'Using lme to generate an MMRM model in R - incompatible formulas for groups in 'random' and 'correlation'
I'm trying to fit an MMRM to a dataset, there are specific covariates that have been pre-specified as random.
Previously, I have experience using gls() and simply accounting for the random effects in an unstructured correlation matrix via the below as an example:
nlme::corSymm(form = ~time | pt_num)
Since gls() doesn't specify random effects I'm trying to use lme, but I'm getting the error:
Error in lme.formula(la_mm2 ~ factor(arm) + factor(partI_bool) + la_base_mm2, :
incompatible formulas for groups in 'random' and 'correlation'
I've pasted some of the dummy data below as well as the model that I'm using, any clarity on what is causing the issue is highly appreciated!
#Model
gather1_mmrm <- lme(la_mm2 ~ factor(arm) + factor(partI_bool) + la_base_mm2,
data = gather1,
method = "REML",
random = ~t_factor + t_factor*factor(arm) + t_factor*factor(partI_bool) + t_factor*la_base_mm2 | pt_id,
na.action = na.omit,
correlation = nlme::corSymm(form= ~ t_factor | pt_num),
weights = nlme::varIdent(form= ~1|t_factor))
run pt_id arm partI_bool la_base_mm2 la_base_mm t_factor t_months la_mm2 la_mm ch_la_mm2 ch_la_mm
1 4 SHAM 1 4.302596153 2.074270029 1 0 4.302596153 2.074270029 0 0
1 4 SHAM 1 4.302596153 2.074270029 2 6 NA NA NA NA
1 4 SHAM 1 4.302596153 2.074270029 3 12 NA NA NA NA
1 12 SHAM 1 14.34691312 3.787731923 1 0 14.34691312 3.787731923 0 0
1 12 SHAM 1 14.34691312 3.787731923 2 6 15.64964748 3.955963533 1.302734357 1.302734357
1 12 SHAM 1 14.34691312 3.787731923 3 12 17.78969962 4.217783733 3.442786498 3.442786498
1 13 SHAM 1 5.356110596 2.314327245 1 0 5.356110596 2.314327245 0 0
1 13 SHAM 1 5.356110596 2.314327245 2 6 7.10663327 2.665826939 1.750522674 1.750522674
1 13 SHAM 1 5.356110596 2.314327245 3 12 9.041039758 3.00683218 3.684929162 3.684929162
1 14 SHAM 1 11.25759063 3.35523332 1 0 11.25759063 3.35523332 0 0
1 14 SHAM 1 11.25759063 3.35523332 2 6 13.61993655 3.690519821 2.362345918 2.362345918
1 14 SHAM 1 11.25759063 3.35523332 3 12 16.42931581 4.053309242 5.171725175 5.171725175
1 19 SHAM 1 2.758491755 1.660870782 1 0 2.758491755 1.660870782 0 0
1 19 SHAM 1 2.758491755 1.660870782 2 6 3.739763552 1.933846828 0.981271798 0.981271798
1 19 SHAM 1 2.758491755 1.660870782 3 12 4.772096698 2.18451292 2.013604943 2.013604943
1 35 SHAM 0 3.268341978 1.80785563 1 0 3.268341978 1.80785563 0 0
1 35 SHAM 0 3.268341978 1.80785563 2 6 3.617463276 1.901963006 0.349121298 0.349121298
1 35 SHAM 0 3.268341978 1.80785563 3 12 4.042171268 2.010515175 0.77382929 0.77382929
1 39 SHAM 0 5.806441903 2.409655972 1 0 5.806441903 2.409655972 0 0
1 39 SHAM 0 5.806441903 2.409655972 2 6 6.668033763 2.582253621 0.86159186 0.86159186
