swh:1:snp:91acd9f2f5b4337f8c431e6680f74dbac9657f2f
Tip revision: 1895b1776e1c50bdf34cff2d1b8413621bad7261 authored by Kamil Bartoń on 31 August 2022, 23:10:02 UTC
version 1.47.1
version 1.47.1
Tip revision: 1895b17
NEWS
- MuMIn package news:
Changes in version 1.47.1 (2022-08-31)
- Pleasing RCheck: updated NEWS file so that it can be parsed by the
`news` function.
Changes in version 1.47.0 (2022-08-30)
- (changed) plot.model.selection: Most notable change is the way the
'col' argument is interpreted. The default colours use now
`hcl.palette` and differ from the previous version. There is no backward
compatibility.
- Long defunct `mod.sel`, `tTable` and `updateable2` have been removed.
`importance` is now defunct (use `sw` instead).
Changes in version 1.46.7 (2022-08-24)
- Rd files have been updated to meet changes in the HTML R help system,
starting with R 4.2.0. Hence, the minimum required version of R is now
4.2.0.
Changes in version 1.46.6 (2022-07-31)
- (fixed) print.model.selection: Abbreviations now only include existing
values (i.e. after subsetting).
- (fixed) merge.model.selection: "modelList" attributes are now preserved.
Changes in version 1.46.5 (2022-06-07)
- (fixed) getAllTerms.gamlss: error with intercept only models and formulas
containing offset (reported multiple times on Stackoverflow)
Changes in version 1.46.4 (2022-06-07)
- (fixed) dredge: in a rare case when intercept terms were passed as "fixed",
some variable combinations were erroneously dropped from the result.
Changes in version 1.46.0 (2022-02-23)
- (fixed) r.squaredGLMM: now gives correct values for negative binomial models
(thanks to Shuang Zhang for research)
Changes in version 1.45.1 (2021-12-08)
- (added) .vcov a wrapper for vcov returning result in a consistent format
(a matrix)
Changes in version 1.45.0 (2021-11-25)
- pdredge is deprecated in favour of `dredge` with "cluster" argument.
Changes in version 1.44.6 (2021-05-19)
- added stringsAsFactors=TRUE to most 'as.data.frame' occurences to bring back
the desired behaviour (which changed in R 4.0.0).
Changes in version 1.44.5 (2021-05-11)
- std.coef: now matches coefficient names with model matrix column names.
Changes in version 1.44.4 (2021-04-20)
- coefTable.betareg - now includes residual df.
Changes in version 1.44.3 (2021-03-05)
- (fixed) getAllTerms.zeroinfl: error when the function was called from non-global
environment (spotted by Richard Shefferson)
Changes in version 1.44.2 (2020-07-14)
- (fixed) error with makeArgs (and hence dredge) with glmmTMB with non-symbol
response.
Changes in version 1.44.1 (2020-06-25)
- importance: is now formally deprecated with a warning. Use `sw` instead.
Changes in version 1.44.0 (2020-05-28)
- (added) plot method for the class "averaging" produces a dot-and-whisker plot of
coefficients. This uses a new general function `coefplot` that can be used
to make plots for arbitrary model types.
Changes in version 1.43.19 (2020-05-22)
- (fixed) plot titles in plot.coefTable.
Changes in version 1.43.18 (2020-05-18)
- r.squaredGLMM: issues a warning about zero-inflation and dispersion model being
ignored in the calculation of R2 rather than an error as before (request
from Alexander Bruckner, inspired by the code by Ben Bolker:
https://github.com/glmmTMB/glmmTMB/blob/master/glmmTMB/inst/misc/rsqglmm.R)
- (fixed) some issues with evaluating in non-global environment (`updateable` and
'na.action' checking)
Changes in version 1.43.17 (2020-04-14)
- Merely refreshing date stamp to please CRAN policies.
Changes in version 1.43.16 (2020-03-12)
- (added) specs for 'unmarkedFitPCount' with mixture = "ZIP" (spotted by Hannah
Clyde)
Changes in version 1.43.15 (2019-12-19)
- (fixed) fatal error with QIC.geem introduced in the previous version
(reported by Lee McDaniel)
Changes in version 1.43.14 (2019-12-18)
- (fixed) example(QIC) causing an error after recent update of 'geepack'.
- Added quasiLik/QIC for the negative binomial family (reportedly supported only
by 'geeM::geem').
Changes in version 1.43.13 (2019-12-14)
- (fixed) get.models: in the absence of a 'global model', the argument 'subset'
was ignored and a list of all models was returned.
Changes in version 1.43.12 (2019-12-11)
- (fixed) [p]dredge: error while formatting the error message about an overlarge
number of predictors (found by a certain 89_Simple on Stackoverflow).
Changes in version 1.43.11 (2019-12-09)
- (fixed) getAllTerms now recognizes structured terms of form `struc(terms|group)`
properly as random effect terms;
- (fixed) dredge, model.sel: delta was not calculated if any rank was NA.
Changes in version 1.43.10 (2019-12-05)
- (removed) conflicting methods which are now defined in their 'survival' package
(nobs.coxph, nobs.survreg). Because of that, MuMIn now depends on
survival >= 3.1.0.
Changes in version 1.43.9 (2019-06-21)
- (fixed) 'r.squaredGLMM' failed when order of interaction components in RE part
of model formula were not in order of appearance (found by
Gabriel Baud-Bovy)
- (removed) 'predict.merMod' replacement to avoid the conflict of registered
methods. Note that the original method does not calculate 'se.fit', so
currently there is no out-of-box way to produce averaged predictions
with standard errors.
Changes in version 1.43.8 (2019-04-15)
- (fixed) methods for 'gamlss' (reported by Andras Farkas)
Changes in version 1.43.6 (2019-04-08)
- (fixed) if conditions with "length > 1 in coercion to logical" error produced by
the new Rcheck.
