glmulti , lmer fit (linear mixed models) and gls fit models(lme package)

Question

Why does functions from the glmulti R package not work well on lmer fit (linear mixed models) and gls fit models(lme package):

A. To extract model averaged coefficients? Its coef function did not work.

I used the glmulti R package on lmer fit models(i.e.mixed models) and ran model selection. But I failed to do model averaging since the coef function did not work even though I applied the wrapper getfit() function mentioned here glmulti and liner mixed models

B. Its level=2 choice i.e. the part dedicated to include pairwise interactions on glmulti objects? It works sometimes and in another case it fails. For instance I got this error message when it fails. I chose the different methods= "h","g","d" to look at if the failure is linked to computational capacity but none of the choice works. "Error in .jnew("glmulti/ModelGenerator", y, .jarray(xc), .jarray(xq), : java.lang.ArrayIndexOutOfBoundsException: 10 " The other problem on this one is once I received this error message on a new glmulti, those well worked previous works will not work again.

C. How much difference would it cause if I use the model averaging function from MuMIn package and base my inference on its output? My concern comes from the critics given by the authors of the glmulti package on MuMIn package. They said that "*MuMIn can handle formulas to include interactions but it treats interactions as standard variables, which raises several issues" look at on page 4 the second last paragraph http://www.jstatsoft.org/v34/i12/paper .

Many thanks for your help :)

Thanks Ben for the quick reply and suggestion. Here is my data. Block and Composition are used as random effect factors and the six variables (TShann, Alt, Slope, CPT, MAT and MARF) are used as fixed effect factors (covariates). I want to investigate the main and pairwise interaction effects of these six variables on Yield.

