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I get an error message when fitting a full random two-level null model with the package R2MLwiN. My dataframe is a subset of a Multiple Indicator Cluster Survey developed by UNICEF for Mozambique. My response variable is agem.18 a binary ("Yes", "No") indicating whether the woman got married before the age of 18 y.o. or not.

> table(moz.20$agem.18, useNA = "ifany")

  No  Yes 
5934 5405

My two levels are, in descending order, province and w.id. This is the code I run

# Random effect
F1 <- logit(agem.18) ~ 1 + (1 | province) + (1 | w.id)
rand.eff <- runMLwiN(Formula = F1, D = "Binomial", data = moz.20)

This is the error message I get

Invalid link function specified: NA 
Error in runMLwiN(Formula = F1, D = "Binomial", data = df) :

I initially thought that the logit function was masked by the car package, but this is not the case. I also thought that the proble was in the denom call in the link function, but I read that R2MLwiN should automatically create the denom as a set of 1s. I do not get any error if I use the package lme4 with the same data, variable and levels:

(fit <- glmer(agem.18 ~ 1 + (1 | province), family = binomial("logit"), data = moz.20)

Generalized linear mixed model fit by maximum likelihood (Laplace
  Approximation) [glmerMod]
 Family: binomial  ( logit )
Formula: agem.18 ~ 1 + (1 | province)
   Data: moz.20
      AIC       BIC    logLik  deviance  df.resid 
14907.498 14922.170 -7451.749 14903.498     11337 
Random effects:
 Groups   Name        Std.Dev.
 province (Intercept) 0.5366  
Number of obs: 11339, groups:  province, 11
Fixed Effects:
(Intercept)  
   -0.04992

I do not encounter the same problem if I use a very similar formula included in the demo UserGuide09.R for the package R2MLwiN. 

(mymodel1 <- runMLwiN(logit(use) ~ 1 + lc, D = "Binomial", data = bang))

My only guess at the moment is that for some reasons, R2MLwiN fails to recognise my response variable agem.18 as binary.

Any suggestion?

Thanks

Manolo

Manolo
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  • What about `runMLwiN(Formula = logit(agem.18) ~ 1 + (1 | province) + (1 | w.id) , D = "Binomial", data = moz.20)`, Is it working? – A. Suliman Oct 07 '18 at 08:25
  • Yes, same error message. Sorry, I forgot to mention that I tried it already, both specifying `Formula = ` and not after the first parenthesis. – Manolo Oct 07 '18 at 08:58

1 Answers1

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Problem solved. It appears there is a bug in R2MLwiN, as noted by Chris Charlton in the R2MLwiN forum (see post here). I replicate the code written by Chris that shows the bug.

> library(R2MLwiN)
> data(bang, package = "R2MLwiN")
> (mymodel1 <- runMLwiN(logit(use) ~ 1 + lc, D = "Binomial", data = bang))

-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.02)  multilevel model (Binomial) 
Estimation algorithm:  IGLS MQL1        Elapsed time : 0.6s 
Number of obs:  2867 (from total 2867)        The model converged after 4 iterations.
Log likelihood:      NA 
Deviance statistic:  NA 
--------------------------------------------------------------------------------------------------- 
The model formula:
logit(use) ~ 1 + lc
Level 1: l1id      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                    Coef.   Std. Err.        z    Pr(>|z|)         [95% Conf.   Interval] 
Intercept        -1.12288     0.08348   -13.45    3.05e-41   ***     -1.28650    -0.95926 
lcOne_child       0.93275     0.12156     7.67   1.676e-14   ***      0.69450     1.17100 
lcTwo_children    1.09250     0.12509     8.73   2.466e-18   ***      0.84733     1.33768 
lcThree_plus      0.87224     0.10302     8.47   2.523e-17   ***      0.67033     1.07416 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the l1id level: 
                Coef.   Std. Err. 
var_bcons_1   1.00000     0.00000 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 

> bang$use.test <- bang$use
> (mymodel1 <- runMLwiN(logit(use.test) ~ 1 + lc, D = "Binomial", data = bang))
Invalid link function specified: NA 
Error in runMLwiN(logit(use.test) ~ 1 + lc, D = "Binomial", data = bang) :
Manolo
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