[R] Mixed models fixed effects
Emma Stone
Emma.Stone at bristol.ac.uk
Fri Mar 13 11:07:53 CET 2009
Hi Thierry,
Thanks, my data are pasted in below: n = 48, with different numbers if site
replicates.
Site passes length width height ohwidth ohheight style shape nogap pgaps
1 1 32 38.21 7.18 2.60 0.00 0.00 1 1 0 0.00
2 1 7 154.38 2.55 2.43 0.00 0.00 2 1 0 0.00
3 2 24 130.00 2.73 4.96 5.83 2.27 1 2 0 1.92
4 2 43 130.00 2.73 4.96 3.45 2.45 1 2 0 1.91
5 2 32 130.00 3.30 4.34 3.67 2.63 3 2 0 0.00
6 2 9 130.00 3.30 4.34 2.13 1.53 2 2 0 0.00
7 2 25 214.00 1.65 6.23 2.80 2.53 3 2 0 0.00
8 2 1 214.00 2.20 1.05 0.00 0.00 2 1 0 0.00
9 2 57 188.00 5.87 4.97 3.23 2.13 2 2 0 0.00
10 2 32 211.00 2.63 6.09 4.37 2.50 2 2 0 0.00
11 2 14 211.00 2.63 6.09 3.50 2.53 2 2 0 0.00
12 3 78 192.00 2.30 2.40 0.33 0.88 2 2 0 2.19
13 3 11 192.00 2.50 2.50 0.13 0.55 2 2 0 2.19
14 3 9 444.00 2.10 1.93 0.00 0.00 2 1 2 6.19
15 4 40 44.00 1.83 2.05 0.00 0.00 1 1 1 31.81
16 4 112 44.00 1.58 1.73 0.00 0.00 1 1 1 31.81
17 4 23 98.00 2.18 1.70 0.00 0.00 1 3 0 2.55
18 4 23 98.00 1.78 1.60 0.00 0.00 1 1 0 2.55
19 4 4 84.00 1.73 1.98 0.00 0.00 1 3 1 17.02
20 4 72 88.00 3.30 5.30 3.30 1.45 1 2 0 0.00
21 5 207 116.00 3.08 3.38 3.65 3.68 1 2 0 0.00
22 5 2 116.00 2.85 2.18 3.18 3.53 1 2 0 0.00
23 5 81 104.00 2.68 2.78 1.00 0.75 2 1 0 0.00
24 5 3 104.00 2.68 2.38 0.00 0.00 2 1 0 0.00
25 5 21 59.00 2.78 4.03 2.23 1.75 2 2 0 6.78
26 5 1 59.00 2.78 3.33 1.38 1.35 2 2 0 6.78
27 6 82 165.56 2.50 4.00 1.00 1.33 1 2 0 0.00
28 6 1 165.56 2.60 3.63 0.50 1.40 1 2 0 0.00
29 6 46 69.35 3.23 10.67 4.73 4.67 1 2 0 0.00
30 6 7 165.56 3.50 10.17 2.67 1.67 1 2 0 0.00
31 6 45 136.00 3.33 3.67 0.00 0.00 1 2 0 2.20
32 6 3 136.00 3.33 2.75 0.00 0.00 1 2 0 3.30
33 6 34 82.00 2.83 12.00 3.33 3.83 1 2 0 0.00
34 7 0 228.00 2.57 2.70 0.30 1.00 2 2 0 0.50
35 7 148 228.00 3.08 4.68 0.75 1.75 2 2 0 0.05
36 7 0 208.00 2.40 2.90 0.00 0.00 2 1 0 1.44
37 7 38 208.00 2.57 2.63 0.00 0.00 2 1 0 1.44
38 7 0 112.00 2.13 1.65 0.00 0.00 2 1 0 0.50
39 7 0 192.00 1.55 1.55 0.00 0.00 2 1 0 0.00
40 7 0 132.00 1.56 1.41 0.00 0.00 2 1 0 0.00
41 8 52 148.00 5.05 7.62 2.55 3.38 2 2 0 0.00
42 8 18 148.00 4.08 5.80 0.65 0.63 2 2 0 0.00
43 8 19 210.00 3.08 4.58 0.70 0.88 2 2 0 1.42
44 8 0 210.00 3.68 4.90 0.25 0.38 3 2 0 1.42
45 8 3 246.00 2.18 2.43 0.00 0.00 2 1 3 15.24
46 8 0 246.00 1.93 2.20 0.00 0.00 2 1 3 15.24
47 8 3 142.00 1.60 2.03 0.00 0.00 1 1 3 26.19
48 8 0 142.00 1.37 1.87 0.00 0.00 1 1 3 26.19
habitat side oharea hvolume
1 1 2 0.00 713.30
2 1 4 0.00 956.62
3 1 2 1720.43 1760.30
4 1 4 1098.83 1760.30
5 1 4 1254.77 1861.86
6 1 2 423.66 1861.86
7 1 1 1515.98 2199.81
8 1 3 0.00 494.34
9 1 2 1293.42 5484.69
10 1 3 2305.18 3379.52
11 1 1 1868.41 3379.52
12 1 2 55.76 1059.84
13 1 4 13.73 1200.00
14 1 1 0.00 1799.53
15 1 1 0.00 165.07
16 1 3 0.00 120.27
17 1 2 0.00 363.19
18 1 4 0.00 279.10
19 1 4 0.00 287.73
20 1 2 421.08 1539.12
21 1 2 1558.11 1207.61
22 2 4 1302.15 720.71
23 2 2 78.00 774.84
24 1 4 0.00 663.35
25 1 2 230.25 661.00
26 1 4 109.92 546.19
27 1 3 220.19 1655.60
28 3 1 115.89 1562.56
29 1 1 1531.88 2390.09
30 1 3 738.22 5893.11
31 2 2 0.00 1662.07
32 4 4 0.00 1245.42
33 5 3 1045.82 2784.72
34 1 2 68.40 1582.09
35 1 4 299.25 3286.48
36 1 2 0.00 1447.68
37 1 4 0.00 1405.89
38 4 3 0.00 393.62
39 4 1 0.00 461.28
40 4 1 0.00 290.35
41 1 4 1275.61 5695.19
42 1 2 60.61 3502.27
43 1 1 129.36 2962.34
44 1 3 19.95 3786.72
45 1 1 0.00 1303.16
46 1 3 0.00 1044.52
47 1 2 0.00 461.22
48 1 4 0.00 363.79
--On 13 March 2009 11:01 +0100 "ONKELINX, Thierry"
<Thierry.ONKELINX at inbo.be> wrote:
> Dear Emma,
>
> Have you tried a simpler model? False convergence can be due to an
> overcomplex model. Can you give a brief outline of your data? E.g. how
> many sites, how many data per site, ... Cross tabulations of all pairs
> of factor variables are usefull too.