Blocks  TShann  Alt Slope   CPT MAT MARF    PlotID  Layer   Composition Yeild
Block1  1.82    87  1   98.65   2.6 625 B1P1    0-10cm  Pa,Ps   37.42
Block1  1.77    138 1   25.71   2.4 638 B1P2    0-10cm  Bp,Pa   42.47
Block1  1.57    139 1   16.5    2.4 638 B1P3    0-10cm  Bp,Pa   54.87
Block1  1.93    138 1   63.3    2.5 637 B1P4    0-10cm  Bp,Pa   51.93
Block1  1.89    114 2   75.11   2.6 631 B1P5    0-10cm  Bp,Ps   27.27
Block1  1.04    112 1   99.39   2.5 631 B1P6    0-10cm  Pa  47.66
Block1  1.02    120 1   0.31    2.3 625 B1P7    0-10cm  Bp  47.62
Block1  1.06    120 1   0.98    2.3 624 B1P8    0-10cm  Bp  41.31
Block1  1.09    119 1   99.08   2.2 623 B1P9    0-10cm  Ps  39.69
Block1  1.07    134 1   98.77   2.1 624 B1P10   0-10cm  Pa  46.55
Block1  1.12    124 2   2.48    2.2 623 B1P11   0-10cm  Bp  40.55
Block1  2.45    233 1   74.2    1.4 639 B1P12   0-10cm  Bp,Pa,Ps    40.28
Block1  2   219 2   79.15   1.4 639 B1P13   0-10cm  Bp,Ps   25.31
Block1  1   101 1   100 1.8 622 B1P14   0-10cm  Ps  22.72
Block1  1.8 97  1   76.35   1.9 622 B1P15   0-10cm  Bp,Ps   28.54
Block1  1.16    143 1   97.95   1.8 634 B1P16   0-10cm  Ps  22.4
Block1  1.73    139 2   100 1.8 633 B1P17   0-10cm  Pa,Ps   24.26
Block1  1.05    110 1   99.19   2   633 B1P18   0-10cm  Pa  33.76
Block1  2.03    130 2   99.75   2.1 634 B1P19   0-10cm  Pa,Ps   36.86
Block1  1.57    119 1   83.18   2.2 628 B1P20   0-10cm  Bp,Pa   42.5
Block1  1.05    135 2   100 2   637 B1P21   0-10cm  Ps  22.44
Block1  1.99    126 1   100 2.1 635 B1P22   0-10cm  Pa,Ps   39.58
Block1  1.18    122 1   100 2.1 634 B1P23   0-10cm  Pa  37.67
Block1  1.9 151 2   74  1.9 637 B1P24   0-10cm  Bp,Pa   49.77
Block1  2.55    136 1   86.87   2.1 635 B1P25   0-10cm  Bp,Pa,Ps    38.21
Block1  2.97    108 1   70.06   2.1 636 B1P26   0-10cm  Bp,Pa,Ps    31.7
Block1  2.31    119 1   91.18   2.5 636 B1P27   0-10cm  Pa,Ps   36.8
Block1  2.13    111 2   51.16   2.5 636 B1P28   0-10cm  Bp,Pa   45.83
Block1  1   422.8   2   0   7.3 711 B2P1    0-10cm  Fs  37.59
Block2  1   389.93  1   0   7.4 697 B2P2    0-10cm  Fs  35.08
Block2  1.68    323.1   1   2.96    7.8 636 B2P3    0-10cm  Ap,Fe   40.07
Block2  1.43    272.7   1   0   7.9 631 B2P4    0-10cm  Fe  38.47
Block2  1.19    337.04  1   0   7.8 637 B2P5    0-10cm  Qp  34.49
Block2  2   284 1   0   7.8 638 B2P6    0-10cm  Fs,Qp   30.55
Block2  1.3 479.9   1   92.69   6.9 755 B2P7    0-10cm  Pa  60.06
Block2  1.27    328.52  1   94.19   7.8 643 B2P8    0-10cm  Pa  35.41
Block2  2.86    371.96  1   0   7.4 697 B2P9    0-10cm  Ap,Fe,Fs    33.21
Block2  2.94    381.31  2   0   7.4 697 B2P10   0-10cm  Ap,Fe,Fs    41.88
Block2  2.36    457.82  1   0   7.1 736 B2P11   0-10cm  Fe,Fs   39.86
Block2  2.29    382.73  1   0   7.3 694 B2P12   0-10cm  Fs,Qp   32.56
Block2  2.8 301.09  1   0   8   611 B2P13   0-10cm  Ap,Fe,Qp    33.91
Block2  2.49    323.66  1   63.24   7.8 643 B2P14   0-10cm  Fs,Pa   39.31
