[R-sig-ME] Trouble looping model using glmmTMB
Viraj Torsekar
viraj.torsekar at gmail.com
Wed May 2 09:03:24 CEST 2018
Hi Bill,
To answer your first question (Deriving confidence interval(s) from the
bootstrap), the following code might help. That should give you a data
frame of the lower CI range of 2.5% and higher range of 97.5%.
CI_values <- data.frame(sapply(1:ncol(X), function(x)
quantile(X[,x],c(0.025,0.975))))
where, X is the data frame containing the bootstrapped values.
As for the second question (Proper interpretation of the resulting output
statistics.) you might want to refer to Nakagawa and Cuthill (2007) and
Cumming and Finch (2005).
Viraj
On 1 May 2018 at 17:41, Bill Poling <Bill.Poling at zelis.com> wrote:
> Hi, I have been following this string as I try to learn how to bootstrap
> using R.
>
>
>
> I am an R novice and this is actually my first post.
>
>
>
> Therefore, I hope I am complying with the posting rules, as I understand
> them, properly.
>
>
>
> I ran the bbolker script From: R-sig-mixed-models [
> mailto:r-sig-mixed-models-bounces at r-project.org
> <r-sig-mixed-models-bounces at r-project.org>] On Behalf Of Ben Bolker,
> Sent: Sunday, April 08, 2018 2:22 PM on this topic
>
>
>
> Therefore I have the 100:
>
>
>
> [,1] [,2] [,3] [,4]
>
> [1,] 1.674036 1.103844 -1.558970 0.20640989
>
> [2,] 1.626733 1.116971 -1.683252 0.09869567
>
> [3,] 1.623758 1.173316 -1.669386 0.21515432
>
> [4,] 1.690359 1.141988 -1.729407 0.17972799
>
> [5,] 1.679417 1.146139 -1.425824 0.19958387
>
>
> etc…..
>
>
>
> AND the bootfit model:
>
>
>
> bootfit
>
>
>
> # Formula: y ~ x + (1 | f)
>
> # Zero inflation: ~1
>
> # Data: bootsamp()
>
> # AIC BIC logLik df.resid
>
> # 13101.717 13130.980 -6545.859 2567
>
> # Random-effects (co)variances:
>
> #
>
> # Conditional model:
>
> # Groups Name Std.Dev.
>
> # f (Intercept) 1.499
>
> #
>
> # Number of obs: 2572 / Conditional model: f, 102
>
> #
>
> # Overdispersion parameter for nbinom2 family (): 1.17
>
> #
>
> # Fixed Effects:
>
> #
>
> # Conditional model:
>
> # (Intercept) x
>
> # 1.578 1.103
>
> #
>
> # Zero-inflation model:
>
> # (Intercept)
>
> # -1.657
>
>
>
> I have reviewed the confint() help and performed the examples: (mtcars and the glm counts).
>
>
>
> However, I am not sure how to apply the confint() function on this bootstrap output.
>
>
>
> My questions pertain to:
>
>
>
> 1. Deriving confidence interval(s) from the bootstrap output.
> 2. Proper interpretation of the resulting output statistics.
>
>
>
> Please advise at your convenience and thank you in advance for any assistance.
>
>
>
> WHP
>
> William H. Poling, Ph.D., MPH
>
>
>
>
>
> *From:* R-sig-mixed-models [mailto:r-sig-mixed-models-
> bounces at r-project.org] *On Behalf Of *Viraj Torsekar
> *Sent:* Monday, April 09, 2018 7:40 AM
> *To:* Houslay, Tom <T.Houslay at exeter.ac.uk>
> *Cc:* r-sig-mixed-models at r-project.org
> *Subject:* Re: [R-sig-ME] Trouble looping model using glmmTMB
>
>
>
> Thanks so much for the suggestion Tom. Yes I was analysing calling effort
> for males, and movement for both males and females in that manner. But I
> was running separate models for each. I'll have a look at these conditional
> two-part models.
