NEWS | R Documentation |
bbmle News
Changes in version 1.0.25.1
CRAN COMPATIBILITY
remove/ignore spurious .Rout files
Changes in version 1.0.25
USER-VISIBLE CHANGES
-
mle2.options()
function is now exported
CRAN COMPATIBILITY
vignettes will build without suggested packages
Changes in version 1.0.24 (2021-08-06)
USER-VISIBLE CHANGES
new
namedrop_args
argument tomle2
(don't drop argument names within sub-lists of data)allow user-specified covariance matrix for importance sampling
Changes in version 1.0.23 (2020-02-03)
suppress some warnings in tests for cross-platform/CRAN compatibility
Changes in version 1.0.22 (2019-12-19)
BUG FIXES
intercept-only parameters were handled wrong (GH #8)
fix error-handling (class vs. inherits) for R 4.0 compatibility
NEW FEATURES
-
pop_pred_samp
to compute population prediction samples, tweaking non-positive-definite covariance matrices and using importance samples if necessary/specified. This is still VERY experimental/in flux! added
dnorm_n
function for Normal densities with the standard deviation parameter profiled outadd
slnorm
function for log-Normal densities (median and mean only for now)IC tables now have an
as.data.frame
method (from @iago-pssjd on GitHub)
USER-VISIBLE CHANGES
the evaluated
start
andfixed
components of the call are now stored in thecall
component (Daniel B. Stouffer)
Changes in version 1.0.20 (2017-10-30)
BUG FIXES
fixed buglet: flipped profile plot axes, confint for negative values
USER-VISIBLE CHANGES
-
summary.mle2
is now exported, for use by other packages small fixes to AIC(c) methods
Changes in version 1.0.19 (2017-04-08)
fixed bug: evaluate
call$method
so that profiling/updating works within a function environmentmake AICtab smarter about NA values
fix BIC bug (infinite recursion)
hessian computation uses gradient function if provided
basic continuation method implemented for profiling (with stubs for smarter methods)
mle2 stores its calling environment for more flexibility when re-evaluating, e.g. in profiling (could lead to occasional surprises, e.g. if saving a fitted mle2 object with large objects in its calling environment)
Changes in version 1.0.18 (2016-02-11)
update slice functionality; allow for explicit ranges
CRAN updates (import from base packages)
Changes in version 1.0.17 (2014-01-01)
new warning if ~dnorm is called with sd implicitly ==1
some internal tweaking to slice functionality
updated to allow for
MuMIn
v 1.10.0 changes
Changes in version 1.0.16 (2014-01-01)
fix
mnames
behaviourslight vignette cleanup
Changes in version 1.0.15 (2013-11-20)
add
logLik
option to IC tables, more use ofnobs
methodsminor improvements to
slice
functionality
Changes in version 1.0.14 (2013-08-24)
more CRAN tweaks
Changes in version 1.0.13 (2013-08-22)
.Rbuildignore tweaks for CRAN
Changes in version 1.0.12 (2013-08-22)
vignette tweaks
add Depends: R>=3.0.0
Changes in version 1.0.11 (2013-08-19)
add .Rbuildignore for CRAN tests
Changes in version 1.0.10 (2013-08-18)
adapt to updated optimx
tweaks for CRAN compliance
Changes in version 1.0.9 (2013-06-23)
switch from aod to aods3 in vignettes
switch vignette to knitr
Changes in version 1.0.8 (2013-04-23)
tweaks to
print.ICtab()
Changes in version 1.0.7
warn on convergence failure
Changes in version 1.0.6
fixed (fairly obscure) bug in assigning data environment to gradient function; replace 'gr' in call with appropriately evaluated version
Changes in version 1.0.5.3 (2012-09-05)
changed some cat() to message()
Changes in version 1.0.5.2 (2012-07-29)
=======
add .Rbuildignore for CRAN tests
Changes in version 1.0.10 (2013-08-18)
adapt to updated optimx
tweaks for CRAN compliance
Changes in version 1.0.9 (2013-06-23)
switch from aod to aods3 in vignettes
switch vignette to knitr
Changes in version 1.0.8 (2013-04-23)
tweaks to
print.ICtab()
Changes in version 1.0.7
warn on convergence failure
Changes in version 1.0.6
fixed (fairly obscure) bug in assigning data environment to gradient function; replace 'gr' in call with appropriately evaluated version
Changes in version 1.0.5.3 (2012-09-05)
changed some cat() to message()
Changes in version 1.0.5.2 (2012-07-29)
>>>>>>> .r116
remove BIC definitions (now unnecessary/should be adequately defined in core R)
add explicit Depends: on stats4
note that development optimx (2012.05.24+) now fails on profiling when reduced model is 1-dimensional (i.e. for a 2-parameter model)
Changes in version 1.0.5.1 (2012-07-17)
remove spurious .RData file; version bump
Changes in version 1.0.5 (2012-05-15)