Block2  1.84    378.12  2   69.99   7.4 699 B2P15   0-10cm  Fe,Pa   59.51
Block2  2.72    331.15  2   47.28   7.6 661 B2P16   0-10cm  Fs,Pa,Qp    35.54
Block2  1.68    364.72  1   0   7.5 678 B2P17   0-10cm  Ap,Fs   31.34
Block2  2.3 494.38  1   1.86    6.9 765 B2P18   0-10cm  Ap,Fe   42.31
Block2  2.17    407.45  1   0   7.3 694 B2P19   0-10cm  Ap,Fs,Qp    34.71
Block2  2.79    324.78  1   0   7.7 637 B2P20   0-10cm  Fe,Fs,Qp    38.69
Block2  2.91    391.97  1   0   7.3 694 B2P21   0-10cm  Ap,Fe,Fs,Qp 37.87
Block2  2.52    382.84  1   4.5 7.4 691 B2P22   0-10cm  Fe,Fs   31.91
Block2  2.78    378.29  1   26.12   7.5 658 B2P23   0-10cm  Fs,Pa,Qp    36.13
Block2  2.84    418.17  2   0   7.2 737 B2P24   0-10cm  Ap,Fe,Fs    37.06
Block2  2.86    368.38  1   0   7.5 671 B2P25   0-10cm  Ap,Fs,Qp    30.2
Block2  3.03    391.77  2   4.01    7   755 B2P26   0-10cm  Ap,Fe,Fs    81.08
Block2  3.38    469.13  1   0   7   746 B2P27   0-10cm  Ap,Fe,Fs,Qp 43.39
Block2  2   282.63  1   0   8   611 B2P28   0-10cm  Ap,Fe   55.47
Block2  3.15    401.12  2   3.27    7.3 699 B2P29   0-10cm  Fe,Fs,Qp    43.54
Block2  2.31    415.49  3   0   7.2 737 B2P30   0-10cm  Fs,Qp   36.96
Block2  2.87    458.57  1   0   6.9 758 B2P31   0-10cm  Fe,Fs   43.75
Block2  3.54    387.87  1   0   7.1 745 B2P32   0-10cm  Ap,Fe,Fs    38.18
Block2  3.81    390.85  1   15.3    7.5 681 B2P33   0-10cm  Ap,Fe,Fs,Pa 56.03
Block2  2.38    353.31  3   13.01   7.4 699 B2P34   0-10cm  Fe,Fs,Pa    57.4
Block2  3.07    331.04  1   7.79    7.8 637 B2P35   0-10cm  Fs,Qp   30.48
Block2  2.21    305.31  1   24.12   7.7 641 B2P36   0-10cm  Fe,Pa   63.12
Block2  4.4 430.02  2   4.04    7.2 713 B2P37   0-10cm  Ap,Fe,Fs,Qp 52.17
Block2  3.07    495.57  1   0.82    6.9 765 B2P38   0-10cm  Ap,Fe,Fs    38.47
Block3  2.06    443 2   0   7   581 B3P1    0-10cm  Qc,Qp   23.8
Block3  3.95    470 2   0   13.6    794 B3P2    0-10cm  Oc,Qc,Qi,Qp 39.86
Block3  1.5 416 2   0   13.4    819 B3P3    0-10cm  Oc,Qi   46.73
Block3  1.46    397 2   0   13.6    794 B3P4    0-10cm  Qp  25.5
Block3  3.3 422 2   0   13.6    794 B3P5    0-10cm  Oc,Qi,Qp    38.88
Block3  1   393 1   0   13.7    792 B3P6    0-10cm  Qi  35.99
Block3  1   402 3   0   13.2    728 B3P7    0-10cm  Cs  23.22
Block3  1.8 383 3   0   13.2    747 B3P8    0-10cm  Oc,Qi   49.01
Block3  3   429 2   0   13.4    700 B3P9    0-10cm  Oc,Qc,Qi    30.94
Block3  2.77    438 2   0   13  697 B3P10   0-10cm  Cs,Qi,Qp    47.88
Block3  3.35    379 2   0   14  709 B3P11   0-10cm  Cs,Oc,Qi,Qp 27.39
Block3  1.03    445 2   0   13  695 B3P12   0-10cm  Cs  43.31
Block3  2.15    479 2   0   13  695 B3P13   0-10cm  Cs,Qc   50.85
Block3  2.9 444 2   0   13.5    699 B3P14   0-10cm  Cs,Qc,Qi    47.67
Block3  1   388 1   0   13.5    699 B3P15   0-10cm  Qc  44.33
Block3  1.11    417 2   0   13.4    698 B3P16   0-10cm  Qi  37.9
Block3  2.37    395 2   0   13.6    794 B3P17   0-10cm  Qi,Qp   30.19
Block3  3.85    425 2   0   13.6    794 B3P18   0-10cm  OC,Qc,Qi,Qp 40.14