- (fixed) updated 'tests' to make up for 'spautolm' moved from 'spdep' to
'spatialreg'.
Changes in version 1.43.4 (2019-04-04)
- (fixed) minor changes to the quasi-likelihood function
Changes in version 1.43.3 (2019-03-19)
- (added) methods for 'gamlss' (suggested by Anne Loosen)
- (fixed) QIC,quasiLik: now gives results compatible with those of
wgeesel::QIC.gee.
Changes in version 1.43.2 (2019-03-16)
- 'sw' (for "Sum of Weights") is now preferred to 'importance' (which is
still available, but is going to be deprecated in future). This is because
of the controversies about SoW being a valid measure of actual variable
importance.
- [p]dredge: max. number of predictors is now correctly calculated (depending on
the number of variants)
Changes in version 1.43.1 (2019-03-06)
- (added) new model structure for unmarkedFitGDS (gdistsamp) with alpha parameter
(thanks to Alba Estrada)
Changes in version 1.43.0 (2019-02-28)
- (fixed) in QICu, the number of parameters was mistaken for number of
observations (reported by Richard Fredrickson)
- (added) some methods for wgeesel::wgee objects.
Changes in version 1.42.5 (2019-01-02)
- r.squaredGLMM: added the argument "envir" which is passed to `.nullFitRE`. This
can be used in case of issues with model data not being found (reported by
Eliot McIntire)
Changes in version 1.42.4 (2018-12-05)
- (fixed) r.squaredGLMM.merMod: error when the function was called in an
environment different than .GlobalEnv (spotted by a certain Martin on
Stackoverflow)
Changes in version 1.42.3 (2018-07-31)
- (added) dredge: the subset expression `.(x)` now accepts an additional argument
for the allowed term orders. For example `.(X, 2:10)` means
"at least one 2nd or 3rd order interaction of 'X'". The `.` pseudo-function
has also a new alias: "with", e.g. `with(X, 2:10)`.
Changes in version 1.42.2 (2018-07-27)
- (fixed) r.squaredGLMM: handle the case when some coefficients are not estimated
and NA
Changes in version 1.42.1 (2018-07-21)
- tests have been modified to prevent CRAN check errors on some systems.
- (fixed) arm.glm, armWeights: now use a random sample to select a training set.
armWeights: no longer give a warning about "longer object length"
Changes in version 1.42.0 (2018-07-17)
- (updated) methods for "unmarkedFit" models have been rewritten and should work
properly with all subclasses. Added missing support for
"unmarked::unmarkedFitOccuFP" (reported by Tara Hohoff)
R2GLMM added an option to disable "null fit warning"
- (fixed) getAllTerms.lme: now gives a correct value for response in "binomial"
glmmPQL ("zz" previously)
- (fixed) testSmoothKConsistency: (used by `model.avg` with 'gam' models) works
now with 'gam's including no smooth terms.
Changes in version 1.41.1 (2018-07-13)
- (fixed) workaround for clmm's (package "ordinal") annoyance: it needs explicit
"1" in the formula if there are no other fixed terms. That resulted in
intercept-only model calls generated by `dredge` being rejected.
(kindly reported by Jörg Albrecht)
Changes in version 1.41.0 (2018-07-12)
- (updated) r.squaredGLMM: revised to incorporate new developments in
Nakagawa et al (2017). Methods exist for merMod, glmmTMB, glmmADMB, glmmPQL,
cpglmm, and lm classes.
Changes in version 1.40.8 (2018-06-18)
- Model description - simplified handling of the model's family description in
the model selection tables, so it does not require `family()$family` string
being an existing function name. The drawback is that now a default link
function is not detected and its name always appears in the column (
before e.g. "binomial(logit)" appeared as "binomial()").
Changes in version 1.40.7 (2018-06-14)
- Addad a workaround to accommodate glmmTMB specific families (which do not have
a matching function) (reported by a certain Gitu on Stackoverflow)
Changes in version 1.40.6 (2018-05-16)
- (fixed) makeArgs, getAllTerms: compatibility with glmmTMB - random terms in
formulas other than cond have not been handled properly (discovered via
Mollie Brooks on GitHub)
Changes in version 1.40.5 (2018-05-14)
- `.checkNAAction` now handles a case of 'na.action' formal argument being a call
(e.g. `getOption(na.action)` in glmmTMB) (spotted by Ben Bolker)
Changes in version 1.40.4 (2018-01-30)
- Elaborated the Description field.
Changes in version 1.40.3 (2018-01-29)
- Removed superfluous method replacements for models from package "survival".
`predict` functions for "gls" and "lme" are no longer registered as S3
methods in NAMESPACE.
Changes in version 1.40.2 (2018-01-19)
- (fixed) getAllTerms.glmmTMB: error with models including offset term
(spotted by Kate Plummer)
Changes in version 1.40.1 (2017-11-30)
- (added) Support for "glmmTMB" models (incentive from Kaitlyn Zerr)
Changes in version 1.40.0 (2017-09-30)
- (fixed) long broken support for "unmarkedFit" models has been restored
(because of the utterly inconsistent structure of these objects it is not
guaranteed to work in all cases).
- (fixed) R.squaredGLMM: error with very long RE formulas (reported by Siti Binte
Faizal)
Changes in version 1.16.7 (2017-08-10)
- A few minor things fixed.
Changes in version 1.16.6 (2017-07-11)
- (fixed) print.summary.averaging: warning when fitting function name was a call
rather than a symbol, e.g. lme4::lme (reported by Chen Lei).
