[R-sig-ME] c++ exception (unknown reason) when using an offset of the slope with glmer
Ben Bolker
bbolker at gmail.com
Wed Jan 28 15:45:27 CET 2015
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Confirmed on
R Under development (unstable) (2015-01-26 r67627)
Platform: i686-pc-linux-gnu (32-bit)
lme4 1.1.8
I will see what I can figure out. I suspect the main problem is that
the doses range from 4 to 6, so with an offset of (1.5*dose), that
says that the logit-probability or log-odds should range from 6 to 9,
which corresponds to a baseline probability of 0.997 to 0.999. Those
are very high probabilities: they're going to make it very hard to
make a sensible model. Can you say a little bit more about what
you're trying to do/why an offset of 1.5 makes sense?
Ben Bolker
On 15-01-27 08:24 AM, xavier.paoletti at curie.fr wrote:
> Thanks for your attention.
>
> Here there are. 180 rows, 4 columns + obs number. Obs patid
> cycle dose DLT 1 1 1 4.1 0 2 2 1 4.8 0 3
> 3 1 5.3 0 4 4 1 5.7 0 5 5 1 6.0 1
> 6 6 1 5.7 1 7 7 1 5.7 0 8 8 1
> 5.3 0 9 9 1 5.3 0 10 10 1 5.7 0 11 11
> 1 5.3 0 12 12 1 5.3 0 13 13 1 5.3 0 14
> 14 1 5.3 0 15 15 1 5.7 0 16 16 1 5.3
> 0 17 17 1 5.3 0 18 18 1 5.3 0 19 19 1
> 5.3 0 20 20 1 5.7 0 21 21 1 5.7 1 22 22
> 1 5.7 1 23 23 1 5.7 0 24 24 1 5.3 0 25
> 25 1 5.3 0 26 26 1 5.3 0 27 27 1 5.3
> 1 28 28 1 5.7 0 29 29 1 5.7 1 30 30 1
> 5.7 0 31 1 2 4.1 0 32 2 2 4.8 0 33 3
> 2 5.3 0 34 4 2 5.7 0 35 5 2 6.0 0 36
> 6 2 5.7 0 37 7 2 5.7 1 38 8 2 5.3 0
> 39 9 2 5.3 0 40 10 2 5.7 0 41 11 2
> 5.3 0 42 12 2 5.3 0 43 13 2 5.3 0 44 14
> 2 5.3 0 45 15 2 5.7 0 46 16 2 5.3 0 47
> 17 2 5.3 0 48 18 2 5.3 0 49 19 2 5.3
> 0 50 20 2 5.7 0 51 21 2 5.7 0 52 22 2
> 5.7 0 53 23 2 5.7 1 54 24 2 5.3 0 55 25
> 2 5.3 0 56 26 2 5.3 0 57 27 2 5.3 0 58
> 28 2 5.7 0 59 29 2 5.7 0 60 30 2 5.7
> 1 61 1 3 4.1 0 62 2 3 4.8 0 63 3 3
> 5.3 0 64 4 3 5.7 0 65 5 3 6.0 1 66 6
> 3 5.7 1 67 7 3 5.7 1 68 8 3 5.3 0 69
> 9 3 5.3 0 70 10 3 5.7 0 71 11 3 5.3 0
> 72 12 3 5.3 0 73 13 3 5.3 0 74 14 3
> 5.3 0 75 15 3 5.7 0 76 16 3 5.3 0 77 17
> 3 5.3 0 78 18 3 5.3 0 79 19 3 5.3 1 80
> 20 3 5.7 0 81 21 3 5.7 0 82 22 3 5.7
> 0 83 23 3 5.7 1 84 24 3 5.3 0 85 25 3
> 5.3 0 86 26 3 5.3 1 87 27 3 5.3 0 88 28
> 3 5.7 0 89 29 3 5.7 0 90 30 3 5.7 1 91
> 1 4 4.1 0 92 2 4 4.8 0 93 3 4 5.3 0
> 94 4 4 5.7 0 95 5 4 6.0 0 96 6 4
> 5.7 0 97 7 4 5.7 0 98 8 4 5.3 0 99 9
> 4 5.3 0 100 10 4 5.7 0 101 11 4 5.3 1 102
> 12 4 5.3 1 103 13 4 5.3 0 104 14 4 5.3
> 0 105 15 4 5.7 1 106 16 4 5.3 0 107 17 4
> 5.3 0 108 18 4 5.3 0 109 19 4 5.3 0 110 20
> 4 5.7 0 111 21 4 5.7 0 112 22 4 5.7 0 113
> 23 4 5.7 0 114 24 4 5.3 0 115 25 4 5.3
> 0 116 26 4 5.3 0 117 27 4 5.3 0 118 28 4
> 5.7 0 119 29 4 5.7 0 120 30 4 5.7 0 121 1
> 5 4.1 0 122 2 5 4.8 0 123 3 5 5.3 0 124
> 4 5 5.7 0 125 5 5 6.0 0 126 6 5 5.7 1
> 127 7 5 5.7 0 128 8 5 5.3 1 129 9 5