Block3  2.02    478 2   0   13.3    793 B3P19   0-10cm  Oc,Qc   41.85
Block3  2.55    508 2   0   13.3    792 B3P20   0-10cm  Qc,Qi,Qp    30.98
Block3  1.94    464 2   0   13.4    700 B3P21   0-10cm  Cs,Qi   77.66
Block3  3.66    410 3   0   13.7    707 B3P22   0-10cm  Cs,Oc,Qc,Qi 41.56
Block3  3.43    523 2   0   12.8    691 B3P23   0-10cm  Cs,Qc,Qi,Qp 39.08
Block3  1.86    416 2   0   13.2    694 B3P24   0-10cm  Qc,Qi   43.99
Block3  2.45    355 2   0   13.4    700 B3P25   0-10cm  Cs,OC,Qi    38.63
Block3  2.94    406 1   0   13.2    728 B3P26   0-10cm  Cs,Qc,Qp    40.76
Block3  1.28    421 2   0   13.2    728 B3P27   0-10cm  Qp  40.24
Block3  1.95    418 3   0   13.2    728 B3P28   0-10cm  Cs,Qp   26.31
Block3  2.52    471 2   0   13.6    794 B3P29   0-10cm  Oc,Qc,Qp    40.11
Block3  2.34    389 2   0   13.3    720 B3P30   0-10cm  Cs,Oc   28.59
Block3  1.33    269 2   0   13.9    721 B3P31   0-10cm  Oc  39.22
Block3  3.57    429 2   0   12.4    687 B3P32   0-10cm  Cs,Oc,Qc,Qi,    34.04
Block3  3.74    519 2   0   12.4    687 B3P33   0-10cm  Cs,Qc,Qi,Qp 42.68
Block3  4.74    480 3   0   12.4    687 B3P34   0-10cm  Cs,Oc,Qc,Qp,Qi  40.75
Block3  1   254 2   0   14.1    731 B3P35   0-10cm  Qc  36.14
Block3  2.47    436 2   0   13.2    728 B3P36   0-10cm  Cs,Qc,Qp    28.27
Block4  1.12    182 1   97.71   7   581 B4P1    0-10cm  Pa  41.27
Block4  1.5 157 1   4.37    6.9 585 B4P2    0-10cm  Cb  24.79
Block4  1.13    163 1   97.37   6.9 580 B4P3    0-10cm  Pa  29.14
Block4  3.66    171 1   26.56   6.8 582 B4P4    0-10cm  Bp,Pa,Qr    27.01
Block4  2   176 1   0   6.9 576 B4P5    0-10cm  Cb,Qr   23.39
Block4  3.1 190 1   42.44   6.8 585 B4P6    0-10cm  Bp,Cb,Pa    29.98
Block4  3.8 190 1   35.89   6.8 585 B4P7    0-10cm  Bp,Cb,Pa,Qr 32.7
Block4  2   180 1   0   6.8 585 B4P8    0-10cm  Bp,Cb   23.3
Block4  2.18    195 1   64.67   6.8 584 B4P9    0-10cm  Cb,Pa   27.27
Block4  1.74    145 1   2.92    6.8 582 B4P10   0-10cm  Cb,Qr   28.13
Block4  1.75    185 1   0   6.8 581 B4P11   0-10cm  Bp,Cb   24.78
Block4  1.23    160 1   5.27    6.8 583 B4P12   0-10cm  Cb  23.16
Block4  2.94    160 1   0   6.9 578 B4P13   0-10cm  Bp,Cb,Qr    26.84
Block4  3.65    150 1   70.67   6.9 578 B4P14   0-10cm  Cb,Pa,Ps,Qr 40.99
Block4  2.95    184 1   33.63   6.8 583 B4P15   0-10cm  Cb,Pa,Qr    40.3
Block4  2.35    186 1   45.55   6.8 583 B4P16   0-10cm  Pa,Qr   52.01
Block4  3.95    155 1   57.64   6.9 586 B4P17   0-10cm  Bp,Cb,Ps,Pa 59.3
Block4  3.23    160 1   46.08   6.9 581 B4P18   0-10cm  Cb,Ps,Qr    21.05
Block4  2.16    175 1   97.97   6.9 582 B4P19   0-10cm  Pa,Ps   26.99
Block4  1.73    173 1   1.72    7   576 B4P20   0-10cm  Cb,Qr   36.26
Block4  1.41    170 1   91.64   6.9 577 B4P21   0-10cm  Ps  36.91
Block4  3.34    160 1   71.93   6.9 581 B4P22   0-10cm  Pa,Ps,Qr    30.89
Block4  2.89    170 1   78.58   6.9 582 B4P23   0-10cm  Cb,Pa,Ps,   23.62
Block4  3.54    170 1   31.2    6.9 581 B4P24   0-10cm  Cb,Ps,Qr    29.85