Changes in version 1.16.5 (2017-05-24)
- (fixed) predict.gls updated to match current version in nlme (reported by a
certain Asteraceae on Stackoverflow)
Changes in version 1.16.4 (2016-11-21)
- (fixed) makeArgs.mark: reverted to a working version (this bug was introduced in
1.15.2/rev. 373. Reported by Jay Rotella)
Changes in version 1.16.3 (2016-09-14)
- (fixed) dredge: recognizes when global model's data is a function in a smarter
way
Changes in version 1.16.2 (2016-09-01)
- (fixed) plot.model.selection: problem in case with only one model in the
table (reported by Ryan Rothman on Stackoverflow)
- dredge: recognizes when global model's data is a function (which is not allowed
as it may cause sub-models being fitted to different datasets)
Changes in version 1.16.1 (2016-07-29)
- New suite of functions to support model averaging. It is based on original
code developed by Carsten Dormann, as an outcome of the model-averaging
workshop held in Freiburg in 2015.
- (added) cos2Weights, BGWeights, jackknifeWeights, stackingWeights: calculate
various types of model weights.
- (added) loo: RMSE/log-likelihood based on leave-one-out cross-validation
- (added) armWeights: similar to `arm.glm` but produces model weights.
- (fixed) model.avg/model.sel: problems with intercept only models
(spotted by a certain Teresa on Stackoverflow)
Changes in version 1.15.8 (2016-07-05)
- (fixed) dredge: no longer produces an error in the rare case when dependency
matrix was an empty matrix [0x0].
- (fixed) r.squaredGLMM: error with naming of variance components in 'lmer'
models. (both problems reported by a certain Teresa on Stackoverflow)
- (added) Weights: has an assignment version, so weights can be applied to an
"averaging" object.
- get.models: now can extract models also from an "averaging" object (only when
it was created with model objects).
Changes in version 1.15.7 (2016-01-21)
- (fixed) dredge: number of variables is limited to 30 to avoid integer overflow
(reported by Sarah Grogan).
Changes in version 1.15.6 (2015-12-21)
- (fixed) get.models, dredge, subset.model.selection: enclosure for the subset
expression evaluation is now `parent.frame()` rather than `.GlobalEnv` as it
was before (incentive from Philipp Maier).
- (fixed) coeffs.survreg, coefTable.survreg: log(scale) added to coefficients,
when it is estimated (suggested by Nicolas Rode).
Changes in version 1.15.5 (2015-11-25)
- (fixed) [p]dredge: error with model with offsets in formula when 'subset'
expression was given (reported by Adam Cummings)
- (fixed) [p]dredge: in some cases the generated combinations did not obey the
subset matrix (reported by Ben Augustine)
- (fixed) model.selection column assignment "[<-" was broken when (spotted by
a certain abmiller8 on Stackoverflow)
- model.avg: warns when averaged 'gam' models have smooths with different
dimension for the same variable.
Changes in version 1.15.4 (2015-10-16)
- (fixed) rbind, merge methods for "model.selection": wrong order of names of
columns and rows (spotted by Ben Augustine)
Changes in version 1.15.3 (2015-09-06)
- (fixed) Weights: bug that caused that NaN's were returned (reported by Carles
Alcaraz)
Changes in version 1.15.2 (2015-07-07)
- (added) summary.coefTable: tries to calculate p-values for coefficients, nicer
printing using printCoefmat
Changes in version 1.15.1 (2015-07-02)
- added imports from all the default packages added to NAMESPACE in order to
satisfy CRAN's new stricter RCheck.
Changes in version 1.15.0 (2015-07-01)
- (added) arm.glm: implements model averaging with weights calculated via ARM
("adaptive regression by mixing") algorithm.
- "averaging" object: the elements "coef.shrinkage" and "coefTable" are
replaced by matrix named "coefficients". The "Pval-tables" are accessed via
summary(averaging)'s elements "coefmat.full" and "coefmat.subset". Objects
created with previous versions will be automatically converted if needed.
- [p]dredge: argument 'm.lim' replaces 'm.min' and 'm.max' (which are still
present, but deprecated).
- "model.selection" object: changing or removing essential columns (i.e.
everything except 'varying' and 'extra') converts the object to a plain
"data.frame" and drops all additional attributes.
- (added) rbind.model.selection: combine multiple "model.selection" objects.
- (added) 'xtable' methods for "averaging" and "model.selection" objects.
- (fixed) updateable: does not cause infinite recursion when the resulting wrapper
has the same name as the wrapped function.
- (fixed) exprApply: now can deal with function expressions and 'expression's
longer than one.
Changes in version 1.14.1 (2015-06-12)
- (fixed) [p]dredge no longer gives coefficient values as NA with [g]lmer
(reported by Aitor Cevidanes).
- Some tidying-up of manual and data (response in 'Cement' and 'Beetle' moved to
first column so that formula(data) is correct).
Changes in version 1.14.0 (2015-06-03)
- (added) partial.sd, std.coef: calculate partial std. deviation and standardize
model coefficients. 'beta.weights' is now deprecated in favour of
'std.coef'.
- dredge, model.avg, model.sel: argument 'beta' is modified to allow for
standardizing with SD or partial SD.
- coefTable, coeffs: method for class 'aodml' (package 'aod3') no longer return
'phi' coefficients. This is for consistency with results of 'vcov' and
'coef', as well as their counterparts for 'glimML' models.
- Removed all methods for 'mer' objects (used in lme4 < 1.0.0)
Changes in version 1.13.10 (2015-06-01)
- (fixed) compatibility with lme4-1.1.8, 'null.fit' now works properly with 'gamm'
objects.
Changes in version 1.13.9 (2015-05-28)
- stdize: improved interpretation of the argument "scale".
- new dataset "GPA" ("First-year college Grade Point Average" referred in Burnham
& Anderson (2002)).
Changes in version 1.13.8 (2015-05-22)
- (added) QIC support for 'geem' models (request from Lee McDaniel).
Changes in version 1.13.7 (2015-05-14)
- coefTable: method for 'averaging' objects gains new arguments "full" and
"adjust.se".
- (fixed) getAllTerms: now correctly names coefficients of 'unmarked::gdistsamp'
models (reported by Nathan Hostetter)
Changes in version 1.13.6 (2015-05-01)
- (fixed) model.avg, model.sel: now better distinguish model objects from lists of
objects.