wrapped eigen() call to prevent failure of eigenvalue ratio summary when hessian is bad
fix bug: forgot to export summary method for mle2
add
exclude.fixed
argument tocoef
methodfix bug: single lower/upper parameter, or prof.lower/prof.upper parameter, not interpreted properly in profile/confint
add and document
slice
methods: change from old (profile-like) behavior, old version is available assliceOld
DESCRIPTION/NAMESPACE fixes, move most Depends: to Imports: instead (except methods package)
Changes in version 1.0.4.2 (2012-02-25)
fix bug in gradient/vecpar/profiling interaction (Daniel Kaschek)
improve (and document) uniroot method for confint: now respects box constraints
fix issue where bobyqa (optimx) strips parameter names from result
Changes in version 1.0.4.1 (2012-01-27)
remove a bit of installed junk; vignette fix
Changes in version 1.0.4 (2012-01-02)
fix imports for latest version of R-devel
Changes in version 1.0.3
modified starting value code and documentation slightly: now allows per-parameter lists. Updated docs.
Fixed bug that would screw things up if 'i' were used as a parameter.
Update vignette to conform to MuMIn changes
Changes in version 1.0.2 (2011-09-07)
fixed buglet in detection of no-intercept models when setting starting values
Changes in version 1.0.1 (2011-08-04)
Turned off some warnings when skip.hessian=TRUE (e.g. in profile)
Calculate max grad and Hessian eigenval ratio, add to "details"
(Should add accessor methods)
Fixed NAMESPACE to export methods etc etc properly; removed universal exportPattern directive
Changes in version 1.0.0 (2011-06-17)
mainly just a version bump for CRAN
added tag for variables in profile/confint warnings
lots more technical information in vignette about profiling algorithm
Changes in version 0.9.9 (2011-05-14)
changed NEWS to NEWS.Rd
fixed bug for "optimize" – profile etc. now respect bounds
eliminated warning about bounds names if all identical
add "try_harder" flag to profiling (ignore flat spots, NAs ...)
Changes in version 0.9.8
gradient functions work better with fixed parameters, hence with profiling
profile plot reverts to linear for non-monotonic profile
added warning in confint for non-monotonic profile, or for non-monotonic spline fit to monotonic profile; revert from spline+linear to linear approximation in this case
various documentation improvements
optimx improvements
require data= argument when using formula interface
turn off hessian computation in profile
allow use of MASS::ginv
Changes in version 0.9.7
bug fix in calc_mle2_function for no-intercept models (thanks to Colin Kremer)
fixed optimx, added 'user' option
Changes in version 0.9.6
changed hessian calculation to use numDeriv code (causes tiny changes to hessian results that could matter in edge cases). Too lazy to provide a backward compatibility mode ...
documented optimizer= choices in ?mle2
Changes in version 0.9.5.1
fixed bug in AICc (David Harris)
Changes in version 0.9.5
added NAMESPACE, various fixes to go with that
beginnings of an RUnit testing framework
tweaked vignette
added prof.lower, prof.upper to profile()
added "optimize" to list of allowed optimizers, some bug fixes
Changes in version 0.9.4.1
tweaked par() resetting in profile plots
Changes in version 0.9.4
more qAICc fixing
Changes in version 0.9.3 (2009-09-18)
tweaked handling of bounds: profile now succeeds on some 1D problems where it didn't before
added deviance, residuals methods
added newparams argument to predict, simulate; newdata argument to simulate
added vignette (stub)
added explicit params argument, to help sort out full parameter specifications when parameters is non-NULL
Changes in version 0.9.2 (2009-08-10)
fixed predict() for case with parameters
added snorm
changed ICtab defaults to weight=TRUE, base=FALSE, sort=TRUE
Changes in version 0.9.1
added simulate method (formula interface only)
fix AICctab bug
remove spurious cat/print in profile
fix qAIC bug
Changes in version 0.9.0 (2008-08-26)
fix Tom Hobbs bug: named lower/upper/parscale/ndeps get rearranged properly, otherwise rearrange in order of "start" and issue a warning
documentation tweak for S4 as.data.frame
added sbeta to list of known distributions
removed nlme requirement & auto-loading
Changes in version 0.8.9 (2008-08-04)
version bump, submit to CRAN
added predict method
Changes in version 0.8.8 (2008-07-10)
added flexibility for profile plotting (main, x labels etc.); added examples
added an instance of "namedrop" to fix naming problem
added tol.newmin to slice etc.