1 39 SHAM 0 5.806441903 2.409655972 3 12 6.657201504 2.580155326 0.850759601 0.850759601
1 51 SHAM 0 6.726560406 2.593561336 1 0 6.726560406 2.593561336 0 0
1 51 SHAM 0 6.726560406 2.593561336 2 6 6.752801108 2.598615229 0.026240702 0.026240702
1 51 SHAM 0 6.726560406 2.593561336 3 12 7.14950777 2.673856348 0.422947364 0.422947364
1 55 SHAM 0 5.281358119 2.298120562 1 0 5.281358119 2.298120562 0 0
1 55 SHAM 0 5.281358119 2.298120562 2 6 3.504983367 1.872160081 -1.776374752 -1.776374752
1 55 SHAM 0 5.281358119 2.298120562 3 12 1.453285056 1.205522732 -3.828073063 -3.828073063
1 103 SHAM 0 14.14175968 3.760553108 1 0 14.14175968 3.760553108 0 0
1 103 SHAM 0 14.14175968 3.760553108 2 6 15.83732887 3.979614161 1.695569189 1.695569189
1 103 SHAM 0 14.14175968 3.760553108 3 12 17.85259321 4.225232918 3.710833529 3.710833529
1 105 SHAM 0 8.118501066 2.849298346 1 0 8.118501066 2.849298346 0 0
1 105 SHAM 0 8.118501066 2.849298346 2 6 NA NA NA NA
1 105 SHAM 0 8.118501066 2.849298346 3 12 NA NA NA NA
1 107 SHAM 0 16.25989413 4.032355903 1 0 16.25989413 4.032355903 0 0
1 107 SHAM 0 16.25989413 4.032355903 2 6 NA NA NA NA
1 107 SHAM 0 16.25989413 4.032355903 3 12 NA NA NA NA
1 110 SHAM 0 3.108610876 1.763125315 1 0 3.108610876 1.763125315 0 0
1 110 SHAM 0 3.108610876 1.763125315 2 6 NA NA NA NA
1 110 SHAM 0 3.108610876 1.763125315 3 12 NA NA NA NA
1 122 2mg 1 14.23013034 3.772284499 1 0 14.23013034 3.772284499 0 0
1 122 2mg 1 14.23013034 3.772284499 2 6 16.31252812 4.038877086 2.082397778 2.082397778
1 122 2mg 1 14.23013034 3.772284499 3 12 17.26079811 4.154611667 3.030667766 3.030667766
1 129 2mg 1 5.839250811 2.416454181 1 0 5.839250811 2.416454181 0 0
1 129 2mg 1 5.839250811 2.416454181 2 6 7.464223376 2.732073091 1.624972565 1.624972565
1 129 2mg 1 5.839250811 2.416454181 3 12 9.640338241 3.104889409 3.80108743 3.80108743
1 133 2mg 1 4.413316452 2.100789483 1 0 4.413316452 2.100789483 0 0
1 133 2mg 1 4.413316452 2.100789483 2 6 5.064445674 2.25043233 0.651129222 0.651129222
1 133 2mg 1 4.413316452 2.100789483 3 12 NA NA NA NA
1 139 2mg 0 11.85320922 3.442848998 1 0 11.85320922 3.442848998 0 0
1 139 2mg 0 11.85320922 3.442848998 2 6 13.7069869 3.702294815 1.853777679 1.853777679
1 139 2mg 0 11.85320922 3.442848998 3 12 14.36968627 3.790736904 2.516477054 2.516477054
1 155 2mg 0 9.226600647 3.037531999 1 0 9.226600647 3.037531999 0 0
1 155 2mg 0 9.226600647 3.037531999 2 6 8.73090644 2.954810728 -0.495694207 -0.495694207
1 155 2mg 0 9.226600647 3.037531999 3 12 9.042412659 3.007060468 -0.184187988 -0.184187988
1 160 2mg 0 12.06173395 3.473000713 1 0 12.06173395 3.473000713 0 0
1 160 2mg 0 12.06173395 3.473000713 2 6 12.47205033 3.531579013 0.410316377 0.410316377