Changes in version 1.13.5 (2015-04-15)
- (fixed) r.squaredGLMM: method for 'lme' class with a multilevel grouping
structure (reported by Alex Gunderson)
Changes in version 1.13.4 (2015-02-24)
- coefTable.coxph: added workaround for the case when variance-covariance matrix
is NA (as in results of 'intcox') (reported by Vanessa Boukili)
Changes in version 1.13.3 (2015-02-19)
- get.models+subset.model.selection: unified 'subset' expression interpretation
- dredge: no longer exceeds memory limit with very complex models, and its
efficiency has somewhat improved. With trace=2 a progress bar is displayed.
- model.sel: has new attribute 'fit'.
- "averaging" object now stores component models.
- model.sel,subset,get.models: unified interpretation of the "subset" expression
- (fixed) extracting random effects formula (affected 'r.squaredGLMM' for 'lmer',
reported by Yevgen Matusevych)
- (fixed) makeArgs (and hence 'dredge'): formulas with no intercept are now
handled correctly in 'zeroinfl' models.
Changes in version 1.13.2 (2015-01-08)
- (fixed) makeArgs (and hence 'dredge'): gave error if no random effects
was specified in 'glmmadmb' model (reported by Szymek Drobniak).
Changes in version 1.13.1 (2015-01-06)
- (fixed) getAllTerms: now properly handles single formula in 'hurdle' and
'zeroinfl' models (package 'pscl').
Changes in version 1.13.0 (2015-01-03)
- (added) get.response: utility to extract response variable.
Changes in version 1.12.4 (2014-12-26)
- (added) stdizeFit: utility to modify model object or a call to modelling
function to use standardized data.
Changes in version 1.12.3 (2014-12-23)
- (fixed) checkModels: workaround for the "dotted argument identity" issue (namely
sometimes equal "..1"s are not identical).
Changes in version 1.12.2 (2014-12-19)
- (fixed) [Q]AICc: previously they ignored REML argument for some model classes.
The code has been rewritten so that most of the core calculation is done by
a common internal function.
Changes in version 1.12.1 (2014-12-16)
- minor corrections to the documentation
Changes in version 1.12.0 (2014-12-16)
- (added) exprApply: new function to manipulate expressions (with example of use
with 'dredge' to manipulate terms inside formula).
- dredge, subset.model.selection: curly braces can be used to indicate complex
terms (e.g. {I(x)} or {s(x,k=2}) instead of backtick quotes. Spacing in
these expressions is irrelevant (as both whitespace and backticks seem to be
a problem for some users).
Changes in version 1.11.3 (2014-12-10)
- (added) stdize: new function for standardizing data
- (fixed) smarter sorting of interaction terms in coefficient names
- print.model.selection: rank function call is added to the output
Changes in version 1.11.2 (2014-12-01)
- (fixed) r.squaredGLMM: in "binomial" family models the residual variance is
used for additive dispersion (thanks to Paul Johnson).
There is still issue with 'lmer' with 'subset' argument, and
observation-level random term has to be specified manually.
- (fixed) some formula-decomposition related functions (that sometimes caused
problems with 'r.squaredGLMM' for 'lmer', reported by Yevgen Matusevych)
- dredge: warns about potentially misspecified arguments
- (added) predict method for 'gamm' class
Changes in version 1.11.1 (2014-11-19)
- dredge: more efficient checking for marginality in model terms (~10x faster in
case of 4-way interaction). The argument 'marg.ex' is removed (exceptions
to marginality rule are inferred from the global model).
- getAllTerms: result has a new attribute 'deps' with a "term dependency matrix".
- nested: new function listing nested models (suggested by Giacomo Assandri).
- updateable: added new argument 'eval.args'
Changes in version 1.10.8 (2014-11-14)
- dredge, subset.model.selection: improved interpretation of 'subset' expressions.
"Term(x)" notation can be used instead of backtick quotes for complex term
names.
Changes in version 1.10.7 (2014-09-24)
- (fixed) coef.multinom: gave a wrong order of coefficients for multiple level
responses (thanks to Alistair Senior who spotted this)
Changes in version 1.10.6 (2014-08-17)
- (added) methods for 'maxlike' (from package with the same name)
- lazy loading of datasets
- plot.model.selection: improved and documented
Changes in version 1.10.5 (2014-08-08)
- get.models: can now use parallel computation if a valid 'cluster' is provided.
It takes over the functionality of 'pget.models', which is now deprecated.
Also, the argument 'subset' must be now explicitely provided (so all models
are no longer fitted by default).
Changes in version 1.10.4 (2014-08-02)
- (fixed) importance, model.avg: wrong order of 'N containing models' attribute
(bug reported by Alba Estrada)
- r.squaredGLMM: should be considerably faster and memory efficient due to
improved calculation of random effects variance (slow performance with large
datasets reported by Daniel Ezra Johnson).
Changes in version 1.10.3 (2014-06-27)
- (fixed) dredge: no longer drops random term in 'glmmadmb' models (spotted by
Carlos Le˘n)
Changes in version 1.10.2
- mystery update
Changes in version 1.10.1 (2014-05-19)
- dredge: more meaningful warning message about misspecified 'fixed' argument
- pdredge: synchronized code with 'dredge'
- documentation: improved formatting
Changes in version 1.10.0 (2014-05-02)
- r.squaredGLMM: throws an error if contrasts that have been used for random
factors in the "merMod" model do not match the ones in model matrix. This
happens if there are factors in random slope formula and user has changed
relevant 'options(contrasts)' since the model was fitted.
- dredge: 'na.action' checking now allows "option(na.action)" to be a function and
not only character string.
Changes in version 1.9.26 (2014-03-16)
- (fixed) dredge: when columns/rows in a subset matrix were in different order
than model terms, the values became wrongly rearranged (spotted by
a certain Frank on Stackoverflow).