>
> Viraj
>
> On 9 April 2018 at 15:50, Houslay, Tom <T.Houslay at exeter.ac.uk> wrote:
>
> > Hi Viraj,
> >
> >
> > This isn't a direct answer to your question so you can feel extremely
> free
> > to ignore it(!), but your question reminded me of an approach I took to
> > modelling calling effort in crickets using zero-altered poisson models in
> > Jarrod's MCMCglmm package. In that case I had a few more predictor
> > variables, but it meant the question could be phrased as two parts: what
> > factors affect whether a male called or not, and - given he did call -
> what
> > factors affect how much time he spent calling? It seems that that might
> be
> > another option for you to model the movement with your crickets, although
> > obviously it depends whether you think that would give you anything more
> > valuable than your current approach (eg, is the decision to move
> something
> > worth modelling separately from how far the cricket travels).
> >
> >
> > Anyway - my paper including this analysis is at http://doi.wiley.com/10.
> > 1111/1365-2435.12766 in case it's of any interest.
>
> >
> >
> > Cheers
> >
> >
> > Tom
> >
> > ----
> >
> > Message: 1
> > Date: Sun, 8 Apr 2018 19:57:53 +0530
> > From: Viraj Torsekar <viraj.torsekar at gmail.com>
> > To: r-sig-mixed-models at r-project.org
> > Subject: [R-sig-ME] Trouble looping model using glmmTMB
> > Message-ID:
> > <CAOJBL42qdVortWMi2xVdqv=4MHUT8zbiOPbU3Y+UxBSjkiAY0Q at mail.
> <CAOJBL42qdVortWMi2xVdqv=4MHUT8zbiOPbU3Y+UxBSjkiAY0Q at mail.%0b>> gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> >
> > Hello all,
> >
> > I'm trying to find out if distance moved by crickets is a function of
> > predation risk. My response variable is 'distance moved' and the
> predictor
> > is probability of spatial proximity with predator, ranging from 0 to 1.
> The
> > response variable is zero-inflated (about 77% values are zeroes) and its
> > variance is far higher than its mean. Hence, I tried running
> zero-inflated
> > negative binomial mixed models using glmmADMB, which failed (mixed
> because
> > I have multiple values per individual). Following was the error I kept
> > encountering: "function maximizer failed" (attaching a text file with
> > details of this model by keeping debug=TRUE).
> >
> > Hence, I shifted to glmmTMB (version: 0.2.0), on Dr. Bolker's advice, and
> > it worked! But the problem is, when I try bootstrapping the model using
> to
> > obtain confidence intervals, I keep getting the following error after
> > varying number of runs: 'Error in optimHess(par.fixed, obj$fn, obj$gr):
> > gradient in optim evaluated to length 1 not 5'. This non-parametric
> > bootstrapping routine involves for loops in which the model is run using
> > bootstrapped groups (belonging to the grouping variable; individual.id
> in
> > my case) and the model coefficients thus obtained constitute the
> confidence
> > intervals. I've tried running 10,000 iterations, but the error pops up
> > within 10 to 100 runs.
> >
> > Does anyone have suggestions regarding what can be changed?
> >
> > Details of the model run singly and not in the loop:
> >
> > Family: nbinom2 ( log )
> > Formula: movement.whole ~ poc + (1 | female.id)
> > Zero inflation: ~1
> > Data: incrisk_females_comm
> >
> > AIC BIC logLik deviance df.resid
> > 1725.1 1745.9 -857.5 1715.1 474
> >
> > Random effects:
> >
> > Conditional model:
> > Groups Name Variance Std.Dev.
> > female.id (Intercept) 0.07924 0.2815
> > Number of obs: 479, groups: female.id, 110
> >
> > Overdispersion parameter for nbinom2 family (): 1.59
> >
> > Conditional model:
> > Estimate Std. Error z value Pr(>|z|)
> > (Intercept) 4.66384 0.14161 32.93 <2e-16 ***
> > poc -0.08815 0.20978 -0.42 0.674
> > ---
> > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> >
> > Zero-inflation model:
> > Estimate Std. Error z value Pr(>|z|)
> > (Intercept) 1.2442 0.1098 11.34 <2e-16 ***
> >
> > Please do mention if you need further details. Thank you in advance.
> >
> > Viraj Torsekar,
> > PhD Candidate,
> > Centre for Ecological Sciences,
> > Indian Institute of Science
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
> > ------------------------------
> >
> > End of R-sig-mixed-models Digest, Vol 136, Issue 19
> > ***************************************************
> >
>
> [[alternative HTML version deleted]]
>
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