[R] Improper coding for an offset in vglm()?
Christopher R. Dolanc
crdolanc at ucdavis.edu
Tue Jun 5 20:08:04 CEST 2012
Hello R-help.
I believe I may be coding the offset incorrectly in my formula. I am
testing significance between different group pairings using the VGAM
package. My data are zero-truncated and poisson-distributed and
overdispersed, so I'm using the posnegbinomial function in vglm (code
below). I've spent a very long time working out this model and am pretty
sure it's the best for my data, but I have several examples of groups
with very similar means that come out significant. I'm looking at
differences in density between 2 data sources (see attached file), but
the plot size varies between the 2, so I am using plot "Area" as an
offset and running tests on "Stems". I've attached a sample where the
means for density are 26.4 vs. 25.2 with clearly overlapping error bars,
yet the test comes out significant. (A Wilcoxan test on density also
comes out significant.) Just to check, I did a t-test on density, which
was non-significant, and a t-test on Stems, which WAS significant. This
leads me to believe that my vglm model is not accounting for the area
offset (and thus density) and is just running the model straight on
"Stems". Here's the code:
vglm(Stems~Data + offset(log(Area)), family=posnegbinomial, data=...)
I've tried changing the family to "pospoisson" and it makes no
difference. I've also tried taking out the log part of the offset, just
to see what would happen, but couldn't get the model to run. I'm
currently working with R 2.14.1.
I'd love any ideas you may have on possible solutions.
Chris
--
Christopher R. Dolanc
Post-doctoral Researcher
University of Montana and UC-Davis
-------------- next part --------------
Data Plot Stems Area Density
FIA 8.87E+12 1 665.0103 15.03736
FIA 2.51E+13 2 672.45 29.74199
FIA 8.94E+12 3 619.9869 48.38812
FIA 2.38E+13 1 601.4576 16.62628
FIA 1.31E+13 2 634.6976 31.51107
FIA 2.30E+13 1 659.3915 15.1655
FIA 2.99E+13 2 634.6976 31.51107
FIA 2.40E+13 1 659.3915 15.1655
FIA 8.87E+12 1 665.0103 15.03736
FIA 2.40E+13 1 665.0103 15.03736
FIA 2.51E+13 1 666.8388 14.99613
FIA 2.30E+13 1 601.4576 16.62628
FIA 2.36E+13 1 599.0423 16.69331
FIA 8.94E+12 1 624.3542 16.01655
FIA 2.51E+13 2 672.45 29.74199
FIA 2.94E+13 1 659.3915 15.1655
FIA 2.51E+13 1 666.8388 14.99613
FIA 2.29E+13 1 661.8141 15.10998
FIA 2.51E+13 1 672.45 14.87099
FIA 2.38E+13 1 669.743 14.9311
FIA 2.99E+13 2 672.45 29.74199
FIA 2.42E+13 1 652.3723 15.32867
FIA 2.29E+13 1 634.6976 15.75554
FIA 2.30E+13 1 628.5952 15.90849
FIA 1.31E+13 3 671.2428 44.69321
FIA 2.36E+13 1 671.611 14.88957
FIA 8.94E+12 2 619.9869 32.25875
FIA 1.31E+13 1 634.6976 15.75554
FIA 2.37E+13 1 659.3915 15.1655
FIA 2.38E+13 1 601.4576 16.62628
FIA 2.38E+13 2 670.3084 29.83701
FIA 2.30E+13 1 669.1128 14.94516
FIA 2.37E+13 2 168.1125 118.96795