Block4  2.13    171 1   63.18   6.9 585 B4P25   0-10cm  Cb,Ps   33.64
Block4  2.04    165 1   2.58    6.9 582 B4P26   0-10cm  Bp,Cb   36.12
Block4  3.74    175 1   51.14   6.8 581 B4P27   0-10cm  Cb,Pa,Ps,Qr 27.97
Block4  2.29    170 1   62.65   6.8 585 B4P28   0-10cm  Bp,Pa   28.34
Block4  3.55    155 1   53.48   6.8 582 B4P29   0-10cm  Bp,Ps,Qr    26.97
Block4  3.8 140 1   62.64   6.9 576 B4P30   0-10cm  Bp,Cb,Ps,Pa 33.39
Block4  3.68    150 1   27.62   6.9 578 B4P31   0-10cm  Bp,Cb,Pa,Qr 31.3
Block4  4.58    177 1   46.72   6.8 584 B4P32   0-10cm  Bp,Pa,Ps,Qr 42.21
Block4  3.4 184 1   52.43   6.9 582 B4P33   0-10cm  Bp,Cb,Ps    38.73
Block4  3.89    189 1   17.97   7   581 B4P34   0-10cm  Bp,Cb,Ps,Qr 24.84
Block4  4.8 188 1   46.77   6.8 582 B4P35   0-10cm  Bp,Cb,Pa,Ps,Qr  30.23
Block4  3.41    160 1   9.58    6.9 578 B4P36   0-10cm  Bp,Cb,Qr    22.46
Block4  4.62    145 1   57.41   6.9 578 B4P37   0-10cm  Bp,Cb,Pa,Ps,Qr  41.43
Block4  2.53    165 1   66.22   7   573 B4P38   0-10cm  Bp,Cb,Ps    26.37
Block4  4.2 170 1   22.62   7   572 B4P39   0-10cm  Bp,Cb,Ps,Qr 35.88
Block4  1.47    175 1   89.39   6.9 580 B4P40   0-10cm  Ps  28.98
Block4  3.7 200 1   34.21   6.7 585 B4P41   0-10cm  Bp,Pa,Ps,Qr 24.59
Block4  3.97    177 1   53.75   6.8 582 B4P42   0-10cm  Bp,Cb,Pa,Ps,    29.49
Block4  3.28    186 1   74.3    7   570 B4P43   0-10cm  Pa,Ps,Qr    23.52
Block5  1.17    838 2   98.88   5.8 675 B5P1    0-10cm  Pa  44.37
Block5  1   865 2   100 5.8 675 B5P2    0-10cm  Pa  44.63
Block5  3.14    869 2   25.95   5.8 675 B5P3    0-10cm  Ap,Fs,Pa    58.27
Block5  2.08    1019    2   98.23   5.6 687 B5P5    0-10cm  Aa,Pa   36.69
Block5  2.64    1045    2   8.05    5.6 687 B5P6    0-10cm  Ap,Fs   36.08
Block5  1.12    1062    2   97.53   5.2 709 B5P7    0-10cm  Aa  39.41
Block5  3.67    1028    2   40.83   5.4 701 B5P8    0-10cm  Aa,Ap,Fs,Pa 35.27
Block5  2.37    984 2   45.68   5.4 701 B5P9    0-10cm  Fs,Pa   45.6
Block5  3.13    968 2   78.33   5.4 701 B5P10   0-10cm  Aa,Ap,Pa    42.73
Block5  3.08    805 2   69.69   5.8 678 B5P11   0-10cm  Aa,Fs,Pa,   44.43
Block5  2   799 2   48.01   5.7 681 B5P12   0-10cm  Fs,Pa   36.94
Block5  1   812 2   0   5.7 681 B5P13   0-10cm  Fs  27.82
Block5  1.93    909 2   0   5.2 709 B5P14   0-10cm  Ap,Fs   38.01
Block5  1.34    930 3   6.81    5.2 709 B5P15   0-10cm  Ap  73.38
Block5  1.4 972 2   3.26    5.2 709 B5P16   0-10cm  Ap  35.49
Block5  1.96    1047    2   97.16   4.6 742 B5P17   0-10cm  Aa,Pa   43.19
Block5  2.97    1012    2   72.72   4.6 742 B5P18   0-10cm  Aa,Fs,Pa,   39.22
Block5  2.18    951 2   30.92   5.7 681 B5P19   0-10cm  Aa,Fs   31.47
Block5  2.94    869 2   26.36   5.7 681 B5P20   0-10cm  Aa,Ap,Fs    31.62
Block5  2.94    718 2   18.25   5.7 681 B5P21   0-10cm  Ap,Fs,Pa    38.54
Block5  2.89    843 2   75.15   6.2 655 B5P22   0-10cm  Aa,Fs,Pa    34.27
Block5  1.06    894 2   98.99   5.6 688 B5P23   0-10cm  Aa  33.8
