susie_get_objective

[stephens999]

I think we should add this as an accessor function to the final elbo achieved

[gaow]

@stephens999 are you suggesting adding:

susie_get_objective = function(s) {
  s$elbo
}

?

[stephens999]

no, only the last value, s$elbo[length(s$elbo)]

we could have an option to get the full vector.... but by default I'm just interested in the value obtained so we can easily compare fits from different initializations.

On Fri, Oct 19, 2018 at 10:46 AM gaow notifications@github.com wrote:

@stephens999 https://github.com/stephens999 are you suggesting adding:

susie_get_objective = function(s) { s$elbo }

?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stephenslab/susieR/issues/58#issuecomment-431408280, or mute the thread https://github.com/notifications/unsubscribe-auth/ABt4xaz_zgM3jHtmLZ2QYO4LIDV35mCpks5umfPbgaJpZM4XwmHq .

[stephens999]

it has been modified so that if it is non-decreasing then the whole thign is returnd with a warning. But the problem is that this non-decreasing check is quite delicate (can be very close to 0). And in programming this behaviour (switching to return whole thing when user did not ask for it) is disruptive.

I suggest: i) change check to some tolerance eg 1e-6 instead of 0. ii) if check fails emit warning, but do not change value of all.

[gaow]

@stephens999 Thanks for the suggestions -- both have been implemented.

[zouyuxin]

@gaow I have a susie fit with elbo at each iteration as -Inf -1941.380 -1914.195 -1914.195. The 3rd and the 4th elements are the same. elbo[3] == elbo[4] is TRUE. But susie_get_objective gives warning: Objective is not non-decreasing.

[gaow]

Sorry @zouyuxin it's an artifact of the patch from 3 days ago (see above). The patch below should have fixed it ...

 susie_get_objective <- function(res, all = FALSE, warning_tol = 1E-6) {
-  if (!all(diff(res$elbo) >= warning_tol)) {
+  if (!all(diff(res$elbo) >= (-1 * warning_tol))) {
     warning('Objective is not non-decreasing')
   }

[stephens999]

Can we close this?