[GenABEL-dev] Tolerance level in GenABEL RUnit test

[L.C. Karssen]

I spoke too early: in fact almost all checks in runit.polylik.R fail:

> checkEquals(h2htNew$h2an$est,h2htOld$h2an$est, tolerance = tol)
Error in checkEquals(h2htNew$h2an$est, h2htOld$h2an$est, tolerance = tol) :
  Mean relative difference: 3.36492e-05

>     checkEquals(h2htNew$h2an$min,h2htOld$h2an$min, tolerance = tol)
Error in checkEquals(h2htNew$h2an$min, h2htOld$h2an$min, tolerance = tol) :
  Mean relative difference: 5.961843e-06

> checkEquals(h2htNew$residualY,h2htOld$residualY, tolerance = tol)
Error in checkEquals(h2htNew$residualY, h2htOld$residualY, tolerance =
tol) :
  Mean relative difference: 4.462787e-05

>     checkEquals(h2htNew$pgresidualY,h2htOld$pgresidualY, tolerance = tol)
Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY, tolerance
= tol) :
  Mean relative difference: 0.001496624

> checkEquals(h2htNew$InvSigma,h2htOld$InvSigma, tolerance = tol)
Error in checkEquals(h2htNew$InvSigma, h2htOld$InvSigma, tolerance = tol) :
  Mean relative difference: 0.004265527

>     checkEquals(h2htNew$measuredIDs,h2htOld$measuredIDs, tolerance = tol)
[1] TRUE


So the question remains: is this to be expected and should the tolerance
be set less strict or is this a true bug that needs fixing?


Thanks,

Lennart.

On 08-05-15 15:26, L.C. Karssen wrote:
> Dear list,
> 
> I just ran the unit tests in GenABEL's /insts/unitTests/ directory and
> get the following error:
> 
>   1 Test Suite :
>   GenABEL unit testing - 21 test functions, 0 errors, 1 failure
>   FAILURE in test.polylik: Error in checkEquals(h2htNew$h2an$est,
> h2htOld$h2an$est, tolerance = tol) :
>     Mean relative difference: 8.295007e-05
>   Error:
> 
>   unit testing failed (#test failures: 1, #R errors: 0)
> 
> 
> This is a test in the runit.polylik.R file. The variable "tol" is set to
>  2*.Machine$double.eps^0.5, which is equal to 2.980232e-08 on my
> machine. As you can see the difference in the unit test is more than
> three orders of magnitude higher.
> 
> The two variables that are compared are calculated like this:
>   h2htOld <- polygenic(formula,kin=gkin,df,llfun="polylik")
>   h2htNew <- polygenic(formula,kin=gkin,df,llfun="polylik_eigen")
> 
> Since I'm not an expert on the finer details of the various functions
> used in polygenic() I was hoping one of you could enlighten me and tell
> me if we should expect the comparison to give a difference of order 1e-8
> or that 1e-4 is good enough.
> 
> 
> Thanks for your help,
> 
> Lennart.
> 
> 
> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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