TODO

SHORT-TERM (release 1.0.22)

check with/add contributors
fix qAICc output
NEWS about start/fixed pull request
revdep checks


BUGS/ISSUES:

* change the way 'better fit found' is handled in profiles.
  with try_harder, push through anyway ... otherwise stop
  WITH AN ERROR and give the user a utility function for how to proceed?
  *Don't* want to return an object with a different structure --
  maybe attributes?

* is there a way to (optionally?) save the environment of the
   call so that fits could be profiled after being removed from
   their original environments? (maybe fixed?)

* consider "data-absent" flag for big data sets?

* remove "quad" method, replace with confint.default [NO]

* move calcslice from emdbook and make it more robust/general
  (different signatures: mle2 fits, numeric vectors)


* prettier multi-parameter profiles a la Bates/lme4
* ggplot2 profiles?

* fix confint plot to use linear interpolation when non-monotonic (done)
* pass parameters through from confint to profile (done?)
* nobs() methods
* filter use.ginv properly
* fix gradient with profile

* work on vignette: ask MM/PD/BDR about mismatch between confint (approx) and profile plot (backspline) ... ?

* DISABLE boundary warning when profiling ...
* try to do something about rescaling when hessian is problematic?
* add ginv for problematic hessians? (done)
* implement 'subset' argument
* check problems with optimizer="optimize" in tests/parscale.R
* allow ICtab etc. to recognize optim(), optimize() fits
  (ASSUMING that the function was a NLL)
* add optimizer() as alternative optimizer [DONE]
* fix par mfrow resetting glitch on plotting profile
* prettier profile plots (with lattice)?  xyplot for profiles?
* make sure numeric deriv modifications are working

* incorporate optimx (done)?  minpack.lm?

* proper initialization of intercept-less parameter()
    entries

* plot methods/fortify, a la ggplot2?

* add deviance() method [need S3-to-S4 conversion]

* make sure subset arg is really working!

* spurious error on mismatched parameter names

* spurious warnings in 1-parameter conf int: [FIXED]

   library(bbmle)
   m1 <- mle2(10~dbinom(prob=p,size=15),start=list(p=0.67))
   c1 <- confint(m1)

* do one-parameter profiles with optimize??

* use numDeriv library hessian() function instead of nlme::fdHess?
(or use nlme::fdHess to avoid loading whole package?)
  [DONE]

* turn off Hessian calculation for profile fits??
  [maybe DONE by virtue of previous fix]

* should print warning immediately if convergence fails

* some weird stuff with returned fit from found-better-fit profile --
treating profiled value as fixed ...

* replace approx() in confint() with backspline?
  general solution for non-monotonic profiles?

BUG:   order of parameters matters for L-BFGS-B
  (fixed)

  adjusting parameter vectors for lower, upper, parscale, ...
    when some params are fixed ...

  sort out names BS -- when can we safely remove names?


TO DO:

model-averaging?

more documentation -- especially S4 methods!
   especially:
     profile
     plot profile
     confint

catch/interpret more error messages?
  (try to filter last.warning?)

add DIC to IC tabs?
lmer?

WISHLIST:
start as FUNCTION (i.e., self-start)
analytic derivatives
relist
subset
plot.predict
drop1, add1, etc.
link functions ("identity","log", "logit", etc.)
delta method standard error calcs
tranformations on LHS of formula (i.e. use
  link rather than inverse-link function?  only
  possible if link is known and invertible:

   inverse 
   log
   logit  (qlogis)
   probit (qnorm)

  etc.

clean up/argue about data handling: closures etc. etc. etc...

document argument handling:

  start must be a named vector or a named list
       [OR?? inherit from parnames(minuslogl)?]
  if start is not a list (i.e. a numeric vector)
  set vecpar TRUE
  convert start to a list

  if missing and default.start is TRUE use formals(minuslogl)