Changes in version 1.9.25 (2014-03-13)
- (added) methods for 'cpglm' and 'cpglmm' (from package 'cplm') (suggested by
Andrew Cooper)
Changes in version 1.9.24 (2014-02-26)
- (fixed) 'getAllTerms.unmarkedFit' gave error when 'alpha' was estimated in
pcount model (reported by Lindsey Garner)
Changes in version 1.9.23 (2014-02-24)
- (added) methods 'model.matrix' and 'model.frame' for 'lme', because the default
ones give wrong results when there is 'subset' or 'contrasts' set, or
'na.omit'ting.
Changes in version 1.9.22 (2014-02-20)
- r.squaredGLMM: can be now applied to models with random slopes (based on idea
and R code by Paul Johnson). Added calculation of conditional R^2 for
Poisson family models.
Changes in version 1.9.21 (2014-02-17)
- logLik.asreml: number of estimated parameters ('df') is now calculated as the
number of fixed effect coefficients + number of variance parameters
(non-fixed and non-constained). This gives comparable numbers to similar
lmer models. In 'Asreml-R manual', however, only the number of variance
components is used as K for AIC calculation (page 15). The log-likelihood
values of asreml are far different from those from lmer(REML = TRUE), even
though coefficients are very close. Note also that REstricted-likelihood is
returned, so model comparisions based on it are invalid.
- r.squaredGLMM: checks if it is applied to a random intercepts model, otherwise
error is given. This is a limitation of the original formula by Nakagawa &
Schiezlich.
Changes in version 1.9.20 (2014-02-12)
- (added) methods for 'phylolm' (suggestion by Rafael Maia)
Changes in version 1.9.19 (2013-12-21)
- (added) 'merge.model.selection' combines two 'model.selection' tables. Note that
this is different than 'merge' for 'data.frame's (requested by Rafael Maia)
Changes in version 1.9.18 (2013-12-18)
- (added) methods for 'asreml' model (in commercial package 'asreml'). Note this
has not been tested extensively (thanks to Emeline Mourocq for an incentive
and testing)
Changes in version 1.9.17 (2013-12-14)
- full-averaged coefficients and standard errors are now calculated by 'model.avg'
and relevant methods (argument full = TRUE) (suggested by Candan Soykan)
- importance: result gives now also number of models containg each variable
Changes in version 1.9.16 (2013-11-24)
- model.sel: now accepts arguments 'extra' and 'beta', like 'dredge' (requested by
D. Duro on R-Forge).
Changes in version 1.9.15 (2013-11-17)
- [p]dredge: improved checking for whether the global model removes missing data
(na.action = "na.omit" or "na.exclude"). Note that code working with
previous versions may give you an error now, setting options(na.action =
"na.fail") prevents it.
Changes in version 1.9.14 (2013-11-03)
- (added) support for 'betareg' (from package 'betareg') (suggested by Marie-Line
Gentes)
- (added) support for 'aodml' and 'aodql' (from package 'aods3') (suggested by
Renaud Lancelot)
[p]dredge: fixed a bug that occurred when there was 'na.action=na.omit' in
global model (spotted by Laura Busia on R-help).
Changes in version 1.9.13 (2013-10-28)
- (fixed) handling response variables with more than two levels in
'nnet::multinom' models (reported by Ludo Duvaux on Stackoverflow)
Changes in version 1.9.12 (2013-10-21)
- further adjustments to deal with unavailability of 'lme4' on CRAN
Changes in version 1.9.11 (2013-09-30)
- Documentation: examples that depend on suggested packages have been made
conditional on availability of the package
- getCall method for 'model.selection' can retrieve a component model call if
index is given as a second argument.
Changes in version 1.9.10 (2013-08-27)
- pdredge: removed global assignments (within cluster nodes).
Changes in version 1.9.9 (2013-05-21)
- (fixed) beta.weights: bug with dimensions dropped (spotted by Dennis Duro,
thanks to Ben Bolker for tracking it down)
Changes in version 1.9.8 (2013-05-02)
- (fixed) handling bar in formulas for 'hurdle' class of models (reported by
Jean-Yves Barnagaud)
Changes in version 1.9.7 (2013-04-19)
- dredge: 'subset' expression now recognizes ".(x)" notation to indicate a
variable rather than a model term. Error message from within a 'rank'
function gives now a more meaningfull call (apparently it is a common
mistake to have some misspelled arguments that get passed to 'rank' function
through '...').
Changes in version 1.9.6 (2013-04-12)
- model.sel: better model naming in the result table
- (fixed) logLik.coxme: 'nobs' attribute now uses a correct number of observations
(model$n[2]). "penalized" log-lik. is the default type now (Note that
"logLik.coxme"'s argument "type" is undocumented).
Changes in version 1.9.5 (2013-04-04)
- (fixed) AICc: now takes number of observations from "nall" (if it is available)
attribute of the 'logLik' object. If not present, "nobs" attribute is used.
- r.squaredGLMM: current implementation does not calculate the marginal variant
correctly for Poisson family models, so until it is resolved 'NA' is
returned, with a warning.
Changes in version 1.9.4 (2013-04-01)
- (fixed) pdredge: bug with wrong number of updated rows.
- Replaced all calls to the soon-to-be deprecated ".find.package" with
"find.package".
Changes in version 1.9.3 (2013-02-21)
- (fixed) method registration for 'getAllTerms.gam' was missing (reported by
Steven Delean).
Changes in version 1.9.2 (2013-02-01)
- updateable: new function to create a wrapper for functions returning
non-updateable objects (adds a 'call' element to the function's result).
- (renamed) removed 'gamm' wrapper, which is now replaced by 'uGamm'.
- (added) 'predict' method replacement for 'gls' models (adds 'se.fit' argument).
- model.avg: no longer returns residuals (this is because residuals for models
other than 'lm' can be calculated in several different ways - with different
results).
