "moist" 98 5.8 15.2
156.6 41.6
"99" 1 "Sf" "control" "moist" 99 7.5
26.5 140.75 36.5
"100" 1 "Sf" "xfull" "moist" 100 4.2
10.4 91 41.2
"101" 1 "Sf" "control" "awater-logged"
101 9 35.8 222.2 43.6
"102" 1 "Sf" "shoot" "awater-logged" 102
10.8 40.6 245.4 47.6
"103" 1 "Sf" "xfull" "awater-logged" 103
4.6 10.6 134.6 47
"104" 1 "Sf" "shoot" "awater-logged" 104
8.2 35.4 263.4 56.2
"105" 1 "Sf" "xfull" "awater-logged" 105
8.4 8 207.8 45.6
"106" 1 "Sf" "control" "awater-logged"
106 8.5 38.5 243.25 45.25
"107" 1 "Sf" "root" "awater-logged" 107
9 41 205 43.2
"108" 1 "Sf" "shoot" "awater-logged" 108
8.4 24.6 170.4 39.2
"109" 1 "Sf" "root" "awater-logged" 109
8.8 29.2 176.4 31.4
"110" 1 "Sf" "control" "awater-logged"
110 7 28.8 167 44
"111" 1 "Sf" "shoot" "awater-logged" 111
10.2 41.2 283.4 50.6
"112" 1 "Sf" "root" "awater-logged" 112
8.6 35.6 211.6 37.4
"113" 1 "Sf" "root" "awater-logged" 113
10.6 39 221 44.6
"114" 1 "Sf" "xfull" "awater-logged" 114
8 11.8 253.6 64.4
"115" 1 "Sf" "shoot" "awater-logged" 115
8.4 25 148 30.6
"116" 1 "Sf" "control" "awater-logged"
116 8.6 37.2 213 46.6
"117" 1 "Sf" "root" "awater-logged" 117
9.8 28 165.4 35.4
"118" 1 "Sf" "xfull" "awater-logged" 118
6.2 2.6 124 34
"119" 1 "Sf" "control" "awater-logged"
119 6.2 25.6 145 39.8
"120" 1 "Sf" "xfull" "awater-logged" 120
8.5 9.75 247.25 62.25
"811" 2 "Sf" "xfull" "moist" 81 4.4 41.6
464.6 217.6
"821" 2 "Sf" "root" "moist" 82 4.6 58.4
800 271.8
"831" 2 "Sf" "control" "moist" 83 7 79.2
967.8 248.8
"841" 2 "Sf" "control" "moist" 84 5.8
68.6 923 256.4
"851" 2 "Sf" "shoot" "moist" 85 4.4 46.4
549.6 263.8
"861" 2 "Sf" "control" "moist" 86 6.8
81.2 1077 309
"871" 2 "Sf" "root" "moist" 87 6.6 72.6
914.8 307.4
"881" 2 "Sf" "shoot" "moist" 88 3 28.25
361 242
"891" 2 "Sf" "xfull" "moist" 89 2.2 19.8
221.8 139.2
"901" 2 "Sf" "control" "moist" 90 5.8
72.4 1038.4 328.6
"911" 2 "Sf" "shoot" "moist" 91 4.5 39
423.25 253.25
"921" 2 "Sf" "root" "moist" 92 4.8 66.8
930.8 296.8
"931" 2 "Sf" "shoot" "moist" 93 7.75
69.5 843 323.25
"941" 2 "Sf" "root" "moist" 94 5.75
56.75 710.75 205
"951" 2 "Sf" "root" "moist" 95
6.666666667 68.33333333 703.6666667 136.3333333
"961" 2 "Sf" "shoot" "moist" 96 4.5 40.5
524.5 235.25
"971" 2 "Sf" "xfull" "moist" 97 4.2 26.4
277.2 159.8
"981" 2 "Sf" "xfull" "moist" 98 2.2 17.6
197.2 143.6
"991" 2 "Sf" "control" "moist" 99 5.8
63.6 660.4 230
"1001" 2 "Sf" "xfull" "moist" 100 2.2
24.8 252.6 179.8
"1011" 2 "Sf" "control" "awater-logged"
101 6.8 87 1356.6 346.6
"1021" 2 "Sf" "shoot" "awater-logged"
102 7.4 73.2 887 350.8
"1031" 2 "Sf" "xfull" "awater-logged"
103 3.8 42 582.4 330
"1041" 2 "Sf" "shoot" "awater-logged"
104 6.2 66.8 818.4 381.8
"1051" 2 "Sf" "xfull" "awater-logged"
105 4.6 28.4 258.8 136
"1061" 2 "Sf" "control" "awater-logged"
106 6.8 78.8 957.8 286
"1071" 2 "Sf" "root" "awater-logged" 107
6.6 85.6 1345.2 351.2
"1081" 2 "Sf" "shoot" "awater-logged"
108 5.6 61 861.6 371
"1091" 2 "Sf" "root" "awater-logged" 109
6.2 71.8 1051.6 337.2
"1101" 2 "Sf" "control" "awater-logged"
110 5.8 67.2 992.4 338
"1111" 2 "Sf" "shoot" "awater-logged"
111 7 74.4 936 362.6
"1121" 2 "Sf" "root" "awater-logged" 112
6.8 110.6 1490.4 369.8
"1131" 2 "Sf" "root" "awater-logged" 113
7.8 89 1328.6 373.8
"1141" 2 "Sf" "xfull" "awater-logged"
114 3.8 28.4 330 165.8
"1151" 2 "Sf" "shoot" "awater-logged"
115 5.8 54 647 301.2
"1161" 2 "Sf" "control" "awater-logged"
116 7 83.4 1332.2 384
"1171" 2 "Sf" "root" "awater-logged" 117
7 83.6 1212 341
"1181" 2 "Sf" "xfull" "awater-logged"
118 4.6 28.2 405.2 193.8
"1191" 2 "Sf" "control" "awater-logged"
119 5.2 70 815.4 271
"1201" 2 "Sf" "xfull" "awater-logged"
120 6 45.25 507 205.75
"812" 3 "Sf" "xfull" "moist" 81 3.4 38.4
635.6 387.8
"822" 3 "Sf" "root" "moist" 82 4.8 64.2
1163 441.2
"832" 3 "Sf" "control" "moist" 83 5.2
78.2 1470.4 481.2
"842" 3 "Sf" "control" "moist" 84 4 72.2
1401.8 499.4
"852" 3 "Sf" "shoot" "moist" 85 2.4 40.8
797.8 519.2
"862" 3 "Sf" "control" "moist" 86 4.8
80.8 1562.6 563.6
"872" 3 "Sf" "root" "moist" 87 3.4 57.8
1224.8 499.4
"882" 3 "Sf" "shoot" "moist" 88 2.6 30
565 430
"892" 3 "Sf" "xfull" "moist" 89 2 25.4
435.2 362.4
"902" 3 "Sf" "control" "moist" 90 3.8
68.4 1353.8 508.4
"912" 3 "Sf" "shoot" "moist" 91 3.25
34.5 593 465.5
"922" 3 "Sf" "root" "moist" 92 4.6 73.8
1406.4 495.8
"932" 3 "Sf" "shoot" "moist" 93 3 43.4
873.2 516.6
"942" 3 "Sf" "root" "moist" 94 5 72.75
1301.25 457
"952" 3 "Sf" "root" "moist" 95
6.333333333 90.33333333 1401.333333 350.6666667
"962" 3 "Sf" "shoot" "moist" 96 2.25
39.75 738.25 433.75
"972" 3 "Sf" "xfull" "moist" 97 3.6 35.6
428.2 281
"982" 3 "Sf" "xfull" "moist" 98 3.4 28.8
412.6 303.8
"992" 3 "Sf" "control" "moist" 99 4.8
89.4 1151.4 443.8
"1002" 3 "Sf" "xfull" "moist" 100 2.2
29.2 467.4 377
"1012" 3 "Sf" "control" "awater-logged"
101 6 83.6 1659.4 473.2
"1022" 3 "Sf" "shoot" "awater-logged"
102 3.4 56.2 1122.4 566.2
"1032" 3 "Sf" "xfull" "awater-logged"
103 2.8 46.4 882.4 633.2
"1042" 3 "Sf" "shoot" "awater-logged"
104 4 58.8 1052.8 636.4
"1052" 3 "Sf" "xfull" "awater-logged"
105 3.6 40.6 516.6 345
"1062" 3 "Sf" "control" "awater-logged"
106 4.6 71.6 1441 509.8
"1072" 3 "Sf" "root" "awater-logged" 107
5.4 92.6 1879 609
"1082" 3 "Sf" "shoot" "awater-logged"
108 2.2 46.8 1038.8 639.2
"1092" 3 "Sf" "root" "awater-logged" 109
5.4 73.6 1364.8 538.4
"1102" 3 "Sf" "control" "awater-logged"
