ENH: Adding in multiplicative replacement

qiime2 / q2-composition

BSD 3-Clause "New" or "Revised" License

5 stars 28 forks source link

ENH: Adding in multiplicative replacement #38

Closed mortonjt closed 7 years ago

mortonjt commented 7 years ago

This is adding a little more flexibility for the pseudocounts. Essentially, this will allow for smaller pseudocounts to be used if necessary.

We are adding the multiplicative flag here in order to maintain the ratios if specified.

ebolyen commented 7 years ago

Couple of questions:

If the multiplicative flag isn't provided then what would it mean to provide 0.01 as the pseudocount?
With the multiplicative strategy, could this method now support FeatureTable[RelativeFrequency]?

Some notes:

Parameter description is missing for multiplicative
Your pseudocount isn't bounded, so it looks like I could provide negative values. (Is that a viable thing to do, I would almost think that it might work pretty well to use -1...)

ebolyen commented 7 years ago

Closing, related functionality should probably go on q2-gneiss's add_pseudocounts

mortonjt commented 7 years ago

On Thu, Aug 17, 2017 at 11:46 AM, Evan Bolyen notifications@github.com wrote:

Closing, related functionality should probably go on q2-gneiss's add_pseudocounts

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/qiime2/q2-composition/pull/38#issuecomment-323160286, or mute the thread https://github.com/notifications/unsubscribe-auth/AD_a3UXLhjwlAxTk7P72VlNZjccdXUWhks5sZIpsgaJpZM4OF773 .