Changes in version 1.9.1 (2013-01-24)
- (fixed) bugs with 'MCMCglmm' models and 'varying' lists in 'dredge'.
Changes in version 1.9.0 (2013-01-23)
- This version brings in more elaborated subsetting of models in 'dredge' and
'model.selection' object, and a new variant of pseudo-R^2.
[p]dredge: 'subset' can use 'varying' variables (as "V(varying.variable)") and
number of model terms (as `*nvar*`). This allows for better fine-tuning of
the selection table.
'fixed' argument can be set to TRUE to fix all terms of 'global.model'.
[p]dredge, subset.model.selection: 'subset' expressions can now make use of a
new function 'dc' ("dependency chain") to make inclusion of variables
conditional on other variables.
- r.squaredGLMM: new function to calculate R^2 statistic for mixed effect models,
described by Nakagawa & Schiezlich (2012).
- (added) support for 'splm' (from package 'splm'), and 'logistf' models (from
package 'logistf').
- Cp: now accepts more than one model (like 'AIC').
- New demos "dredge.varying", "dredge.subset" and "gees".
Changes in version 1.8.2 (2012-12-07)
- (added) support for models of class 'mark' (from package 'RMark'). 'dredge'
can currently only manipulate 'formula' element of argument
'model.parameters'.
- simplify.formula, expand.formula: new functions to convert formula between
expanded and shorthand notation (i.e. between 'a+b+a:b' and 'a*b').
- model.names: has new argument "use.letters".
Changes in version 1.8.1 (2012-11-23)
- (added) methods for class 'merMod' to accommodate recent changes in
lme4_0.99999911-0.
- getAllTerms: now recognizes random effects in 'MCMCglmm'.
Changes in version 1.8.0 (2012-11-21)
- This version introduces support for GEE models ('gee','geeglm' and 'yags')
ranked by QIC (note that 'yags' seems to be still quite buggy).
Also 'clmm' and 'clm' from package 'ordinal' are now handled properly.
- QIC, quasiLik: new functions for use with GEE models.
[p]dredge: argument 'subset' can be now a logical matrix representing allowed
parameter combinations. Some improvements for speed have been made.
[p]dredge, model.avg: new argument 'ct.args' for passing extra arguments
to 'coefTable'.
Changes in version 1.7.12 (2012-11-11)
- tests/classes.R: fixed compatibility spdep-0.5.53. (spdep::spautolm now uses
method = "eigen", was "full")
Changes in version 1.7.11 (2012-07-13)
- coefTable.multinom: fixed an error when coefficients and standard errors were
matrices.
- get.models: now checks for the object class of the passed arguments.
Changes in version 1.7.10 (2012-06-07)
- (fixed) dredge: bug with an error message when number of predictor exceeded
maximum (thanks to Corina Logan for spotting this).
- manual: added 'glmmADMB' to the list of supported classes (reported by Rocio
Jana).
'coxme' moved from 'Suggested' to 'Enhances' (to avoid build error when the
dependency is missing).
Changes in version 1.7.9 (2012-04-03)
- (added) 'predict' methods for 'lme' and 'lmer' (both can calculate 'se.fit').
'predict.lme' is a wrapper for its namesake from 'nlme' package (it is
not exported, so it's visibility depends on the order the packages were
loaded - but is always visible from MuMIn namespace).
Changes in version 1.7.8 (2012-04-01)
- (fixed) 'coef.model.selection' returns now proper coefficients
Changes in version 1.7.7 (2012-04-01)
- (fixed) dependencies in tests
Changes in version 1.7.6 (2012-04-01)
- dredge: with nested formula designs, 'marg.ex' is now found automatically
- predict.averaging: is now more flexible in how the predictions from generalized
models are calculated (new attribute "backtransform").
Changes in version 1.7.5 (2012-03-27)
- (added) methods for 'MCMCglmm' class, and function 'DIC': works with 'model.sel'
and 'dredge' (but not 'model.avg').
'unmarked' is removed from 'Suggested' packages (recently it is often
unavailable on CRAN and causes errors during R CHECK). Added workarounds to
pass (=cheat) the R CHECK.
Changes in version 1.7.3 (2012-02-01)
- (added) methods for 'glimML' class from package 'aod'
Changes in version 1.7.2 (2012-01-30)
- (fixed) 'nobs.coxme' returned the number of events was returned rather than
the number of observations.
- (fixed) 'coefTable' gave an error for 'coxph' null model.
- (fixed) 'r.squaredLR' was evaluating the null model for 'lme' in a wrong
environment.
- (fixed) 'getAllTerms' method for 'zeroinfl' was not registered.
- dredge: checks each generated model for the correct number of observations.
Changes in version 1.7.1 (2012-01-26)
- (added) methods for 'hurdle' and 'zeroinfl' classes (package 'pscf').
- coef, coefTable: new methods to extract coefficients from model selection
tables.
- Documentation: list of supported models put into a separate page.
Changes in version 1.7.0 (2012-01-25)
- This version adds possibility to model average and re-rank (with another IC) a
model selection table without recreating the fitted models. Models from
package 'coxme' are now supported. Model selection tables include now extra
columns showing differences in attributes of the modelling function call.
- model.avg: use 'model.selection' without refitting the models. Fixed a problem
with averaging different types of models together (happened when 'df's were
available only for some of component models).
- dredge: coefficient tables added to the result (attribute "coefTables"). The
code has been simplified.
- print.model.selection: now reports random terms also for objects generated by
'model.sel'.
- get.models: can handle 'model.selection' objects from 'model.sel'
- model.sel: re-ranking 'model.selection' without recreating original models
(works only if the IC can be applied to logLik). Output has additional
columns showing differences between models (based on call's arguments)
- (added) generic methods for 'coxme' and 'lmekin' classes (package 'coxme').
Changes in version 1.6.6 (2012-01-07)
- model.avg: fixed error occurring when non-estimable coefficients existed in the
component models (problem reported by Annabel Smith)
Changes in version 1.6.5 (2011-11-28)
- pdredge example changed to use SOCK cluster type (portability issue).