>
> HTH,
>
> Thierry
>
>
> ------------------------------------------------------------------------
> ----
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest
> Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
> methodology and quality assurance
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
> tel. + 32 54/436 185
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: Emma Stone [mailto:Emma.Stone at bristol.ac.uk]
> Verzonden: vrijdag 13 maart 2009 10:50
> Aan: ONKELINX, Thierry; Emma Stone; r-help at r-project.org
> Onderwerp: RE: [R] Mixed models fixed effects
>
> Hi Thierry,
>
> That's great thanks!
>
> I have done as you have said but I keep getting a warning message here
> is
> my code:
>
> G1Hvol<-glmer(passes~hvolume+style+habitat(1|Site),family = poisson)
>
> And this is the message i get:
> Warning message:
> In mer_finalize(ans) : false convergence (8)
>
> any ideas??
>
> Emma
>
>
> --On 11 March 2009 15:45 +0100 "ONKELINX, Thierry"
> <Thierry.ONKELINX at inbo.be> wrote:
>
>> Hi Emma,
>>
>> Continuous predictors are no problem at all. You can mix both
> continuous
>> and categorial predictors if needed. I suppose your response are
> counts
>> (the number of bats that passes)? In that case a generalised linear
>> mixed model is more appropriate. With the lme4 package you could try
>> something like this:
>>
>> library(lme4)
>> Model <- glmer(BatPasses ~ Width + Height + (1|Site), family =
> poisson)
>>
>> HTH,
>>
>> Thierry
>>
>> PS There is a mailing list dedicated to mixed models:
> R-Sig-MixedModels
>>
> ------------------------------------------------------------------------
>> ----
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
>> and Forest
>> Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
>> methodology and quality assurance
>> Gaverstraat 4
>> 9500 Geraardsbergen
>> Belgium
>> tel. + 32 54/436 185
>> Thierry.Onkelinx at inbo.be
>> www.inbo.be
>>
>> To call in the statistician after the experiment is done may be no
> more
>> than asking him to perform a post-mortem examination: he may be able
> to
>> say what the experiment died of.
>> ~ Sir Ronald Aylmer Fisher
>>
>> The plural of anecdote is not data.
>> ~ Roger Brinner
>>
>> The combination of some data and an aching desire for an answer does
> not
>> ensure that a reasonable answer can be extracted from a given body of
>> data.
>> ~ John Tukey
>>
>> -----Oorspronkelijk bericht-----
>> Van: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org]
>> Namens Emma Stone
>> Verzonden: woensdag 11 maart 2009 15:29
>> Aan: r-help at r-project.org
>> Onderwerp: Re: [R] Mixed models fixed effects
>>
>> Dear All,
>>
>> This may sound like a dumb question but I am trying to use a mixed
> model
>> to
>> determine the predictors of bat activity along hedges within 8 sites.
> So
>> my
>> response is continuous (bat passes) my predictors fixed effects are
>> continuous (height metres), width (metres) etc and the random effect
> is
>> site - can you tell me if the fixed effects can be continuous as all
>> the
>> examples I have read show them as categorical, but this is not covered
>> in
>> any documents I can find.
>>
>> Help!
>>
>> Emma
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
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>> bevestigd is door een geldig ondertekend document. The views expressed
> in
>> this message and any annex are purely those of the writer and may not
> be
>> regarded as stating an official position of INBO, as long as the
> message
>> is not confirmed by a duly signed document.
>
>
>
> ----------------------
> Emma Stone
> Postgraduate Researcher
> Bat Ecology and Bioacoustics Lab
> & Mammal Research Unit
> School of Biological Sciences,
> University of Bristol, Woodland Road,
> Bristol, BS8 1UG
> Email: emma.stone at bristol.ac.uk
>
>
>
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver
> weer en binden het INBO onder geen enkel beding, zolang dit bericht niet
> bevestigd is door een geldig ondertekend document. The views expressed in
> this message and any annex are purely those of the writer and may not be
> regarded as stating an official position of INBO, as long as the message
> is not confirmed by a duly signed document.
----------------------
Emma Stone
Postgraduate Researcher
Bat Ecology and Bioacoustics Lab
& Mammal Research Unit
School of Biological Sciences,
University of Bristol, Woodland Road,
Bristol, BS8 1UG
Email: emma.stone at bristol.ac.uk
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