added check for numeric return from profile within confint
fixed bugs in profile plotting when profile is restricted to a subset of variables
added tests for par() to reset to original on exit
improved profile documentation
replicate std.err if specified in profile
add as.data.frame
tweak tol.newmin (better fit found during profile) code
Changes in version 0.8.7 (2008-05-12)
version bump, moved to R-forge.
reordered NEWS file (most recent first)
Changes in version 0.8.6.1 (2008-03-22)
tweaked stop-on-better-fit code
fixed (?) qAIC(c) methods
Changes in version 0.8.6 (2008-03-26)
tweak/fix to ICtab documentation (thanks to Tom Hobbs)
added qAIC(c) methods (not working yet!)
Changes in version 0.8.5.1
oops. Fixed infelicity (bug?) in new environment manipulation
Changes in version 0.8.5
tweaked environment/data assignment to preserve original minuslogl environment better
Changes in version 0.8.4
changed plot.profile.mle2 options (added onepage etc., made plot.confstr=TRUE by default)
Changes in version 0.8.3
added warning about too-short lower/upper
added documentation
Changes in version 0.8.2
fixed bug in AICctab
cosmetic change to printing – save call.orig
moved ChangeLog to NEWS
Changes in version 0.8.1
fixed (?) environment bug
tried to use built-in relist, but failed: renamed relist to "relist2" (try again later)
documented get.mnames (auxiliary function for ICtabs)
started to add gr (gradient) capability – NOT TESTED
Changes in version 0.8
changed ICtab to allow either ICtab(x,y,z) or ICtab(list(x,y,z)) (L <- list(...); if is.list(L[[1]]) && length(L)==1)
Changes in version 0.7.7
fix bug in profiling: all optim() methods EXCEPT L-BFGS-B. return the value of the objective function if given a function with no arguments/zero-length starting parameter vector (this is the situation with "profiling" a 1-D function). L-BFGS-B gives funky answers. added a check for this case. (may need to check behavior for alternate optimizers (nlm etc)) [this behavior triggered a "found better fit" error when profiling 1D functions with L-BFGS-B]
changed behavior when finding better fit during profiling to return new parameters
Changes in version 0.7.6
tweak vignette
fixed second major AICc bug (was fixed in mle2 method, but not in logLik method)
Changes in version 0.7.5
change "ll" to "LL" in examples for clarity
tweaked anova reporting of models (wrap instead of truncating)
added (undocumented) show.points option to profile plot to display actual locations of profile evaluation
tweaked profile to behave better when profiling variables with constraints (upper, lower)
moved vignette to inst/doc where it belongs
ICtab hack to protect against package:aod definition of AIC(logLik)
added submit stub
tweaked slice.mle2-class docs for consistency
fiddled with vignette
preliminary code to allow non-monotonic profiles
preliminary add nlm to list of optimizers (untested)
add aod, Hmisc, emdbook to VignetteDepends and Suggests:
Changes in version 0.7
better df extraction in ICtab
minor bug fix for AICc (allows AICc of nls objects)
handle models with -1 in formula better: starting values set "all equal"
made ANOVA formula line-length accessible
added skip.hessian and trace arguments to mle2
messed around with BIC definition – attempt at consistency with nlme
added rudimentary support for nlminb, constrOptim
nlme now required for fdHess (which is required for nlminb since it doesn't compute a finite-diff Hessian)
Changes in version 0.6
add experimental formula interface
change all names from mle to mle2 to avoid confusion/conflicts
with stats4 version of mle
change internal structure of data evaluation
worked on vignette
added optimizer slot (stub)
Changes in version 0.5
fix AICc bug! (was deviance+2*k*(k+1)/(n-k-1), not AIC+2*k*(k+1)/(n-k-1))
Changes in version 0.4
change AIC to AICc for corrections
add AICtab for weights, delta, sort ... options
expose error messages occuring within profile()
uniroot tries harder to find a valid endpoint
truncate terms in anova.mle at 80 characters
Changes in version 0.3
enhanced anova method, works with print.anova
tweaked namedrop() code – ??
Changes in version 0.2
added parnames, parnames<-
minor fix to allow "profiles" of 1-parameter models (skip fdHess call)
minor change to print method for mle results
tweaking "vecpar" (to allow parameter vectors in objective function)
removed fdHess/nlme dependency