Changes in version 1.6.4 (2011-11-26)
- coefTable: replaces 'tTable' (which still exists, but is deprecated), it
accepts an argument 'dispersion'. The dispersion parameter can be also
passed from 'model.avg'.
- pdredge: collects all the warnings and errors which occur during fitting, and
stores them. They are printed below the table.
The function does more thorough checking of the cluster nodes' environment,
for possible missing variables and functions.
- get.models: "subset" argument can be now a character vector giving model names.
- (added) demos for model selection with models from 'unmarked' package using
'dredge' and 'pdredge'.
Changes in version 1.6.3 (2011-11-15)
- pget.models: new function, parallel version of 'get.models'.
- (p)get.models: important change of the default behaviour: without the 'subset'
argument, ALL models are returned. Also the '...' arguments were not used to
update the returned models - this is corrected now.
Changes in version 1.6.2 (2011-11-13)
- pdredge: new function, a parallel version of dredge (experimental).
Changes in version 1.6.1 (2011-11-11)
- dredge: added generic support for all 'unmarked' models, and fixed some bugs
with it.
- model.names: new function (previously was internal only)
- CAICF: adds to the collection of rarely used information criteria.
Changes in version 1.6.0 (2011-11-07)
- dredge: most important change (although invisible to the user) is in the way the
model objects are updated. The new function 'makeArgs' is used to generate
the updated call. This results in a very flexible interface to the modelling
functions. The default method updates the 'formula' argument, other methods
can be used to deal with more problematic calls (the models from package
'unmarked' were a challenge). Apart from the model classes previously
supported by 'dredge', support for 'unmarkedFitOccu', 'unmarkedFitColExt'
and several other 'unmarkedFit' objects has been added.
- dredge: has new argument 'extra' to add additional statistics into the model
selection table.
- r.squared: new function to calculate likelihood-ratio based pseudo-R-squared
- subset method for 'model.selection': accepts a shorthand notation "has(x)" to
select rows where a variable is present.
- (added) support for 'survreg' and 'rq' models (packages 'survival' and
'quantreg')
Changes in version 1.5.2 (2011-10-21)
- dredge: fixed a bug with wrong ordering of column names in the returned
data.frame (thanks to Staffan Roos for reporting this).
Changes in version 1.5.1 (2011-10-20)
- compatibility with R prior to 2.13.0: added workarounds for missing generic
function 'nobs'.
Changes in version 1.5.0 (2011-10-18)
- model.avg: removed the argument "method", the standard errors and confidence
intervals are calculated only for coefficients averaged within a subset of
models where they are present (method = "NA"). The "full" coefficients are
also returned, but without std. errors.
- plot.model.selection: new function to visualize the model selection table
- manuals expanded, examples revised
- getAllTerms: should work for most of the classes derived from 'unmarkedFit'
- a load of small improvements, polishings and fixes, generally invisible to the
user.
Changes in version 1.4.4 (2011-10-16)
- QAIC: no longer uses model deviance, as it gave biased values.
- ICOMP, Cp: new information criteria
- model.avg: now performs a smarter check for duplicate models, fixed calculation
of importance values
- model.sel: new alias to 'mod.sel' (eventually will replace 'mod.sel').
Changes in version 1.4.3 (2011-10-13)
- Beetle: new data - beetle mortality, with examples from B&A's book
- dredge: new arguments 'varying', 'm.min' and 'evaluate'
- manuals modified and corrected
- tests/gamm.R: tests for 'gamm'/'gamm4' support.
Changes in version 1.4.2 (2011-10-11)
- support for 'gamm' and 'gamm4'
- gamm: added a wrapper for gamm, that allows for updating the object (hopefully
needed only temporarily)
Changes in version 1.4.1 (2011-10-10)
- A few changes to vignette 'gamm'
Changes in version 1.4.0 (2011-10-05)
- importance: new function
- mod.sel: added method for a 'model.selection' object
Changes in version 1.3.10 (2011-09-23)
- Reverted changes made in previous version (package dependencies) to succesfully
pass checks.
Changes in version 1.3.9 (2011-09-17)
- removed *.lmer *.glmer methods, added dependency on lme4 >= 0.999375-16
- tTable.mer: minor change
Changes in version 1.3.8 (2011-09-17)
- Restored compatibility with R 2.12.2
- getAllTerms: new attribute 'intercept'
Changes in version 1.3.7 (2011-09-16)
- handling double intercept (phi(Int) and p(Int)) in 'unmarked'
Changes in version 1.3.6 (2011-09-12)
- changes in the documentation and vignette
Changes in version 1.3.5 (2011-08-05)
- mod.sel: new function
- added methods for 'unmarkedFit' objects (package 'unmarked'), to provide
(limited) support in 'model.avg'
Changes in version 1.3.4 (2011-08-03)
- Added vignette document on model selection with 'gamm' and 'gamm4'
(thanks to Graham MacDonald for an incentive)
Changes in version 1.3.3 (2011-08-01)
- dredge: small improvements, no longer dependent on 'bitops'
- Polished the documentation
Changes in version 1.3.2 (2011-08-01)
- nobs: updated methods
Changes in version 1.3.1 (2011-07-31)
- dredge: bugs fixed
Changes in version 1.3.0 (2011-07-29)
- model.avg: now may be used directly with 'model.selection' object
- summary.averaging: gives now more information
Changes in version 1.2.4 (2011-07-29)
- fixed handling of spatial parameters (lambda, rho) in models from package
'spdep'
- dredge: modified for better performance
- dredge, get.models: can deal with glms with starting values provided ('start'
argument)
- QAIC: added a note in documentation stating that is uses deviance rather than
logLik in the calculation
Changes in version 1.2.3 (2011-04-07)
- fixed some REML/ML issues, AICc rewritten (based on the new AIC code in stats)
Changes in version 1.2.2 (2011-04-06)
- nobs: corrected methods for mixed models, added documentation page
Changes in version 1.2.1 (2011-04-05)
- .GetLogLik - hidden helper function (returns the proper logLik to use)
Changes in version 1.2.0 (2011-04-04)
- AICc has new argument REML used with mixed models. Thanks to Benjamin Augustine
for suggestion.
