[R] How shall one present LRT test statistic in a scientific journal ?

[Peter Dalgaard]

David Winsemius wrote:
> 
> On Nov 26, 2009, at 12:14 PM, JVezilier wrote:
> 
>>
>> Hello !!
>>
>> I'm recently having a debate with my PhD supervisor regarding how to
>> write
>> the result of a likelihood ratio test in an article I'm about to submit.
>>
>> I analysed my data using "lme" mixed modelling.
>>
>> To get some p-values for my fixed effect I used model simplification
>> and the
>> typical output R gives looks like this:
>>
>> model2 = update ( model1,~.-factor A)
>> anova (model1, model2)
>>
>>       Model df       AIC             BIC         logLik         Test
>> L.Ratio     p-value
>> model 1     1 26  -78.73898   15.29707     65.36949
>> model 2     2 20  -73.70539   -1.36997     56.85270   1 vs 2    17.03359
>> 0.0092
>>
>> I thought about presenting it very simply copying/pasting R table and
>> writing it like: "factor A had a significant effect on the response
>> variable
>> (Likelihood ratio test, L-ratio = 17.033, p = 0.0092)"
>>
>> But my boss argued that it's too unusual (at least in our field of
>> evolutionary biology) and that I should present instead the LR statistic
>> together with the corresponding Chi^2 statistic since the likelihood
>> ratio
>> is almost distributed like a Chi2 (df1-df2), and then write down the
>> p-value
>> corresponding to this value of Chi.
>>
>> I looked up in the current litterature but cannot really find a proper
>> answer to that dilmena.
>>
>> So, dear evolutionary biologists R users, how would you present it ?
> 
> I am not an evolutionary biologist, but presumably your supervisor is
> one. Why are you picking a fight not only with him but with your
> prospective audience when there is no meaningful difference? Here is the
> p-value you would get with his method:
> 
>>> 1-pchisq( 2*(65.36949 -  56.85270), df=6)
> [1] 0.009160622
> 

As I understood the question, it *is* purely formalistic. I.e., what to
write, not what to do.

I'd say "L-ratio" is plain wrong, since this is not a ratio, but the log
of a ratio. "-2lnQ" or "-2logQ" is what my old teachers would write, but
pragmatically, I'd expect the best chances with editors and reviewers to
be "LRT: chi-square=17.03, df=6, p=0.092", possibly with LRT spelled
out. (Some journals like to have the df because it allows reviewers to
catch glaring mistakes like categorical variables treated as numeric.)

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
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