110 4.4 80.4 1382.6 548.6
"1112" 3 "Sf" "shoot" "awater-logged"
111 3.4 67.6 1403.4 632.4
"1122" 3 "Sf" "root" "awater-logged" 112
6.4 103.6 1917.2 504.2
"1132" 3 "Sf" "root" "awater-logged" 113
5 89.8 1817.8 606
"1142" 3 "Sf" "xfull" "awater-logged"
114 2.2 27.8 424.8 347
"1152" 3 "Sf" "shoot" "awater-logged"
115 1.6 30.8 646 523.4
"1162" 3 "Sf" "control" "awater-logged"
116 5.2 84.4 1804.8 598.2
"1172" 3 "Sf" "root" "awater-logged" 117
5.8 80 1388.4 461.2
"1182" 3 "Sf" "xfull" "awater-logged"
118 3.4 42.8 630.4 341.4
"1192" 3 "Sf" "control" "awater-logged"
119 3.8 82.4 1276.8 541.6
"1202" 3 "Sf" "xfull" "awater-logged"
120 3.75 57 870.75 483.75
"1" 1 "Sv" "control" "moist" 1 8.8 37.8
211.2 60.6
"2" 1 "Sv" "xfull" "moist" 2 7 8 174.8
62.8
"3" 1 "Sv" "control" "moist" 3 9 42
255.2 66
"4" 1 "Sv" "root" "moist" 4 7.8 35 225.8
78.2
"5" 1 "Sv" "root" "moist" 5 7.8 31.4
182.6 59.4
"6" 1 "Sv" "shoot" "moist" 6 8.8 50.8
247.6 53.4
"7" 1 "Sv" "root" "moist" 7 7 26.2 169.2
63
"8" 1 "Sv" "xfull" "moist" 8 4.6 4 71.8
35.8
"9" 1 "Sv" "root" "moist" 9 8.8 40 246.8
69.4
"10" 1 "Sv" "shoot" "moist" 10 8 48.2
266.8 67.6
"11" 1 "Sv" "control" "moist" 11 15 71.8
380.2 53.6
"12" 1 "Sv" "shoot" "moist" 12 10.4 41.2
271.8 58.6
"13" 1 "Sv" "shoot" "moist" 13 8.2 44
243.8 53.4
"14" 1 "Sv" "xfull" "moist" 14 6.2 10
171.6 67.2
"15" 1 "Sv" "root" "moist" 15 9.6 42.2
187.6 57.8
"16" 1 "Sv" "xfull" "moist" 16 6.2 7.8
164 63.6
"17" 1 "Sv" "control" "moist" 17 11 53.4
262.4 59.6
"18" 1 "Sv" "control" "moist" 18 8.8 45
245.4 63.8
"19" 1 "Sv" "xfull" "moist" 19 6.2 7.4
161 61.6
"20" 1 "Sv" "shoot" "moist" 20 9.4 38.4
209 74.8
"21" 1 "Sv" "root" "awater-logged" 21
8.6 42 252 75.2
"22" 1 "Sv" "shoot" "awater-logged" 22
7.8 34.8 238.8 80.8
"23" 1 "Sv" "control" "awater-logged" 23
9.75 37.25 182.25 55.5
"24" 1 "Sv" "control" "awater-logged" 24
8.2 51 287.2 77.8
"25" 1 "Sv" "control" "awater-logged" 25
8.5 45.25 290.5 85
"26" 1 "Sv" "xfull" "awater-logged" 26
8.8 11.6 204.4 58.8
"27" 1 "Sv" "shoot" "awater-logged" 27
6.6 22 138.6 68.6
"28" 1 "Sv" "shoot" "awater-logged" 28
10.4 34.4 225.2 70
"29" 1 "Sv" "root" "awater-logged" 29 5
22.4 113.4 60.2
"30" 1 "Sv" "control" "awater-logged" 30
7.4 38 220.4 73.8
"31" 1 "Sv" "xfull" "awater-logged" 31
7.6 5 143.8 54.8
"32" 1 "Sv" "xfull" "awater-logged" 32
3.6 10.2 124.6 74.2
"33" 1 "Sv" "xfull" "awater-logged" 33
7.2 6 162.6 60.8
"34" 1 "Sv" "shoot" "awater-logged" 34
7.4 26.4 210.4 86.2
"35" 1 "Sv" "root" "awater-logged" 35
8.6 34.8 257.6 81.6
"36" 1 "Sv" "root" "awater-logged" 36
9.4 31 196.2 70.4
"37" 1 "Sv" "root" "awater-logged" 37
6.8 34.2 204.4 85.4
"38" 1 "Sv" "xfull" "awater-logged" 38
7.2 6.6 151.6 66
"39" 1 "Sv" "shoot" "awater-logged" 39
7.6 39.6 227.4 63.8
"40" 1 "Sv" "control" "awater-logged" 40
8.4 51.6 257.6 78.6
"41" 2 "Sv" "control" "moist" 1 5.4
100.8 1104.4 392.6
"42" 2 "Sv" "xfull" "moist" 2 5.2 33.6
404.4 182.4
"43" 2 "Sv" "control" "moist" 3 6.4
108.6 1060 364.2
"44" 2 "Sv" "root" "moist" 4 5 91.4
1017.6 394.4
"45" 2 "Sv" "root" "moist" 5 5.2 78.4
772.4 312.4
"46" 2 "Sv" "shoot" "moist" 6 5.6 77.6
775.6 318
"47" 2 "Sv" "root" "moist" 7 4.6 73.2
730.2 314.4
"48" 2 "Sv" "xfull" "moist" 8 3.6 17.4
238.8 136.6
"49" 2 "Sv" "root" "moist" 9 4.6 94.2
980.4 366.8
"50" 2 "Sv" "shoot" "moist" 10 7.75 96.5
876.25 327
"51" 2 "Sv" "control" "moist" 11 10
127.2 1209.6 327.2
"52" 2 "Sv" "shoot" "moist" 12 7.4 83.4
818.6 314
"53" 2 "Sv" "shoot" "moist" 13 6.8 83.8
812.4 283.6
"54" 2 "Sv" "xfull" "moist" 14 3.8 29.8
325 183.4
"55" 2 "Sv" "root" "moist" 15 4.6 72.2
734.8 378
"56" 2 "Sv" "xfull" "moist" 16 2.6 24.4
282 189
"57" 2 "Sv" "control" "moist" 17 8 124.6
1246.8 371.4
"58" 2 "Sv" "control" "moist" 18 4.4
84.4 1061.4 377.2
"59" 2 "Sv" "xfull" "moist" 19 4.2 29
353.8 193.4
"60" 2 "Sv" "shoot" "moist" 20 5.6 74.4
743.2 378.8
"61" 2 "Sv" "root" "awater-logged" 21
6.6 93.6 912.4 351.6
"62" 2 "Sv" "shoot" "awater-logged" 22 4
62 714.8 401
"63" 2 "Sv" "control" "awater-logged" 23
5 82 881.6 323.2
"64" 2 "Sv" "control" "awater-logged" 24
5.6 110.8 1264.8 424.8
"65" 2 "Sv" "control" "awater-logged" 25
5.8 89.6 930.8 346.2
"66" 2 "Sv" "xfull" "awater-logged" 26 4
39.6 455.2 268.8
"67" 2 "Sv" "shoot" "awater-logged" 27
3.4 55.4 614.6 384.2
"68" 2 "Sv" "shoot" "awater-logged" 28
5.4 71 698 320.6
"69" 2 "Sv" "root" "awater-logged" 29 3
66.4 757.4 427.8
"70" 2 "Sv" "control" "awater-logged" 30
4.8 83 990.4 413.4
"71" 2 "Sv" "xfull" "awater-logged" 31
3.2 23.2 300.6 238.8
"72" 2 "Sv" "xfull" "awater-logged" 32
1.4 24.6 210.8 192.8
"73" 2 "Sv" "xfull" "awater-logged" 33
3.2 28.6 344.8 185.8
"74" 2 "Sv" "shoot" "awater-logged" 34
3.6 59.6 631 402
"75" 2 "Sv" "root" "awater-logged" 35
5.2 86.4 826.4 289.8
"76" 2 "Sv" "root" "awater-logged" 36
7.2 87.4 918.8 351
"77" 2 "Sv" "root" "awater-logged" 37
4.2 84.8 840 422
"78" 2 "Sv" "xfull" "awater-logged" 38
2.4 29.8 355.6 239.6
"79" 2 "Sv" "shoot" "awater-logged" 39
6.2 71.2 683.8 282
"80" 2 "Sv" "control" "awater-logged" 40
5.4 106.4 1083.6 388.6
"813" 3 "Sv" "control" "moist" 1 5.2
149.6 1863.8 682
"823" 3 "Sv" "xfull" "moist" 2 2.5 42.25
427.5 344.5
"833" 3 "Sv" "control" "moist" 3 4.2 134
1496.2 572
"843" 3 "Sv" "root" "moist" 4 3.6 121
1488.8 706.8
"853" 3 "Sv" "root" "moist" 5 4 115
1340.2 587.2
"863" 3 "Sv" "shoot" "moist" 6 2.6 80
976 613.2