Block5  1.96    919 2   59.5    5.6 688 B5P24   0-10cm  Aa,Fs   32.04
Block5  3.12    1030    2   18.55   4.6 742 B5P25   0-10cm  Aa,Ap,Fs    39.01
Block5  1.14    782 2   2.49    5.9 671 B5P26   0-10cm  Fs  37.58
Block5  2.77    738 2   42.01   6.3 652 B5P27   0-10cm  Ap,Pa   55.18
Block5  2.21    655 1   78.03   6.5 643 B5P28   0-10cm  Aa,Fs   44
Block5  3.9 893 2   43.94   5.2 708 B5P29   0-10cm  Aa,Ap,Fs,Pa 50.26
Block6  2.34    1224    2   61.84   9.7 545 B6P1    0-10cm  Ps,Qf   74.58
Block6  3.09    1238    1   28.63   9.7 545 B6P2    0-10cm  Pn,Ps,Qf    73.84
Block6  1.86    1228    2   31.43   9.7 549 B6P3    0-10cm  Pn,Qf   86.92
Block6  1.85    1286    1   30.8    9.7 549 B6P4    0-10cm  Ps,Qf   40.69
Block6  1.83    1283    1   70.89   9.7 549 B6P5    0-10cm  Ps,Qf   67.12
Block6  1.93    1306    2   36.77   9.7 549 B6P6    0-10cm  Pn,Qf   70.71
Block6  2.37    1291    2   10.51   9.7 548 B6P7    0-10cm  Pn,Ps   64.21
Block6  2   1207    2   49.13   9.6 553 B6P8    0-10cm  Pn,Qf   68.93
Block6  1   1211    2   100 9.6 553 B6P9    0-10cm  Qf  38.62
Block6  1   1270    2   100 9.6 553 B6P10   0-10cm  Qf  56.26
Block6  1   1187    2   100 9.9 537 B6P11   0-10cm  Qf  47.39
Block6  1   1073    2   0   10  526 B6P12   0-10cm  Pn  82.37
Block6  2.84    1010    2   73.39   10.8    491 B6P13   0-10cm  Pn,Qf,Qi    98.04
Block6  2.17    999 2   33.5    10.8    491 B6P14   0-10cm  Pn,Qi   84.62
Block6  1.1 980 2   1.87    10.8    491 B6P15   0-10cm  Pn  33.39
Block6  2.12    1032    2   32.46   10.8    491 B6P16   0-10cm  Pn,Qi   68.97
Block6  1.02    960 1   0.34    10.8    491 B6P17   0-10cm  Pn  83.84
Block6  1   1403    1   0   9.1 573 B6P18   0-10cm  Ps  46.3
Block6  1   1310    1   0   9.2 566 B6P19   0-10cm  Ps  93.55
Block6  1   1311    1   0   9.1 569 B6P20   0-10cm  Ps  95.7
Block6  1.98    1404    1   0   9   572 B6P21   0-10cm  Pn,Ps   60.85
Block6  1.99    1325    1   0   9   570 B6P22   0-10cm  Pn,Ps   75.42
Block6  2.32    1388    2   5.1 9.1 569 B6P23   0-10cm  Pn,Ps   61.78
Block6  3.87    1377    1   45.55   9.1 557 B6P24   0-10cm  Pn,Ps,Qf,Qi 82.94
Block6  3.58    1314    2   28.88   9.1 557 B6P25   0-10cm  Pn,Ps,Qf    94.59
Block6  3.87    1387    2   47.63   9.1 557 B6P26   0-10cm  Pn,Ps,Qf,Qi 92.18
Block6  2.98    1322    1   61.02   9.3 551 B6P27   0-10cm  Pn,Qf,Qi    73.52
Block6  1.75    1360    1   100 9.4 541 B6P28   0-10cm  Qf,Qi   47.47
Block6  3.44    1354    2   25.76   9.4 541 B6P29   0-10cm  Pn,Ps,Qf,Qi 30.52
Block6  1.97    1350    1   100 9.4 541 B6P30   0-10cm  Qf,Qi   37.82
Block6  1.85    1342    1   100 9.3 545 B6P31   0-10cm  Qf,Qi   30.81
Block6  1   1236    2   100 10.3    504 B6P32   0-10cm  Qi  64.2
Block6  1   1251    2   100 10.3    504 B6P33   0-10cm  Qi  60.76
Block6  1.59    1250    2   100 10.7    484 B6P34   0-10cm  Qf,Qi   30.09
Block6  2.57    1267    2   49.04   9.9 525 B6P35   0-10cm  Pn,Qi   38.79
Block6  1.99    1211    2   44.14   10.2    511 B6P36   0-10cm  Pn,Qi   60.9

