[R-sig-ME] diagnostic test meta analysis using glmer

[Nathan Pace]

Hi Thierry,

Your link to the description of multiple comparisons in glht with custom K matrices for GLMM was much appreciated.

It helped me think clearly about my contrast vectors.

Thanks again,

Nathan

From: Thierry Onkelinx <thierry.onkelinx at inbo.be>
Date: Tuesday, November 14, 2017 at 01:29
To: Nathan L Pace <n.l.pace at utah.edu>
Cc: R-sig-mixed-models <r-sig-mixed-models at r-project.org>
Subject: Re: [R-sig-ME] diagnostic test meta analysis using glmer

Dear Nathan,

You can use the glht() function from the multcomp package to do post-hoc tests on contrasts. You should create a custom K matrix. See https://thebiobucket.blogspot.be/2011/06/glmm-with-custom-multiple-comparisons.html#more

Best regards,

Thierry


ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be<mailto:thierry.onkelinx at inbo.be>
Kliniekstraat 25, B-1070 Brussel
www.inbo.be<http://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
///////////////////////////////////////////////////////////////////////////////////////////

[Van 14 tot en met 19 december 20]<https://overheid.vlaanderen.be/mobiliteitsplan-herman-teirlinckgebouw>
Van 14 tot en met 19 december 2017 verhuizen we uit onze vestiging in Brussel naar het Herman Teirlinckgebouw op de site Thurn & Taxis.
Vanaf dan ben je welkom op het nieuwe adres: Havenlaan 88 bus 73, 1000 Brussel.

///////////////////////////////////////////////////////////////////////////////////////////
[https://inbo-website-prd-532750756126.s3-eu-west-1.amazonaws.com/inbologoleeuw_nl.png]<https://www.inbo.be>

2017-11-14 7:04 GMT+01:00 Nathan Pace <n.l.pace at utah.edu<mailto:n.l.pace at utah.edu>>:
Hi,

I am modeling the sensitivity and specificity of 7 diagnostic tests in a bivariate binomial model using glmer.

glmer(formula = cbind(true, n - true) ~ 0 + seM + spM + seMM + spMM + seMouth + spMouth +
                          seSM + spSM + seTM + spTM + seULBT + spULBT + seW + spW +
                          (0 + sens + spec | studyName), data = Compare_DL.df, family = binomial, nAGQ = 1)

The model without separating diagnostic tests is

glmer(formula = cbind(true, n - true) ~  0 + sens + spec + (0 + sens + spec | studyName),
                      data = Compare_DL.df, family = binomial, nAGQ = 1)

The 7 test model assumes equal variances across tests.

The dataset includes sens, spec, seM, spM, etc as dummy index variables.
Both models can run and converge.

ANOVA shows improved fit:

                          Df   AIC      BIC        logLik     deviance  Chisq Chi Df    Pr(>Chisq)
Simple model    5 8987.8 9007.6 -4488.9   8977.8
Separate tests 17 6878.5 6945.8 -3422.3   6844.5      2133.3     12     < 2.2e-16 ***

I need to identify any separation of sensitivity and specificity properties among the 7 tests.

One possibility would be to jointly contrast seTesti – seTestj  = 0 and spTesti – spTestj = 0 for all pairwise comparisons of the 7 tests (with multiplicity adjustment).

However, I am unable to construct such tests in lme4. Is this possible in lme4? If so, what is the code?

I have looked at other packages (multcomp) without success.

As usual, all help will be appreciated.

Nathan Pace, MD, MStat
University of Utah
Salt Lake City, UT
n.l.pace at utah.edu<mailto:n.l.pace at utah.edu>



---


_________
____________________________________
    R-sig-mixed-models at r-project.org<mailto:R-sig-mixed-models at r-project.org> mailing list
    https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

_______________________________________________
R-sig-mixed-models at r-project.org<mailto:R-sig-mixed-models at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models


	[[alternative HTML version deleted]]