"873" 3 "Sv" "root" "moist" 7 3.6 94.4
1187.2 555
"883" 3 "Sv" "xfull" "moist" 8 3.5 41.75
367 195.5
"893" 3 "Sv" "root" "moist" 9 3.6 120.2
1450.4 630.6
"903" 3 "Sv" "shoot" "moist" 10 2.6 85
1007.2 586
"913" 3 "Sv" "control" "moist" 11 4
118.8 1386 626.6
"923" 3 "Sv" "shoot" "moist" 12 2.2 72.4
942.6 578.4
"933" 3 "Sv" "shoot" "moist" 13 2.2 80.6
957.6 606
"943" 3 "Sv" "xfull" "moist" 14 1.25 27
308 297
"953" 3 "Sv" "root" "moist" 15 2.6 85.8
1080.2 676.8
"963" 3 "Sv" "xfull" "moist" 16
1.666666667 41 475.6666667 374
"973" 3 "Sv" "control" "moist" 17 4.4
148 1795.6 681.8
"983" 3 "Sv" "control" "moist" 18 3.4
107.8 1484.4 653.6
"993" 3 "Sv" "xfull" "moist" 19 2.4 49.8
450.6 326.2
"1003" 3 "Sv" "shoot" "moist" 20 2.8
73.6 896.2 663.8
"1013" 3 "Sv" "root" "awater-logged" 21
4.8 119 1431.6 585
"1023" 3 "Sv" "shoot" "awater-logged" 22
1.8 61.2 896.8 654
"1033" 3 "Sv" "control" "awater-logged"
23 4.6 123.8 1471.6 552
"1043" 3 "Sv" "control" "awater-logged"
24 5 144 1906.6 734.2
"1053" 3 "Sv" "control" "awater-logged"
25 3.4 107.8 1388.4 639
"1063" 3 "Sv" "xfull" "awater-logged" 26
1.8 53.2 586.8 439.4
"1073" 3 "Sv" "shoot" "awater-logged" 27
1.8 68.4 910.6 704.4
"1083" 3 "Sv" "shoot" "awater-logged" 28
3.4 88.2 1092 615
"1093" 3 "Sv" "root" "awater-logged" 29
2.8 101.2 1342.8 740.4
"1103" 3 "Sv" "control" "awater-logged"
30 4 125.4 1556.6 769.6
"1113" 3 "Sv" "xfull" "awater-logged" 31
2 52.2 534.8 451
"1123" 3 "Sv" "xfull" "awater-logged" 32
1.8 40.4 428.6 375.6
"1133" 3 "Sv" "xfull" "awater-logged" 33
2 41.2 420.6 295.6
"1143" 3 "Sv" "shoot" "awater-logged" 34
1.8 74.6 978.8 760.6
"1153" 3 "Sv" "root" "awater-logged" 35
4 110.8 1262.8 494.4
"1163" 3 "Sv" "root" "awater-logged" 36
6.4 129.2 1518.8 590.4
"1173" 3 "Sv" "root" "awater-logged" 37
4.6 124.6 1389.8 746
"1183" 3 "Sv" "xfull" "awater-logged" 38
2 39 472.6 398.4
"1193" 3 "Sv" "shoot" "awater-logged" 39
1.6 59.8 809.4 576.4
"1203" 3 "Sv" "control" "awater-logged"
40 4.4 134.6 1622.6 664.4
"413" 1 "St" "root" "moist" 41 4.6 17.6
83 35.2
"423" 1 "St" "xfull" "moist" 42 3 4.6
29.6 15.6
"433" 1 "St" "root" "moist" 43
5.333333333 26.33333333 110.3333333 52.33333333
"443" 1 "St" "control" "moist" 44 8 38
187 63.4
"453" 1 "St" "control" "moist" 45 5.6
23.8 96.4 38.8
"463" 1 "St" "root" "moist" 46 7.5 18.75
92.25 33
"473" 1 "St" "xfull" "moist" 47
6.333333333 8 73 23
"483" 1 "St" "shoot" "moist" 48 6.4 20.6
93.4 22.4
"493" 1 "St" "xfull" "moist" 49 6 2.6 63
15
"503" 1 "St" "xfull" "moist" 50 5.4 2.8
56.4 21.2
"513" 1 "St" "shoot" "moist" 51 8
24.33333333 117 42.33333333
"523" 1 "St" "shoot" "moist" 52 7 13.4
80 25.8
"533" 1 "St" "root" "moist" 53 4.5 16
66.25 31
"543" 1 "St" "control" "moist" 54 6.8
19.4 83.8 32.6
"553" 1 "St" "control" "moist" 55 9.25
36.75 158.5 34.25
"563" 1 "St" "control" "moist" 56 5.2
18.2 97.6 39
"573" 1 "St" "shoot" "moist" 57 6.25
12.75 55.75 25
"583" 1 "St" "shoot" "moist" 58
6.333333333 30.66666667 131.3333333 39
"593" 1 "St" "xfull" "moist" 59 5.8 7.8
69.2 28.6
"603" 1 "St" "root" "moist" 60 5 19.8 84
27.6
"613" 1 "St" "xfull" "awater-logged" 61
6.2 3.2 73.4 21
"623" 1 "St" "control" "awater-logged"
62 7.2 15 89.2 32
"633" 1 "St" "shoot" "awater-logged" 63
6.5 15.25 85.25 35
"643" 1 "St" "root" "awater-logged" 64
4.666666667 18.66666667 99 40.33333333
"653" 1 "St" "control" "awater-logged"
65 5.8 16.8 75.8 26.2
"663" 1 "St" "xfull" "awater-logged" 66
5.666666667 4 62.33333333 28.33333333
"673" 1 "St" "control" "awater-logged"
67 9 33.25 120 37
"683" 1 "St" "root" "awater-logged" 68 6
16 70 24.25
"693" 1 "St" "shoot" "awater-logged" 69
7 15.4 71.6 31.4
"703" 1 "St" "xfull" "awater-logged" 70
5.2 1.2 57.4 23.6
"713" 1 "St" "control" "awater-logged"
71 7.25 23.5 114 33
"723" 1 "St" "shoot" "awater-logged" 72
6.75 30.5 125 40.75
"733" 1 "St" "shoot" "awater-logged" 73
7.25 13.75 81.5 29.5
"743" 1 "St" "root" "awater-logged" 74
8.2 18.2 89.8 35.6
"753" 1 "St" "shoot" "awater-logged" 75
5.6 15.8 69.6 29.4
"763" 1 "St" "control" "awater-logged"
76 7.4 27.8 100.2 28.8
"773" 1 "St" "root" "awater-logged" 77
6.4 15.4 79.2 36
"783" 1 "St" "xfull" "awater-logged" 78
6.2 0.6 42.6 13.4
"793" 1 "St" "xfull" "awater-logged" 79
3.8 3.8 46.4 22.6
"803" 1 "St" "root" "awater-logged" 80
5.2 26 92.4 25.6
"411" 2 "St" "root" "moist" 41 3 45.6
658.4 364.8
"421" 2 "St" "xfull" "moist" 42 3.4 9.2
130 93.2
"431" 2 "St" "root" "moist" 43 3.25 36
520.75 382.25
"441" 2 "St" "control" "moist" 44 5.6
68.2 966.2 456.4
"451" 2 "St" "control" "moist" 45 4.8
60.4 765.4 347.8
"461" 2 "St" "root" "moist" 46 6.8 57.2
631.4 282.8
"471" 2 "St" "xfull" "moist" 47 4.8 10
133.8 50.8
"481" 2 "St" "shoot" "moist" 48 6.6 61.2
547.4 233.6
"491" 2 "St" "xfull" "moist" 49 7.6 24.6
241.2 88
"501" 2 "St" "xfull" "moist" 50 5.4 19.4
138.2 43
"511" 2 "St" "shoot" "moist" 51 5 42.4
353.8 188
"521" 2 "St" "shoot" "moist" 52 4.6 39.2
417 256
"531" 2 "St" "root" "moist" 53 3.75 51
607.75 298.25
"541" 2 "St" "control" "moist" 54 6.2
66.8 771.4 303.4
"551" 2 "St" "control" "moist" 55 7 79
998 398
"561" 2 "St" "control" "moist" 56 4.6
58.8 782.4 365
"571" 2 "St" "shoot" "moist" 57 4.4 37.6
331 143
"581" 2 "St" "shoot" "moist" 58 4.25
44.25 466.5 261.25
"591" 2 "St" "xfull" "moist" 59 6.6 18.8
160.6 64.6
"601" 2 "St" "root" "moist" 60 3.8 49
668.8 311
"611" 2 "St" "xfull" "awater-logged" 61
6 17.8 204.2 96.4