FIA 1.32E+13 3 644.0903 46.57732
FIA 2.99E+13 1 645.8406 15.4837
FIA 2.37E+13 1 649.2028 15.40351
FIA 2.94E+13 2 659.3915 30.331
FIA 2.30E+13 3 659.3915 45.49649
FIA 8.87E+12 1 669.1128 14.94516
FIA 2.42E+13 1 525.0952 19.04416
FIA 1.31E+13 3 589.2114 50.91551
FIA 8.94E+12 3 624.3542 48.04965
FIA 2.29E+13 1 613.2216 16.30732
FIA 2.43E+13 2 498.7577 40.09963
FIA 1.32E+13 2 659.3915 30.331
FIA 2.43E+13 1 550.8925 18.15236
FIA 1.31E+13 1 613.2216 16.30732
FIA 2.29E+13 1 634.6976 15.75554
FIA 2.37E+13 4 613.2216 65.22927
FIA 2.30E+13 3 661.8141 45.32995
FIA 2.43E+13 2 525.0952 38.08833
FIA 1.31E+13 1 512.3661 19.51729
FIA 8.89E+12 1 463.7586 21.56294
FIA 2.29E+13 1 634.6976 15.75554
FIA 2.50E+13 1 550.8925 18.15236
FIA 8.92E+12 1 672.45 14.87099
FIA 2.38E+13 1 669.1128 14.94516
FIA 1.31E+13 1 634.6976 15.75554
FIA 2.30E+13 4 659.3915 60.66199
FIA 2.40E+13 1 659.3915 15.1655
FIA 2.29E+13 1 667.66 14.97768
FIA 1.32E+13 4 576.6211 69.36964
FIA 2.38E+13 1 576.6211 17.34241
FIA 2.37E+13 1 487.5259 20.51173
FIA 2.43E+13 1 608.5832 16.43161
FIA 2.42E+13 1 525.0952 19.04416
FIA 2.29E+13 1 601.4576 16.62628
FIA 8.94E+12 1 634.6976 15.75554
FIA 1.31E+13 1 589.2114 16.97184
FIA 2.36E+13 1 634.6976 15.75554
FIA 8.94E+12 1 632.6997 15.80529
FIA 2.38E+13 2 589.2114 33.94368
FIA 8.94E+12 1 624.3542 16.01655
VTM 56F54 3 785.2601 38.2039
VTM 56D51 1 793.7091 12.59907
VTM 55E414 4 793.7091 50.3963
VTM 39F41 1 763.985 13.08926
VTM 56F54 1 785.2601 12.73463
VTM 69C119 1 785.2601 12.73463
VTM 69C18 1 785.2601 12.73463
VTM 69C216 2 785.2601 25.46927
VTM 69D29 3 800.4724 37.47787
VTM 68C514 1 709.2333 14.09973
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VTM 3.90E+26 1 800.4724 12.49262
VTM 5.60E+53 1 694.0784 14.40759
VTM 39C12 1 738.1344 13.54767
VTM 3.90E+33 1 793.7091 12.59907
VTM 39D33 2 763.985 26.17852
VTM 40B44 3 808.4177 37.10953
VTM 40B513 1 806.1692 12.40434
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VTM 68C65 1 808.4177 12.36984
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VTM 51F43 1 723.9741 13.81265
VTM 56B43 2 694.0784 28.81519
VTM 56C414 2 808.4177 24.73969
VTM 56D46 1 751.5347 13.30611
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VTM 3.90E+27 2 800.4724 24.98525
VTM 40C64 5 783.3059 63.83202
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VTM 40B58 5 809.0636 61.79984
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VTM 56E512 1 793.7091 12.59907
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VTM 56F42 1 763.985 13.08926
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VTM 68C616 1 723.9741 13.81265
VTM 69C11 3 751.5347 39.91832
VTM 78D510 1 775.291 12.89838
VTM 40A412 3 809.2658 37.07064
VTM 40B67 2 809.4276 24.70882
VTM 89A37 1 803.6619 12.44304
VTM 40C52 2 783.3059 25.53281
VTM 56D49 1 809.4276 12.35441
VTM 39D12 18 783.3059 229.79529
VTM 3.90E+35 5 751.5347 66.53053
