Output for % error in BF package/JASP

Comments

• EJ

  October 2016

  Great question. Let's ask Richard.
  Richard, can you explain how this is computed exactly?
  We will also mention this in our new paper on JASP which will be on my website soon.
  Cheers,
  E.J.
• EJ

  October 2016

  So Quentin kindly looked into the R code for the BayesFactor package. It seems that the following function is used to calculate the error for the cases where the package does not use the integrate function
  (obtained from https://github.com/richarddmorey/BayesFactor/blob/df23df41bea16e45c4e766c9104cc2a0ecc86e64/pkg/BayesFactor/R/common.R):

  propErrorEst = function(logX){
  logX = logX[!is.na(logX)]
  summaries = logSummaryStats(logX)
  exp( ( summaries$logVar - log(length(logX)) )/2 - summaries$logMean)
  }

  So this seems like a coefficient of variation (i.e., SD/mean).
  For the t-test, the relevant code features "err = exp(log(intgl[[2]]) - val)", where intgl[[2]] corresponds to an "estimate of the modulus of the absolute error" (from the integrate function documentation) and we think "val" corresponds to the log Bayes factor.

  Cheers,
  E.J.
• duplex_

  October 2016

  Trying to make sense here...it's a measure of the quality of the MCMC process? How much the BF varies between different chains? Seems to me that it is not absolutely necessary to report it?!
• EJ

  October 2016

  As long as the % is reasonably small (and it almost always is) there's no reason to report it. For ANOVA it can sometimes be a little bigger, but there we added the option to collect more samples to decrease the %. So is a a measure of the quality of the approximation. Sometimes the approximation requires MCMC, sometimes we use something else.
  Cheers,
  E.J.
• duplex_

  October 2016

  alright, thank you very much for the support!
• Markus

  January 2017

  Hi,

  I have the problem that when I conduct a paired samples t-test my %error is >7.000e-8. My BF is therefore not really valid and should not be interpreted, right?

  Best,
  Markus
• EJ

  January 2017

  7e-8 is a really small number!
  E.J.