"621" 2 "St" "control" "awater-logged"
62 4.2 56.8 800.4 353.6
"631" 2 "St" "shoot" "awater-logged" 63
3.5 45 534 305
"641" 2 "St" "root" "awater-logged" 64
4.666666667 61.33333333 665.6666667 338.6666667
"651" 2 "St" "control" "awater-logged"
65 4.2 58.8 759 323.2
"661" 2 "St" "xfull" "awater-logged" 66
4.5 14.25 171 97
"671" 2 "St" "control" "awater-logged"
67 5.5 72 851.5 363
"681" 2 "St" "root" "awater-logged" 68
5.75 62.75 616.75 262.25
"691" 2 "St" "shoot" "awater-logged" 69
3.2 41.6 587.8 415.4
"701" 2 "St" "xfull" "awater-logged" 70
3.8 14 141.4 79.8
"711" 2 "St" "control" "awater-logged"
71 4.2 57 774 298.2
"721" 2 "St" "shoot" "awater-logged" 72
3.8 41.4 468.4 227.2
"731" 2 "St" "shoot" "awater-logged" 73
3.75 42.25 492.25 235
"741" 2 "St" "root" "awater-logged" 74
4.4 52.4 691.2 342
"751" 2 "St" "shoot" "awater-logged" 75
2.4 30.6 379.4 294.2
"761" 2 "St" "control" "awater-logged"
76 6.6 80.2 966.6 340.6
"771" 2 "St" "root" "awater-logged" 77
3.4 38 526.8 361.2
"781" 2 "St" "xfull" "awater-logged" 78
4.6 17.4 198.2 107.4
"791" 2 "St" "xfull" "awater-logged" 79
3 14.2 166.6 104.4
"801" 2 "St" "root" "awater-logged" 80
5.4 63.8 636.6 292.6
"412" 3 "St" "root" "moist" 41 2.6 60.6
1161 617.6
"422" 3 "St" "xfull" "moist" 42 3.4 16.8
313.8 250.6
"432" 3 "St" "root" "moist" 43 2.75 46
906 707.25
"442" 3 "St" "control" "moist" 44 3 74.8
1550.4 742.4
"452" 3 "St" "control" "moist" 45 3.8 73
1324.6 627.6
"462" 3 "St" "root" "moist" 46 4.4 62.2
1096 496.4
"472" 3 "St" "xfull" "moist" 47 3.2 13.8
133.6 64.4
"482" 3 "St" "shoot" "moist" 48 3.2 53
776.8 447.2
"492" 3 "St" "xfull" "moist" 49 3.8 21.4
303.4 239.6
"502" 3 "St" "xfull" "moist" 50 7.5
18.75 207.5 58
"512" 3 "St" "shoot" "moist" 51 4.6 56.8
689 421.8
"522" 3 "St" "shoot" "moist" 52 1.6 34.6
640.4 575.8
"532" 3 "St" "root" "moist" 53 3.75 67.5
1164.25 586.75
"542" 3 "St" "control" "moist" 54 3 73.4
1325 617.2
"552" 3 "St" "control" "moist" 55 4.75
99 1730.75 678
"562" 3 "St" "control" "moist" 56 3.6
75.4 1386.6 713.8
"572" 3 "St" "shoot" "moist" 57 2.25 31
463.5 343
"582" 3 "St" "shoot" "moist" 58 2.5 47
799 551.5
"592" 3 "St" "xfull" "moist" 59 5.5 14.5
243 155
"602" 3 "St" "root" "moist" 60 2.8 55.6
1086.6 513
"612" 3 "St" "xfull" "awater-logged" 61
5.4 27 345 220
"622" 3 "St" "control" "awater-logged"
62 4 80.4 1154.4 496.2
"632" 3 "St" "shoot" "awater-logged" 63
2.25 50.5 835.5 425.25
"642" 3 "St" "root" "awater-logged" 64
4.333333333 83.33333333 1354.333333 551.6666667
"652" 3 "St" "control" "awater-logged"
65 4 71.4 1351.4 576.4
"662" 3 "St" "xfull" "awater-logged" 66
3.75 17 224.5 160.25
"672" 3 "St" "control" "awater-logged"
67 4.25 78.5 1268.5 549.75
"682" 3 "St" "root" "awater-logged" 68
5.25 92.75 1189.5 462
"692" 3 "St" "shoot" "awater-logged" 69
2.2 45 865.6 642.8
"702" 3 "St" "xfull" "awater-logged" 70
3.6 22.4 246.2 181.6
"712" 3 "St" "control" "awater-logged"
71 3.8 74.6 1284 545.4
"722" 3 "St" "shoot" "awater-logged" 72
2.2 42.2 647 405.2
"732" 3 "St" "shoot" "awater-logged" 73
2.25 47.25 798.75 491.75
"742" 3 "St" "root" "awater-logged" 74 3
61 1105.8 551.4
"752" 3 "St" "shoot" "awater-logged" 75
1.8 36.6 585.8 534.4
"762" 3 "St" "control" "awater-logged"
76 5.8 98 1633.8 640.4
"772" 3 "St" "root" "awater-logged" 77
3.4 51.6 876.8 572.6
"782" 3 "St" "xfull" "awater-logged" 78
4.8 25.6 295.6 175.6
"792" 3 "St" "xfull" "awater-logged" 79
2.6 21.4 295.2 228.2
"802" 3 "St" "root" "awater-logged" 80 4
72.2 1072.8 576

Anna Radtke

2010-Oct-29 16:14 UTC

head link

[R] Tukey post hoc comparison (glht?) after 3factorial mixed model (lmer)

Hello, dear R-community.

This is a question about TukeyHSD between factor combinations of a Three-Way
ANOVA, which is - since it is a multi measure ANOVA - not a simple ANOVA but
a Generalised Linear Mixed Model (GLMM), calculated with "lmer".
> growth <-
groupedData(length~meas|box_id,outer=~spec*comp*water,data=all.spec)> model <- lmer(length~spec*comp*water+(meas|box_id),data=growth)
> summary(model)
This works fine. But now, I would like to calculate Tukey HSD among certain
factor combinations. Formerly (before version 1.0), Tukey contrasts
including all levels of interactions could be calculated with the multcomp
package more or less automatically like this:
> summary (glht (model, linfct = mcp (spec*comp*water = "Tukey")))
Now, Mr Hothorn et al. have changed the function and it is "suggestet to
the
users that they write out, manually, the set of contrasts they want". I
think that is not a bad idea, but I got problems with the syntax in my case.
And I would really grateful if anybody could help me. So far I tried:
> K <- cbind(0,diag(length(fixef(model))-1))
> rownames(K) <- names(fixef(model))[-1]
> model_glht <- glht(model,linfct=K)
> summary(model_glht)  # but actually this is not what I want
I'm rather looking for a Tukey output like this

specSt:compControl - specSt:compRoot         p that they are equal < 0.05
specSt:compControl - specSt:compShoot
specSt:compControl - specSt:compFull
specSt:compRoot - specSt:compShoot
specSt:compRoot - specSt:compFull
specSt:compShoot - specSt:compFull

and that for each of the 3 studied species, i.e. compare all-pairwise
combinations of the levels of the second factor within each level of the
first factor. We are not interested in the third factor, so data can be
averaged over that.