> 5.3 0 130 10 5 5.7 0 131 11 5 5.3 0 132 12
> 5 5.3 0 133 13 5 5.3 1 134 14 5 5.3 0 135
> 15 5 5.7 0 136 16 5 5.3 0 137 17 5 5.3
> 0 138 18 5 5.3 0 139 19 5 5.3 0 140 20 5
> 5.7 0 141 21 5 5.7 1 142 22 5 5.7 0 143 23
> 5 5.7 0 144 24 5 5.3 0 145 25 5 5.3 0 146
> 26 5 5.3 0 147 27 5 5.3 0 148 28 5 5.7
> 0 149 29 5 5.7 0 150 30 5 5.7 0 151 1 6
> 4.1 0 152 2 6 4.8 0 153 3 6 5.3 0 154 4
> 6 5.7 1 155 5 6 6.0 1 156 6 6 5.7 0 157
> 7 6 5.7 0 158 8 6 5.3 0 159 9 6 5.3 0
> 160 10 6 5.7 1 161 11 6 5.3 0 162 12 6
> 5.3 0 163 13 6 5.3 0 164 14 6 5.3 0 165 15
> 6 5.7 0 166 16 6 5.3 0 167 17 6 5.3 0 168
> 18 6 5.3 0 169 19 6 5.3 0 170 20 6 5.7
> 1 171 21 6 5.7 1 172 22 6 5.7 0 173 23 6
> 5.7 0 174 24 6 5.3 0 175 25 6 5.3 0 176 26
> 6 5.3 1 177 27 6 5.3 0 178 28 6 5.7 0 179
> 29 6 5.7 1 180 30 6 5.7 0
>
>
>
>
> Ben Bolker <bbolker at gmail.com> 27/01/2015 14:14
>
> A <xavier.paoletti at curie.fr> cc "r-sig-mixed-models at r-project.org"
> <r-sig-mixed-models at r-project.org> Objet Re: [R-sig-ME] c++
> exception (unknown reason) when using an offset of the slope with
> glmer
>
>
>
>
>
>
> Your posted data set got removed by the mailing list machinery.
> Can you post it somewhere publicly accessible?
>
>
> On Tue, Jan 27, 2015 at 3:45 AM, <xavier.paoletti at curie.fr>
> wrote:
>>
>> Dear all,
>>
>> I am new on this forum and I hope my request follows the right
>> format.
>>
>> I use R 3.1.2 and lme1.7 on a mac OS X (snow leopard) or Windows
>> OS.
>>
>> I try to fit a longitudinal logistic mixed effect model on
>> dose-time response data where the response is measured several
>> times at the same dose. The probability of response increases
>> with the dose. There is a set of discrete doses (let's say 6) but
>> most of the data are measured at 1 or 2 doses.
>>
>> I use a very simple logstic model with a random intercept and the
>> dose effect. In the simplest case, there is not time effect.
>> Furthermore, I would like to set the slope of the dose to some
>> value
> using
>> offset slope=1.5.
>>
>> The command line, glmer(DLTb ~ offset(slope*dose) + (1 | patid),
>> family=binomial,data=dataAllCRM,nAGQ=10) gives the following
>> error: Under Mac OSX: (function (fr, X, reTrms, family, nAGQ =
>> 1L, verbose =
> 0L,
>> control = glmerControl(), : c++ exception (unknown reason)
>>
>> Under Windows: Error: (maxstephalfit) PIRLS step-halvings failed
>> to
> reduce
>> deviance in pwrssUpdate
>>
>> Whatever the value of the offset, I get the same error. If I
>> remove the offset or if I remove the variable, some estimates
>> are obtained.
>>
>> Please find attached an example of dataset as an illustration; I
>> get the same error for all tested datasets.
>>
>>
>> Thank you very much for your help.
>>
>> Best regards,
>>
>> Xavier _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
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