VTM 6.90E+212 4 709.2333 56.39893
VTM 38F115 1 738.1344 13.54767
VTM 39F12 5 775.291 64.49191
VTM 39F32 3 808.4177 37.10953
VTM 50A32 2 808.4177 24.73969
VTM 50B44 2 808.4177 24.73969
VTM 50D54 3 805.4106 37.24808
VTM 50D61 1 808.4177 12.36984
VTM 50D62 2 793.7091 25.19815
VTM 50F69 1 763.985 13.08926
VTM 56A11 3 808.4177 37.10953
VTM 56A21 1 775.291 12.89838
VTM 56A32 2 738.1344 27.09534
VTM 56B11 1 763.985 13.08926
VTM 56B22 1 793.7091 12.59907
VTM 56C410 1 751.5347 13.30611
VTM 56E414 2 805.4106 24.83206
VTM 56F54 1 785.2601 12.73463
VTM 68B614 1 808.4177 12.36984
VTM 68B616 3 809.4276 37.06323
VTM 69B112 1 793.7091 12.59907
VTM 69C12 3 763.985 39.26779
VTM 69C216 2 785.2601 25.46927
VTM 69E310 1 751.5347 13.30611
VTM 69F17 3 763.985 39.26779
VTM 69F214 2 808.4177 24.73969
VTM 69F24 3 694.0784 43.22278
VTM 77F113 1 775.291 12.89838
VTM 89A14 1 785.2601 12.73463
VTM 51F19 1 785.2601 12.73463
VTM 69B17 1 785.2601 12.73463
VTM 6.90E+29 2 723.9741 27.6253
VTM 6.80E+68 3 775.291 38.69515
VTM 5.60E+70 1 793.7091 12.59907
VTM 40A411 3 775.291 38.69515
VTM 40B511 2 808.4177 24.73969
VTM 40B56 1 775.291 12.89838
VTM 50A52 2 775.291 25.79676
VTM 50A62 3 775.291 38.69515
VTM 50A64 4 793.7091 50.3963
VTM 50F67 1 805.4106 12.41603
VTM 51C12 2 805.4106 24.83206
VTM 51F12 1 793.7091 12.59907
VTM 56C413 2 793.7091 25.19815
VTM 56F58 2 775.291 25.79676
VTM 68D64 1 738.1344 13.54767
VTM 69B16 1 785.2601 12.73463
VTM 69E317 2 785.2601 25.46927
VTM 78C44 2 763.985 26.17852
VTM 78C614 1 763.985 13.08926
VTM 89A36 2 808.4177 24.73969
VTM 89A35 1 800.4724 12.49262
VTM 68B53 2 709.2333 28.19946
VTM 68B64 1 793.7091 12.59907
VTM 56D56 3 751.5347 39.91832
VTM 6.90E+19 1 775.291 12.89838
VTM 3.90E+26 2 800.4724 24.98525
VTM 3.90E+32 6 805.4106 74.49617
VTM 7.70E+118 1 785.2601 12.73463
VTM 39C11 1 751.5347 13.30611
VTM 39D21 3 775.291 38.69515
VTM 40D62 1 775.291 12.89838
VTM 40D67 4 808.4177 49.47937
VTM 50B45 3 805.4106 37.24808
VTM 50F68 2 805.4106 24.83206
VTM 51B15 3 785.2601 38.2039
VTM 51B16 1 785.2601 12.73463
VTM 51F43 2 723.9741 27.6253
VTM 56A33 1 709.2333 14.09973
VTM 56A37 1 775.291 12.89838
VTM 56B16 1 775.291 12.89838
VTM 56B26 1 793.7091 12.59907
VTM 56B43 3 694.0784 43.22278
VTM 56C414 2 808.4177 24.73969
VTM 56D32 1 785.2601 12.73463
VTM 56D34 2 723.9741 27.6253
VTM 56D46 6 751.5347 79.83664
VTM 56E415 1 805.4106 12.41603
VTM 68C510 1 723.9741 13.81265
VTM 68C67 2 738.1344 27.09534
VTM 69C17 3 763.985 39.26779
VTM 69D28 2 738.1344 27.09534
VTM 69F26 3 800.4724 37.47787
VTM 69F29 3 800.4724 37.47787
VTM 78B410 5 751.5347 66.53053
VTM 78C62 1 763.985 13.08926
VTM 39D24 7 783.3059 89.36483
VTM 5.10E+17 1 808.4177 12.36984
VTM 3.90E+24 8 785.2601 101.87707
VTM 3.90E+33 4 793.7091 50.3963
VTM 38F23 2 793.7091 25.19815
VTM 39C14 6 800.4724 74.95574
VTM 39F31 2 723.9741 27.6253
VTM 39F42 5 738.1344 67.73834
