[GenABEL-dev] Tolerance level in GenABEL RUnit test

[L.C. Karssen]

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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L.C. Karssen
Utrecht
The Netherlands

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