THANKS A LOT FOR ANY ADVICE, Sincerely

Anna Radtke



-----> model output:

Linear mixed model fit by REML
Formula: length ~ spec * comp * water + (meas | box_id)
   Data: growth
  AIC  BIC logLik deviance REMLdev
 4800 4909  -2372     4988    4744
Random effects:
 Groups   Name        Variance Std.Dev. Corr
 box_id   (Intercept)      0.0   0.000
          meas        222484.2 471.682    NaN
 Residual               9439.4  97.157
Number of obs: 360, groups: box_id, 120

Fixed effects:
                            Estimate Std. Error t value
(Intercept)                 -353.554     65.777  -5.375
specSt                      -103.111     93.023  -1.108
specSv                        -4.485     93.023  -0.048
comproot                     -41.686     93.023  -0.448
compshoot                    241.847     93.023   2.600
compxfull                    316.849     93.023   3.406
watermoist                   -48.620     93.023  -0.523
specSt:comproot               97.168    131.554   0.739
specSv:comproot               54.849    131.554   0.417
specSt:compshoot              10.416    131.554   0.079
specSv:compshoot               6.584    131.554   0.050
specSt:compxfull              90.949    131.554   0.691
specSv:compxfull              43.284    131.554   0.329
specSt:watermoist              9.222    131.554   0.070
specSv:watermoist            104.229    131.554   0.792
comproot:watermoist           15.931    131.554   0.121
compshoot:watermoist          28.999    131.554   0.220
compxfull:watermoist          39.363    131.554   0.299
specSt:comproot:watermoist    45.513    186.046   0.245
specSv:comproot:watermoist   -24.350    186.046  -0.131
specSt:compshoot:watermoist   46.027    186.046   0.247
specSv:compshoot:watermoist    1.232    186.046   0.007
specSt:compxfull:watermoist   23.749    186.046   0.128
specSv:compxfull:watermoist  -57.109    186.046  -0.307
-------------- next part --------------
"meas" "spec" "comp" "water"
"box_id" "sprouts" "leaves" "length"
"long.sprout"
"81" 1 "Sf" "xfull" "moist" 81 6.8 13.6
150.4 43.8
"82" 1 "Sf" "root" "moist" 82 6.5 18.5
104.25 25.75
"83" 1 "Sf" "control" "moist" 83 9.25 29
146 27
"84" 1 "Sf" "control" "moist" 84 6.8
31.4 163.8 46.6
"85" 1 "Sf" "shoot" "moist" 85 4.8 19.8
127.6 32.8
"86" 1 "Sf" "control" "moist" 86 8.2
30.6 144.4 31.6
"87" 1 "Sf" "root" "moist" 87 7.8 32.8
174 38.8
"88" 1 "Sf" "shoot" "moist" 88 5 8.5 54
22.25
"89" 1 "Sf" "xfull" "moist" 89 2.25 7
54.25 27
"90" 1 "Sf" "control" "moist" 90 5.6
21.2 103 30
"91" 1 "Sf" "shoot" "moist" 91 4.25 18
84.25 29.25
"92" 1 "Sf" "root" "moist" 92 5.8 26.4
133.2 33
"93" 1 "Sf" "shoot" "moist" 93 11.25
35.25 215 44.25
"94" 1 "Sf" "root" "moist" 94 6
17.33333333 90.66666667 19.33333333
"95" 1 "Sf" "root" "moist" 95
4.666666667 5.333333333 33.66666667 9.333333333
"96" 1 "Sf" "shoot" "moist" 96 6.5 11.5
88.25 25.5
"97" 1 "Sf" "xfull" "moist" 97 9.8 13
184.4 40.2
"98" 1 "Sf" "xfull" "moist" 98 5.8 15.2
156.6 41.6
"99" 1 "Sf" "control" "moist" 99 7.5
26.5 140.75 36.5
"100" 1 "Sf" "xfull" "moist" 100 4.2
10.4 91 41.2
"101" 1 "Sf" "control" "awater-logged"
101 9 35.8 222.2 43.6
"102" 1 "Sf" "shoot" "awater-logged" 102
10.8 40.6 245.4 47.6
"103" 1 "Sf" "xfull" "awater-logged" 103
4.6 10.6 134.6 47
"104" 1 "Sf" "shoot" "awater-logged" 104
8.2 35.4 263.4 56.2
"105" 1 "Sf" "xfull" "awater-logged" 105
8.4 8 207.8 45.6
"106" 1 "Sf" "control" "awater-logged"
106 8.5 38.5 243.25 45.25
"107" 1 "Sf" "root" "awater-logged" 107
9 41 205 43.2
"108" 1 "Sf" "shoot" "awater-logged" 108
8.4 24.6 170.4 39.2
"109" 1 "Sf" "root" "awater-logged" 109
8.8 29.2 176.4 31.4
"110" 1 "Sf" "control" "awater-logged"
110 7 28.8 167 44
"111" 1 "Sf" "shoot" "awater-logged" 111
10.2 41.2 283.4 50.6
"112" 1 "Sf" "root" "awater-logged" 112
8.6 35.6 211.6 37.4
"113" 1 "Sf" "root" "awater-logged" 113
10.6 39 221 44.6
"114" 1 "Sf" "xfull" "awater-logged" 114
8 11.8 253.6 64.4
"115" 1 "Sf" "shoot" "awater-logged" 115
8.4 25 148 30.6
"116" 1 "Sf" "control" "awater-logged"
116 8.6 37.2 213 46.6
"117" 1 "Sf" "root" "awater-logged" 117
9.8 28 165.4 35.4
"118" 1 "Sf" "xfull" "awater-logged" 118
6.2 2.6 124 34
"119" 1 "Sf" "control" "awater-logged"
119 6.2 25.6 145 39.8
"120" 1 "Sf" "xfull" "awater-logged" 120
8.5 9.75 247.25 62.25
"811" 2 "Sf" "xfull" "moist" 81 4.4 41.6
464.6 217.6
"821" 2 "Sf" "root" "moist" 82 4.6 58.4
800 271.8
"831" 2 "Sf" "control" "moist" 83 7 79.2
967.8 248.8
"841" 2 "Sf" "control" "moist" 84 5.8
68.6 923 256.4
"851" 2 "Sf" "shoot" "moist" 85 4.4 46.4
549.6 263.8
"861" 2 "Sf" "control" "moist" 86 6.8
81.2 1077 309
"871" 2 "Sf" "root" "moist" 87 6.6 72.6
914.8 307.4
"881" 2 "Sf" "shoot" "moist" 88 3 28.25
361 242
"891" 2 "Sf" "xfull" "moist" 89 2.2 19.8
221.8 139.2
"901" 2 "Sf" "control" "moist" 90 5.8
72.4 1038.4 328.6
"911" 2 "Sf" "shoot" "moist" 91 4.5 39
423.25 253.25
"921" 2 "Sf" "root" "moist" 92 4.8 66.8
930.8 296.8
"931" 2 "Sf" "shoot" "moist" 93 7.75
69.5 843 323.25
"941" 2 "Sf" "root" "moist" 94 5.75
56.75 710.75 205
"951" 2 "Sf" "root" "moist" 95
6.666666667 68.33333333 703.6666667 136.3333333
"961" 2 "Sf" "shoot" "moist" 96 4.5 40.5
524.5 235.25
"971" 2 "Sf" "xfull" "moist" 97 4.2 26.4
277.2 159.8
"981" 2 "Sf" "xfull" "moist" 98 2.2 17.6
197.2 143.6
"991" 2 "Sf" "control" "moist" 99 5.8
63.6 660.4 230
"1001" 2 "Sf" "xfull" "moist" 100 2.2
24.8 252.6 179.8
"1011" 2 "Sf" "control" "awater-logged"
101 6.8 87 1356.6 346.6
"1021" 2 "Sf" "shoot" "awater-logged"
102 7.4 73.2 887 350.8
"1031" 2 "Sf" "xfull" "awater-logged"
103 3.8 42 582.4 330
"1041" 2 "Sf" "shoot" "awater-logged"
104 6.2 66.8 818.4 381.8
