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stephens999 / ashr

An R package for adaptive shrinkage
GNU General Public License v3.0
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optimization method options should be better documented #140

Open willwerscheid opened 6 months ago

willwerscheid commented 6 months ago

even a basic description of what the options mean would be helpful; at present there is nothing

pcarbo commented 6 months ago

@willwerscheid I pushed a couple commits. How's this?

optmethod: The method used to compute maximum-likelihood estimates of the mixture weights. The default setting, “mixSQP”, uses the fast sequential quadratric programming (SQP) method implemented in the mixsqp package. Alternative methods include the interior-point method implemented in the REBayes package (optmethod = "mixIP"), and a simple Expectation Maximization (EM) algorithm (optmethod = "mixEM"). For more details on the different options, see the help for functions estimate_mixprop, mixSQP, mixIP, mixEM, w_mixEM and mixVBEM.

pcarbo commented 6 months ago

@stephens999 Your review on this change is welcome, but not necessary.

willwerscheid commented 6 months ago

@pcarbo Looks great! Those functions mentioned at the end are all linked, correct?

pcarbo commented 6 months ago

They should be, yes. You can reinstall the package if you want to check this.