1 160 2mg 0 12.06173395 3.473000713 3 12 NA NA NA NA
1 161 2mg 0 6.051340791 2.459947315 1 0 6.051340791 2.459947315 0 0
1 161 2mg 0 6.051340791 2.459947315 2 6 NA NA NA NA
1 161 2mg 0 6.051340791 2.459947315 3 12 5.371776645 2.317709353 -0.679564146 -0.679564146
1 168 2mg 0 13.47495294 3.670824559 1 0 13.47495294 3.670824559 0 0
1 168 2mg 0 13.47495294 3.670824559 2 6 15.60077961 3.949782224 2.125826674 2.125826674
1 168 2mg 0 13.47495294 3.670824559 3 12 17.56628938 4.19121574 4.091336443 4.091336443
1 184 4mg 0 11.41583874 3.378733304 1 0 11.41583874 3.378733304 0 0
1 184 4mg 0 11.41583874 3.378733304 2 6 13.27277419 3.643181877 1.856935451 1.856935451
1 184 4mg 0 11.41583874 3.378733304 3 12 15.59128977 3.948580729 4.175451032 4.175451032
1 189 4mg 0 5.743634485 2.396588092 1 0 5.743634485 2.396588092 0 0
1 189 4mg 0 5.743634485 2.396588092 2 6 5.228250162 2.286536718 -0.515384323 -0.515384323
1 189 4mg 0 5.743634485 2.396588092 3 12 4.484122564 2.117574689 -1.259511921 -1.259511921
1 197 4mg 0 9.077401292 3.012872598 1 0 9.077401292 3.012872598 0 0
1 197 4mg 0 9.077401292 3.012872598 2 6 NA NA NA NA
1 197 4mg 0 9.077401292 3.012872598 3 12 NA NA NA NA
1 214 4mg 0 11.90323176 3.450106051 1 0 11.90323176 3.450106051 0 0
1 214 4mg 0 11.90323176 3.450106051 2 6 13.60561692 3.688579255 1.70238516 1.70238516
1 214 4mg 0 11.90323176 3.450106051 3 12 15.36408886 3.9197052 3.460857095 3.460857095
1 218 4mg 0 10.8365073 3.291885068 1 0 10.8365073 3.291885068 0 0
1 218 4mg 0 10.8365073 3.291885068 2 6 12.0130533 3.465985184 1.176545997 1.176545997
1 218 4mg 0 10.8365073 3.291885068 3 12 13.63051081 3.691952168 2.794003509 2.794003509
1 231 4mg 0 10.32451428 3.213178221 1 0 10.32451428 3.213178221 0 0
1 231 4mg 0 10.32451428 3.213178221 2 6 11.11654749 3.33414869 0.792033208 0.792033208
1 231 4mg 0 10.32451428 3.213178221 3 12 11.13792298 3.33735269 0.813408696 0.813408696
1 235 4mg 0 6.26445047 2.502888425 1 0 6.26445047 2.502888425 0 0
1 235 4mg 0 6.26445047 2.502888425 2 6 NA NA NA NA
1 235 4mg 0 6.26445047 2.502888425 3 12 7.748527082 2.783617625 1.484076612 1.484076612
1 237 4mg 0 5.393093093 2.322303402 1 0 5.393093093 2.322303402 0 0
1 237 4mg 0 5.393093093 2.322303402 2 6 6.382859882 2.526432244 0.989766789 0.989766789
1 237 4mg 0 5.393093093 2.322303402 3 12 6.65907103 2.58051759 1.265977937 1.265977937
1 250 4mg 0 3.578464204 1.891682903 1 0 3.578464204 1.891682903 0 0
1 250 4mg 0 3.578464204 1.891682903 2 6 3.922992029 1.980654445 0.344527825 0.344527825
1 250 4mg 0 3.578464204 1.891682903 3 12 4.405971911 2.099040712 0.827507707 0.827507707
Sources
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Source: Stack Overflow
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