"1051" 2 "Sf" "xfull" "awater-logged"
105 4.6 28.4 258.8 136
"1061" 2 "Sf" "control" "awater-logged"
106 6.8 78.8 957.8 286
"1071" 2 "Sf" "root" "awater-logged" 107
6.6 85.6 1345.2 351.2
"1081" 2 "Sf" "shoot" "awater-logged"
108 5.6 61 861.6 371
"1091" 2 "Sf" "root" "awater-logged" 109
6.2 71.8 1051.6 337.2
"1101" 2 "Sf" "control" "awater-logged"
110 5.8 67.2 992.4 338
"1111" 2 "Sf" "shoot" "awater-logged"
111 7 74.4 936 362.6
"1121" 2 "Sf" "root" "awater-logged" 112
6.8 110.6 1490.4 369.8
"1131" 2 "Sf" "root" "awater-logged" 113
7.8 89 1328.6 373.8
"1141" 2 "Sf" "xfull" "awater-logged"
114 3.8 28.4 330 165.8
"1151" 2 "Sf" "shoot" "awater-logged"
115 5.8 54 647 301.2
"1161" 2 "Sf" "control" "awater-logged"
116 7 83.4 1332.2 384
"1171" 2 "Sf" "root" "awater-logged" 117
7 83.6 1212 341
"1181" 2 "Sf" "xfull" "awater-logged"
118 4.6 28.2 405.2 193.8
"1191" 2 "Sf" "control" "awater-logged"
119 5.2 70 815.4 271
"1201" 2 "Sf" "xfull" "awater-logged"
120 6 45.25 507 205.75
"812" 3 "Sf" "xfull" "moist" 81 3.4 38.4
635.6 387.8
"822" 3 "Sf" "root" "moist" 82 4.8 64.2
1163 441.2
"832" 3 "Sf" "control" "moist" 83 5.2
78.2 1470.4 481.2
"842" 3 "Sf" "control" "moist" 84 4 72.2
1401.8 499.4
"852" 3 "Sf" "shoot" "moist" 85 2.4 40.8
797.8 519.2
"862" 3 "Sf" "control" "moist" 86 4.8
80.8 1562.6 563.6
"872" 3 "Sf" "root" "moist" 87 3.4 57.8
1224.8 499.4
"882" 3 "Sf" "shoot" "moist" 88 2.6 30
565 430
"892" 3 "Sf" "xfull" "moist" 89 2 25.4
435.2 362.4
"902" 3 "Sf" "control" "moist" 90 3.8
68.4 1353.8 508.4
"912" 3 "Sf" "shoot" "moist" 91 3.25
34.5 593 465.5
"922" 3 "Sf" "root" "moist" 92 4.6 73.8
1406.4 495.8
"932" 3 "Sf" "shoot" "moist" 93 3 43.4
873.2 516.6
"942" 3 "Sf" "root" "moist" 94 5 72.75
1301.25 457
"952" 3 "Sf" "root" "moist" 95
6.333333333 90.33333333 1401.333333 350.6666667
"962" 3 "Sf" "shoot" "moist" 96 2.25
39.75 738.25 433.75
"972" 3 "Sf" "xfull" "moist" 97 3.6 35.6
428.2 281
"982" 3 "Sf" "xfull" "moist" 98 3.4 28.8
412.6 303.8
"992" 3 "Sf" "control" "moist" 99 4.8
89.4 1151.4 443.8
"1002" 3 "Sf" "xfull" "moist" 100 2.2
29.2 467.4 377
"1012" 3 "Sf" "control" "awater-logged"
101 6 83.6 1659.4 473.2
"1022" 3 "Sf" "shoot" "awater-logged"
102 3.4 56.2 1122.4 566.2
"1032" 3 "Sf" "xfull" "awater-logged"
103 2.8 46.4 882.4 633.2
"1042" 3 "Sf" "shoot" "awater-logged"
104 4 58.8 1052.8 636.4
"1052" 3 "Sf" "xfull" "awater-logged"
105 3.6 40.6 516.6 345
"1062" 3 "Sf" "control" "awater-logged"
106 4.6 71.6 1441 509.8
"1072" 3 "Sf" "root" "awater-logged" 107
5.4 92.6 1879 609
"1082" 3 "Sf" "shoot" "awater-logged"
108 2.2 46.8 1038.8 639.2
"1092" 3 "Sf" "root" "awater-logged" 109
5.4 73.6 1364.8 538.4
"1102" 3 "Sf" "control" "awater-logged"
110 4.4 80.4 1382.6 548.6
"1112" 3 "Sf" "shoot" "awater-logged"
111 3.4 67.6 1403.4 632.4
"1122" 3 "Sf" "root" "awater-logged" 112
6.4 103.6 1917.2 504.2
"1132" 3 "Sf" "root" "awater-logged" 113
5 89.8 1817.8 606
"1142" 3 "Sf" "xfull" "awater-logged"
114 2.2 27.8 424.8 347
"1152" 3 "Sf" "shoot" "awater-logged"
115 1.6 30.8 646 523.4
"1162" 3 "Sf" "control" "awater-logged"
116 5.2 84.4 1804.8 598.2
"1172" 3 "Sf" "root" "awater-logged" 117
5.8 80 1388.4 461.2
"1182" 3 "Sf" "xfull" "awater-logged"
118 3.4 42.8 630.4 341.4
"1192" 3 "Sf" "control" "awater-logged"
119 3.8 82.4 1276.8 541.6
"1202" 3 "Sf" "xfull" "awater-logged"
120 3.75 57 870.75 483.75
"1" 1 "Sv" "control" "moist" 1 8.8 37.8
211.2 60.6
"2" 1 "Sv" "xfull" "moist" 2 7 8 174.8
62.8
"3" 1 "Sv" "control" "moist" 3 9 42
255.2 66
"4" 1 "Sv" "root" "moist" 4 7.8 35 225.8
78.2
"5" 1 "Sv" "root" "moist" 5 7.8 31.4
182.6 59.4
"6" 1 "Sv" "shoot" "moist" 6 8.8 50.8
247.6 53.4
"7" 1 "Sv" "root" "moist" 7 7 26.2 169.2
63
"8" 1 "Sv" "xfull" "moist" 8 4.6 4 71.8
35.8
"9" 1 "Sv" "root" "moist" 9 8.8 40 246.8
69.4
"10" 1 "Sv" "shoot" "moist" 10 8 48.2
266.8 67.6
"11" 1 "Sv" "control" "moist" 11 15 71.8
380.2 53.6
"12" 1 "Sv" "shoot" "moist" 12 10.4 41.2
271.8 58.6
"13" 1 "Sv" "shoot" "moist" 13 8.2 44
243.8 53.4
"14" 1 "Sv" "xfull" "moist" 14 6.2 10
171.6 67.2
"15" 1 "Sv" "root" "moist" 15 9.6 42.2
187.6 57.8
"16" 1 "Sv" "xfull" "moist" 16 6.2 7.8
164 63.6
"17" 1 "Sv" "control" "moist" 17 11 53.4
262.4 59.6
"18" 1 "Sv" "control" "moist" 18 8.8 45
245.4 63.8
"19" 1 "Sv" "xfull" "moist" 19 6.2 7.4
161 61.6
"20" 1 "Sv" "shoot" "moist" 20 9.4 38.4
209 74.8
"21" 1 "Sv" "root" "awater-logged" 21
8.6 42 252 75.2
"22" 1 "Sv" "shoot" "awater-logged" 22
7.8 34.8 238.8 80.8
"23" 1 "Sv" "control" "awater-logged" 23
9.75 37.25 182.25 55.5
"24" 1 "Sv" "control" "awater-logged" 24
8.2 51 287.2 77.8
"25" 1 "Sv" "control" "awater-logged" 25
8.5 45.25 290.5 85
"26" 1 "Sv" "xfull" "awater-logged" 26
8.8 11.6 204.4 58.8
"27" 1 "Sv" "shoot" "awater-logged" 27
6.6 22 138.6 68.6
"28" 1 "Sv" "shoot" "awater-logged" 28
10.4 34.4 225.2 70
"29" 1 "Sv" "root" "awater-logged" 29 5
22.4 113.4 60.2
"30" 1 "Sv" "control" "awater-logged" 30
7.4 38 220.4 73.8
"31" 1 "Sv" "xfull" "awater-logged" 31
7.6 5 143.8 54.8
"32" 1 "Sv" "xfull" "awater-logged" 32
3.6 10.2 124.6 74.2
"33" 1 "Sv" "xfull" "awater-logged" 33
7.2 6 162.6 60.8
"34" 1 "Sv" "shoot" "awater-logged" 34
7.4 26.4 210.4 86.2
"35" 1 "Sv" "root" "awater-logged" 35
8.6 34.8 257.6 81.6
"36" 1 "Sv" "root" "awater-logged" 36
9.4 31 196.2 70.4
"37" 1 "Sv" "root" "awater-logged" 37
6.8 34.2 204.4 85.4
"38" 1 "Sv" "xfull" "awater-logged" 38
7.2 6.6 151.6 66
"39" 1 "Sv" "shoot" "awater-logged" 39
7.6 39.6 227.4 63.8
"40" 1 "Sv" "control" "awater-logged" 40
8.4 51.6 257.6 78.6
"41" 2 "Sv" "control" "moist" 1 5.4
100.8 1104.4 392.6
"42" 2 "Sv" "xfull" "moist" 2 5.2 33.6
404.4 182.4
"43" 2 "Sv" "control" "moist" 3 6.4