Answer 1

This works for me with sessionInfo() as follows:

R Under development (unstable) (2014-09-17 r66626)
Platform: i686-pc-linux-gnu (32-bit)

other attached packages:
[1] glmulti_1.0.7 rJava_0.9-6   lme4_1.1-8    Rcpp_0.11.2   Matrix_1.1-4 

loaded via a namespace (and not attached):
[1] compiler_3.2.0  grid_3.2.0      lattice_0.20-29 MASS_7.3-34    
[5] minqa_1.2.3     nlme_3.1-117    nloptr_1.0.4    splines_3.2.0  
[9] tools_3.2.0  

With the following code:

library("lme4")
library("glmulti")
dd <- read.table("SO_glmulti.dat",header=TRUE)
m1 <- lmer(Yeild~ (TShann+Alt+Slope+CPT+MAT+MARF)^2+
               (1|Blocks)+(1|Composition),
           data=dd)

Note I get a warning about predictor scaling here -- probably harmless

From previous SO question:

setMethod('getfit', 'merMod', function(object, ...) {
    summ <- coef(summary(object))
    summ1 <- summ[,1:2,drop=FALSE]
    ## if (length(dimnames(summ)[[1]])==1) {
    ##     summ1 <- matrix(summ1, nr=1,
    ##                     dimnames=list(c("(Intercept)"),
    ##                     c("Estimate","Std. Error")))
    ## }
    cbind(summ1, df=rep(10000,length(fixef(object))))
})

This is the old version of glmulti -- quick and dirty but depends on deparsing the formula.

lmer.glmulti<-function(formula,data,random="",...) {
    lmer(paste(deparse(formula),random),data=data,
         REML=FALSE,...)
}

Harder to grok but more robust:

lmer.glmulti<-function(formula,data,random="",...) {
    newf <- formula
    newf[[3]] <- substitute(f+r,
                            list(f=newf[[3]],
                                 r=reformulate(random)[[2]]))
    lmer(newf,data=data,
         REML=FALSE,...)
}

This is what I ended up with:

glmulti_lmm <- glmulti(formula(m1,fixed.only=TRUE),
                     random="+(1|Blocks)+(1|Composition)",
                       data=dd,method="g",
                       deltaM=0.5, 
                       fitfunc=lmer.glmulti,
                       intercept=TRUE,marginality=FALSE,level=2)

I initially tried the default method="h", gave up after 2650 models. My first run with method="g" got to a fairly stable IC after 50 generations, but the mean IC kept going down slowly, so I got impatient and boosted deltaM to 0.5.

For the first run I got IC=1651.69761603866 with the model Yeild~1+CPT+CPT:TShann+CPT:Alt+MAT:Alt+MARF:CPT

On the second run (with deltaM increased), I got a little bit luckier (IC=1649.61044009369, Yeild~1+TShann+CPT+CPT:Alt+MAT:CPT+MARF:CPT). (I don't know whether there's a way to set seed/ensure reproducibility with glmulti). The model claimed to converge after 120 generations.

coef(glmulti_lmm) worked fine for me. The bottom of the output (highest-weighted variables) were:

                  Estimate Uncond. variance Nb models   Importance
[... skip ...]
CPT:MARF      1.334119e-03     5.491836e-07        11 0.7875438701
CPT:MAT       4.051261e-02     5.215084e-04        18 0.7995790960
TShann        1.260082e+00     1.650145e+00        35 0.8111493166
CPT          -9.923303e-01     2.764638e-01        74 0.9600979205
Alt:CPT      -2.465917e-04     7.937155e-09        72 0.9765910742
(Intercept)   3.754893e+01     5.988814e+01       100 1.0000000000

By the way, you might be interested in "Ecologists overestimate the importance of predictor variables in model averaging: a plea for cautious interpretations", Galipaud et al. http://dx.doi.org/10.1111/2041-210X.12251