VTM 39F64 7 805.4106 86.91219
VTM 51B12 4 751.5347 53.22442
VTM 51B37 1 723.9741 13.81265
VTM 51C11 1 785.2601 12.73463
VTM 51D210 1 808.4177 12.36984
VTM 56C52 3 808.4177 37.10953
VTM 56C58 1 793.7091 12.59907
VTM 56D47 3 738.1344 40.643
VTM 56D53 5 785.2601 63.67317
VTM 69C115 1 800.4724 12.49262
VTM 69F313 3 808.4177 37.10953
VTM 89A34 1 806.8498 12.39388
VTM 3.90E+22 2 793.7091 25.19815
VTM 39D37 2 751.5347 26.61221
VTM 39F56 3 808.4177 37.10953
VTM 40A57 1 775.291 12.89838
VTM 40B45 10 809.2658 123.5688
VTM 40B63 1 800.4724 12.49262
VTM 50B62 6 805.4106 74.49617
VTM 51A111 1 793.7091 12.59907
VTM 55C114 7 751.5347 93.14274
VTM 56B24 1 763.985 13.08926
VTM 56C49 4 805.4106 49.66411
VTM 56D43 1 785.2601 12.73463
VTM 56F410 3 785.2601 38.2039
VTM 68C64 2 723.9741 27.6253
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VTM 56B23 1 785.2601 12.73463
VTM 39F65 1 647.5421 15.44301
VTM 68C619 1 751.5347 13.30611
VTM 69C122 2 723.9741 27.6253
VTM 68C627 2 800.4724 24.98525
VTM 5.60E+55 3 785.2601 38.2039
VTM 38F24 2 793.7091 25.19815
VTM 39D33 11 763.985 143.98188
VTM 39D34 3 805.4106 37.24808
VTM 40A612 1 809.0636 12.35997
VTM 40A69 1 763.985 13.08926
VTM 40B44 1 808.4177 12.36984
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VTM 40D64 2 808.4177 24.73969
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VTM 56C51 1 775.291 12.89838
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VTM 68C512 1 751.5347 13.30611
VTM 69C118 2 785.2601 25.46927
VTM 77F115 1 785.2601 12.73463
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VTM 5.10E+22 3 779.4497 38.48869
VTM 3.90E+34 6 800.4724 74.95574
VTM 6.90E+38 2 775.291 25.79676
VTM 39D32 1 793.7091 12.59907
VTM 50B41 4 793.7091 50.3963
VTM 56B35 1 805.4106 12.41603
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VTM 56D410 2 775.291 25.79676
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VTM 78A21 3 800.4724 37.47787
VTM 40B57 3 809.2658 37.07064
VTM 69B115 1 793.7091 12.59907
VTM 5.10E+25 1 808.4177 12.36984
VTM 40A410 1 809.2658 12.35688
VTM 40B53 1 803.6619 12.44304
VTM 56C45 2 785.2601 25.46927
VTM 68C610 1 751.5347 13.30611
VTM 78A28 2 729.7176 27.40786
VTM 7.70E+16 1 785.2601 12.73463
VTM 68F67 1 751.5347 13.30611
VTM 69F214 2 808.4177 24.73969
VTM 69F24 2 694.0784 28.81519
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VTM 69F16 1 775.291 12.89838
VTM 68D65 1 793.7091 12.59907
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VTM 56E413 1 808.4177 12.36984
VTM 78B519 1 793.7091 12.59907
VTM 78D65 1 694.0784 14.40759
VTM 6.90E+40 1 775.291 12.89838
VTM 69F216 2 808.4177 24.73969
VTM 78B215 1 805.4106 12.41603
VTM 56B21 1 808.4177 12.36984
VTM 78B49 1 793.7091 12.59907
VTM 50D52 1 805.4106 12.41603
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VTM 78B314 2 709.2333 28.19946
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