108.6 1060 364.2
"44" 2 "Sv" "root" "moist" 4 5 91.4
1017.6 394.4
"45" 2 "Sv" "root" "moist" 5 5.2 78.4
772.4 312.4
"46" 2 "Sv" "shoot" "moist" 6 5.6 77.6
775.6 318
"47" 2 "Sv" "root" "moist" 7 4.6 73.2
730.2 314.4
"48" 2 "Sv" "xfull" "moist" 8 3.6 17.4
238.8 136.6
"49" 2 "Sv" "root" "moist" 9 4.6 94.2
980.4 366.8
"50" 2 "Sv" "shoot" "moist" 10 7.75 96.5
876.25 327
"51" 2 "Sv" "control" "moist" 11 10
127.2 1209.6 327.2
"52" 2 "Sv" "shoot" "moist" 12 7.4 83.4
818.6 314
"53" 2 "Sv" "shoot" "moist" 13 6.8 83.8
812.4 283.6
"54" 2 "Sv" "xfull" "moist" 14 3.8 29.8
325 183.4
"55" 2 "Sv" "root" "moist" 15 4.6 72.2
734.8 378
"56" 2 "Sv" "xfull" "moist" 16 2.6 24.4
282 189
"57" 2 "Sv" "control" "moist" 17 8 124.6
1246.8 371.4
"58" 2 "Sv" "control" "moist" 18 4.4
84.4 1061.4 377.2
"59" 2 "Sv" "xfull" "moist" 19 4.2 29
353.8 193.4
"60" 2 "Sv" "shoot" "moist" 20 5.6 74.4
743.2 378.8
"61" 2 "Sv" "root" "awater-logged" 21
6.6 93.6 912.4 351.6
"62" 2 "Sv" "shoot" "awater-logged" 22 4
62 714.8 401
"63" 2 "Sv" "control" "awater-logged" 23
5 82 881.6 323.2
"64" 2 "Sv" "control" "awater-logged" 24
5.6 110.8 1264.8 424.8
"65" 2 "Sv" "control" "awater-logged" 25
5.8 89.6 930.8 346.2
"66" 2 "Sv" "xfull" "awater-logged" 26 4
39.6 455.2 268.8
"67" 2 "Sv" "shoot" "awater-logged" 27
3.4 55.4 614.6 384.2
"68" 2 "Sv" "shoot" "awater-logged" 28
5.4 71 698 320.6
"69" 2 "Sv" "root" "awater-logged" 29 3
66.4 757.4 427.8
"70" 2 "Sv" "control" "awater-logged" 30
4.8 83 990.4 413.4
"71" 2 "Sv" "xfull" "awater-logged" 31
3.2 23.2 300.6 238.8
"72" 2 "Sv" "xfull" "awater-logged" 32
1.4 24.6 210.8 192.8
"73" 2 "Sv" "xfull" "awater-logged" 33
3.2 28.6 344.8 185.8
"74" 2 "Sv" "shoot" "awater-logged" 34
3.6 59.6 631 402
"75" 2 "Sv" "root" "awater-logged" 35
5.2 86.4 826.4 289.8
"76" 2 "Sv" "root" "awater-logged" 36
7.2 87.4 918.8 351
"77" 2 "Sv" "root" "awater-logged" 37
4.2 84.8 840 422
"78" 2 "Sv" "xfull" "awater-logged" 38
2.4 29.8 355.6 239.6
"79" 2 "Sv" "shoot" "awater-logged" 39
6.2 71.2 683.8 282
"80" 2 "Sv" "control" "awater-logged" 40
5.4 106.4 1083.6 388.6
"813" 3 "Sv" "control" "moist" 1 5.2
149.6 1863.8 682
"823" 3 "Sv" "xfull" "moist" 2 2.5 42.25
427.5 344.5
"833" 3 "Sv" "control" "moist" 3 4.2 134
1496.2 572
"843" 3 "Sv" "root" "moist" 4 3.6 121
1488.8 706.8
"853" 3 "Sv" "root" "moist" 5 4 115
1340.2 587.2
"863" 3 "Sv" "shoot" "moist" 6 2.6 80
976 613.2
"873" 3 "Sv" "root" "moist" 7 3.6 94.4
1187.2 555
"883" 3 "Sv" "xfull" "moist" 8 3.5 41.75
367 195.5
"893" 3 "Sv" "root" "moist" 9 3.6 120.2
1450.4 630.6
"903" 3 "Sv" "shoot" "moist" 10 2.6 85
1007.2 586
"913" 3 "Sv" "control" "moist" 11 4
118.8 1386 626.6
"923" 3 "Sv" "shoot" "moist" 12 2.2 72.4
942.6 578.4
"933" 3 "Sv" "shoot" "moist" 13 2.2 80.6
957.6 606
"943" 3 "Sv" "xfull" "moist" 14 1.25 27
308 297
"953" 3 "Sv" "root" "moist" 15 2.6 85.8
1080.2 676.8
"963" 3 "Sv" "xfull" "moist" 16
1.666666667 41 475.6666667 374
"973" 3 "Sv" "control" "moist" 17 4.4
148 1795.6 681.8
"983" 3 "Sv" "control" "moist" 18 3.4
107.8 1484.4 653.6
"993" 3 "Sv" "xfull" "moist" 19 2.4 49.8
450.6 326.2
"1003" 3 "Sv" "shoot" "moist" 20 2.8
73.6 896.2 663.8
"1013" 3 "Sv" "root" "awater-logged" 21
4.8 119 1431.6 585
"1023" 3 "Sv" "shoot" "awater-logged" 22
1.8 61.2 896.8 654
"1033" 3 "Sv" "control" "awater-logged"
23 4.6 123.8 1471.6 552
"1043" 3 "Sv" "control" "awater-logged"
24 5 144 1906.6 734.2
"1053" 3 "Sv" "control" "awater-logged"
25 3.4 107.8 1388.4 639
"1063" 3 "Sv" "xfull" "awater-logged" 26
1.8 53.2 586.8 439.4
"1073" 3 "Sv" "shoot" "awater-logged" 27
1.8 68.4 910.6 704.4
"1083" 3 "Sv" "shoot" "awater-logged" 28
3.4 88.2 1092 615
"1093" 3 "Sv" "root" "awater-logged" 29
2.8 101.2 1342.8 740.4
"1103" 3 "Sv" "control" "awater-logged"
30 4 125.4 1556.6 769.6
"1113" 3 "Sv" "xfull" "awater-logged" 31
2 52.2 534.8 451
"1123" 3 "Sv" "xfull" "awater-logged" 32
1.8 40.4 428.6 375.6
"1133" 3 "Sv" "xfull" "awater-logged" 33
2 41.2 420.6 295.6
"1143" 3 "Sv" "shoot" "awater-logged" 34
1.8 74.6 978.8 760.6
"1153" 3 "Sv" "root" "awater-logged" 35
4 110.8 1262.8 494.4
"1163" 3 "Sv" "root" "awater-logged" 36
6.4 129.2 1518.8 590.4
"1173" 3 "Sv" "root" "awater-logged" 37
4.6 124.6 1389.8 746
"1183" 3 "Sv" "xfull" "awater-logged" 38
2 39 472.6 398.4
"1193" 3 "Sv" "shoot" "awater-logged" 39
1.6 59.8 809.4 576.4
"1203" 3 "Sv" "control" "awater-logged"
40 4.4 134.6 1622.6 664.4
"413" 1 "St" "root" "moist" 41 4.6 17.6
83 35.2
"423" 1 "St" "xfull" "moist" 42 3 4.6
29.6 15.6
"433" 1 "St" "root" "moist" 43
5.333333333 26.33333333 110.3333333 52.33333333
"443" 1 "St" "control" "moist" 44 8 38
187 63.4
"453" 1 "St" "control" "moist" 45 5.6
23.8 96.4 38.8
"463" 1 "St" "root" "moist" 46 7.5 18.75
92.25 33
"473" 1 "St" "xfull" "moist" 47
6.333333333 8 73 23
"483" 1 "St" "shoot" "moist" 48 6.4 20.6
93.4 22.4
"493" 1 "St" "xfull" "moist" 49 6 2.6 63
15
"503" 1 "St" "xfull" "moist" 50 5.4 2.8
56.4 21.2
"513" 1 "St" "shoot" "moist" 51 8
24.33333333 117 42.33333333
"523" 1 "St" "shoot" "moist" 52 7 13.4
80 25.8
"533" 1 "St" "root" "moist" 53 4.5 16
66.25 31
"543" 1 "St" "control" "moist" 54 6.8
19.4 83.8 32.6
"553" 1 "St" "control" "moist" 55 9.25
36.75 158.5 34.25
"563" 1 "St" "control" "moist" 56 5.2
18.2 97.6 39
"573" 1 "St" "shoot" "moist" 57 6.25
12.75 55.75 25
"583" 1 "St" "shoot" "moist" 58
6.333333333 30.66666667 131.3333333 39
"593" 1 "St" "xfull" "moist" 59 5.8 7.8
69.2 28.6
"603" 1 "St" "root" "moist" 60 5 19.8 84
27.6
"613" 1 "St" "xfull" "awater-logged" 61
6.2 3.2 73.4 21
"623" 1 "St" "control" "awater-logged"
62 7.2 15 89.2 32
"633" 1 "St" "shoot" "awater-logged" 63
6.5 15.25 85.25 35
"643" 1 "St" "root" "awater-logged" 64
4.666666667 18.66666667 99 40.33333333
"653" 1 "St" "control" "awater-logged"
65 5.8 16.8 75.8 26.2
"663" 1 "St" "xfull" "awater-logged" 66
5.666666667 4 62.33333333 28.33333333
"673" 1 "St" "control" "awater-logged"
67 9 33.25 120 37
"683" 1 "St" "root" "awater-logged" 68 6
16 70 24.25
"693" 1 "St" "shoot" "awater-logged" 69
7 15.4 71.6 31.4
"703" 1 "St" "xfull" "awater-logged" 70
5.2 1.2 57.4 23.6
"713" 1 "St" "control" "awater-logged"
71 7.25 23.5 114 33
"723" 1 "St" "shoot" "awater-logged" 72
6.75 30.5 125 40.75
"733" 1 "St" "shoot" "awater-logged" 73
7.25 13.75 81.5 29.5
"743" 1 "St" "root" "awater-logged" 74
8.2 18.2 89.8 35.6
"753" 1 "St" "shoot" "awater-logged" 75
5.6 15.8 69.6 29.4
"763" 1 "St" "control" "awater-logged"
76 7.4 27.8 100.2 28.8
"773" 1 "St" "root" "awater-logged" 77
6.4 15.4 79.2 36
"783" 1 "St" "xfull" "awater-logged" 78
6.2 0.6 42.6 13.4
"793" 1 "St" "xfull" "awater-logged" 79
3.8 3.8 46.4 22.6
"803" 1 "St" "root" "awater-logged" 80
5.2 26 92.4 25.6
"411" 2 "St" "root" "moist" 41 3 45.6
658.4 364.8
"421" 2 "St" "xfull" "moist" 42 3.4 9.2
130 93.2
"431" 2 "St" "root" "moist" 43 3.25 36
520.75 382.25
"441" 2 "St" "control" "moist" 44 5.6
68.2 966.2 456.4
"451" 2 "St" "control" "moist" 45 4.8
60.4 765.4 347.8
"461" 2 "St" "root" "moist" 46 6.8 57.2
631.4 282.8
"471" 2 "St" "xfull" "moist" 47 4.8 10
133.8 50.8
"481" 2 "St" "shoot" "moist" 48 6.6 61.2
547.4 233.6
"491" 2 "St" "xfull" "moist" 49 7.6 24.6
241.2 88
"501" 2 "St" "xfull" "moist" 50 5.4 19.4
138.2 43
"511" 2 "St" "shoot" "moist" 51 5 42.4
353.8 188
"521" 2 "St" "shoot" "moist" 52 4.6 39.2
417 256
"531" 2 "St" "root" "moist" 53 3.75 51
607.75 298.25
"541" 2 "St" "control" "moist" 54 6.2
66.8 771.4 303.4
"551" 2 "St" "control" "moist" 55 7 79
998 398
"561" 2 "St" "control" "moist" 56 4.6
58.8 782.4 365
"571" 2 "St" "shoot" "moist" 57 4.4 37.6
331 143
"581" 2 "St" "shoot" "moist" 58 4.25
44.25 466.5 261.25
"591" 2 "St" "xfull" "moist" 59 6.6 18.8
160.6 64.6
"601" 2 "St" "root" "moist" 60 3.8 49
668.8 311
"611" 2 "St" "xfull" "awater-logged" 61
6 17.8 204.2 96.4
"621" 2 "St" "control" "awater-logged"
62 4.2 56.8 800.4 353.6
"631" 2 "St" "shoot" "awater-logged" 63
3.5 45 534 305
"641" 2 "St" "root" "awater-logged" 64
4.666666667 61.33333333 665.6666667 338.6666667
"651" 2 "St" "control" "awater-logged"
65 4.2 58.8 759 323.2
"661" 2 "St" "xfull" "awater-logged" 66
4.5 14.25 171 97
"671" 2 "St" "control" "awater-logged"
67 5.5 72 851.5 363
"681" 2 "St" "root" "awater-logged" 68
5.75 62.75 616.75 262.25
"691" 2 "St" "shoot" "awater-logged" 69
3.2 41.6 587.8 415.4
"701" 2 "St" "xfull" "awater-logged" 70
3.8 14 141.4 79.8
"711" 2 "St" "control" "awater-logged"
71 4.2 57 774 298.2
"721" 2 "St" "shoot" "awater-logged" 72
3.8 41.4 468.4 227.2
"731" 2 "St" "shoot" "awater-logged" 73
3.75 42.25 492.25 235
"741" 2 "St" "root" "awater-logged" 74
4.4 52.4 691.2 342
"751" 2 "St" "shoot" "awater-logged" 75
2.4 30.6 379.4 294.2
"761" 2 "St" "control" "awater-logged"
76 6.6 80.2 966.6 340.6
"771" 2 "St" "root" "awater-logged" 77
3.4 38 526.8 361.2
"781" 2 "St" "xfull" "awater-logged" 78
4.6 17.4 198.2 107.4
"791" 2 "St" "xfull" "awater-logged" 79
3 14.2 166.6 104.4
"801" 2 "St" "root" "awater-logged" 80
5.4 63.8 636.6 292.6
"412" 3 "St" "root" "moist" 41 2.6 60.6
1161 617.6
"422" 3 "St" "xfull" "moist" 42 3.4 16.8
313.8 250.6
"432" 3 "St" "root" "moist" 43 2.75 46
906 707.25
"442" 3 "St" "control" "moist" 44 3 74.8
1550.4 742.4
"452" 3 "St" "control" "moist" 45 3.8 73
1324.6 627.6
"462" 3 "St" "root" "moist" 46 4.4 62.2
1096 496.4
"472" 3 "St" "xfull" "moist" 47 3.2 13.8
133.6 64.4
"482" 3 "St" "shoot" "moist" 48 3.2 53
776.8 447.2
"492" 3 "St" "xfull" "moist" 49 3.8 21.4
303.4 239.6
"502" 3 "St" "xfull" "moist" 50 7.5
18.75 207.5 58
"512" 3 "St" "shoot" "moist" 51 4.6 56.8
689 421.8
"522" 3 "St" "shoot" "moist" 52 1.6 34.6
640.4 575.8
"532" 3 "St" "root" "moist" 53 3.75 67.5
1164.25 586.75
"542" 3 "St" "control" "moist" 54 3 73.4
1325 617.2
"552" 3 "St" "control" "moist" 55 4.75
99 1730.75 678
"562" 3 "St" "control" "moist" 56 3.6
75.4 1386.6 713.8
"572" 3 "St" "shoot" "moist" 57 2.25 31
463.5 343
"582" 3 "St" "shoot" "moist" 58 2.5 47
799 551.5
"592" 3 "St" "xfull" "moist" 59 5.5 14.5
243 155
"602" 3 "St" "root" "moist" 60 2.8 55.6
1086.6 513
"612" 3 "St" "xfull" "awater-logged" 61
5.4 27 345 220
"622" 3 "St" "control" "awater-logged"
62 4 80.4 1154.4 496.2
"632" 3 "St" "shoot" "awater-logged" 63
2.25 50.5 835.5 425.25
"642" 3 "St" "root" "awater-logged" 64
4.333333333 83.33333333 1354.333333 551.6666667
"652" 3 "St" "control" "awater-logged"
65 4 71.4 1351.4 576.4
"662" 3 "St" "xfull" "awater-logged" 66
3.75 17 224.5 160.25
"672" 3 "St" "control" "awater-logged"
67 4.25 78.5 1268.5 549.75
"682" 3 "St" "root" "awater-logged" 68
5.25 92.75 1189.5 462
"692" 3 "St" "shoot" "awater-logged" 69
2.2 45 865.6 642.8
"702" 3 "St" "xfull" "awater-logged" 70
3.6 22.4 246.2 181.6
"712" 3 "St" "control" "awater-logged"
71 3.8 74.6 1284 545.4
"722" 3 "St" "shoot" "awater-logged" 72
2.2 42.2 647 405.2
"732" 3 "St" "shoot" "awater-logged" 73
2.25 47.25 798.75 491.75
"742" 3 "St" "root" "awater-logged" 74 3
61 1105.8 551.4
"752" 3 "St" "shoot" "awater-logged" 75
1.8 36.6 585.8 534.4
"762" 3 "St" "control" "awater-logged"
76 5.8 98 1633.8 640.4
"772" 3 "St" "root" "awater-logged" 77
3.4 51.6 876.8 572.6
"782" 3 "St" "xfull" "awater-logged" 78
4.8 25.6 295.6 175.6
"792" 3 "St" "xfull" "awater-logged" 79
2.6 21.4 295.2 228.2
"802" 3 "St" "root" "awater-logged" 80 4
72.2 1072.8 576

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