Changes in version 1.1.2 (2011-03-19)
- removed arguments 'alpha' and 'level' from model.avg. 'confint' is used instead
to obtain CI
Changes in version 1.1.1 (2011-03-18)
- the printed output of 'averaging' has been made consistent with that of lm and
glm: 'print' gives concise information and 'summary' gives more details.
- confint.averaging: new function.
- print.summary.averaging: new function.
Changes in version 1.1.0 (2011-03-10)
- added z-statistic, p-values (with significance stars) to model.avg output
Changes in version 1.0.0 (2011-02-10)
- get.models: fixed - arguments in ... were not passed to updated models
- predict.averaging: predictions on response scale can be calculated
(type=response)
- new functions (not exported): nobs, coefDf
- model.avg: now makes use of correct DF from component models in calculation of
adjusted SE
- par.avg: calculates ASE if df are provided, example(QAIC) now demonstrates
predictions with confidence intervals
Changes in version 0.14.2 (2011-02-05)
- dredge: small changes, slightly faster
- manual corrected
Changes in version 0.14.1 (2011-02-04)
- vcov.averaging, logLik.averaging: new methods,
- revised formula for unconditional variance
- manual reworked
Changes in version 0.14.0 (2011-01-19)
- TODO: model.avg: added npar to the selection table
- predict.averaging: now can return averaged SE
- par.avg: may use revised formula for calculating averaged SE
Changes in version 0.13.21 (2011-01-16)
- dredge: handling of update'd lmer models improved
- QAICc: new function
Changes in version 0.13.20 (2011-01-16)
- Namespace exports updated (coxph methods)
- dredge: uses now QAIC for glms with 'quasi*' family, and if no rank is specified
Changes in version 0.13.19 (2011-01-15)
- model.avg: fixed wrong ordering of model names (thanks to Dennis Jonason for
noticing this)
Changes in version 0.13.18 (2010-10-16)
- Support for coxph (package survival)
Changes in version 0.13.17 (2010-09-13)
- model.avg: fixed a bug with models with binary response;
- dredge: added checking for na.omit'ting in the global model.
- new tests: varia.R
Changes in version 0.13.16 (2010-09-07)
- dredge, model.avg: broken support for several types of models was fixed
Changes in version 0.13.15 (2010-09-06)
- support for 'MASS::multinom'
Changes in version 0.13.14 (2010-09-03)
- print.model.selection: empty columns are not printed now
Changes in version 0.13.13 (2010-09-02)
- dredge: handling of models with no intercept, added "call" attribute
- update.model.selection: new function
Changes in version 0.13.12 (2010-08-29)
- dredge, getAllTerms, dredge.Rd: small modifications
Changes in version 0.13.11 (2010-08-28)
- getAllTerms: improved handling of interactions, random terms (lmer) and
"offset()"
- formulaAllowed: now allows for exceptions in margins presence checking (new
argument: "except")
- dredge: now tries to call fitting function directly rather than through update
(more effective in case when model not passed as a variable). New arguments:
"trace", and "marg.ex" - marginality checking exceptions.
Changes in version 0.13.10 (2010-08-26)
- getAllTerms: fixed a bug with with wrong ordering of interaction terms (resulted
with a:b or b:a depending on the set of terms). Improved handling of random
terms in lme.
Changes in version 0.13.9 (2010-08-24)
- dredge: fixed bugs introduced in the previous version
Changes in version 0.13.8 (2010-08-03)
- QAIC: examples expanded
Changes in version 0.13.7 (2010-08-02)
- dredge: prints errors generated by models as warnings (previously these were
skipped silently)
Changes in version 0.13.6 (2010-08-01)
- print.model.selection: improved column abbreviation.
Changes in version 0.13.5 (2010-07-31)
- dredge: fixed a bug causing interaction coefficients to be stripped from
model.selection table, new function 'fixCoefNames' (not exported) handles proper
ordering of interaction components in coefficient names.
Changes in version 0.13.4 (2010-07-21)
- 'beta.weights' now uses 'tTable' (support for more model types), 'dredge' with
beta=TRUE tries out if it can get beta.weights working.
- Manual: added gls and rlm to the list of supported models
Changes in version 0.13.3 (2010-07-15)
- Bug fixed in print.averaging
Changes in version 0.13.2 (2010-07-14)
- Attributes for custom rank function in "dredge" and "model.avg" are now
evaluated model-wise, if provided as expressions.
Changes in version 0.13.0-1 (2010-07-12)
- Fixed compatibility issues with models of class "lme" and "sarlm".
- "model.avg" does now some checking whether all models were fitted to the same
data and have the same response.
Changes in version 0.12.13 (2010-07-09)
- 'recalc.weights' argument added to "subset.model.selection".
- Small bug fixed in dredge.
Changes in version 0.12.12 (2010-07-08)
- New in "dredge": Subsetting models a priori according to a formula
Changes in version 0.12.11 (2010-07-07)
- Subset/extract methods for 'model.selection' object
Changes in version 0.12.10 (2010-07-05)
- Fixed "predict.averaging" for missing 'newdata' handling; Table returned by
"dredge" now has factors for terms with more than one level (they were
previously shown as '1')
Changes in version 0.12.9 (2010-07-03)
- Finally fixed problems with variable exporting and hidden methods
Changes in version 0.12.7-8 (2010-07-02)
- Small changes in namespace and documentation
Changes in version 0.12.6 (2010-06-26)
- Tidying up the code, small changes.
Changes in version 0.12.4 (2010-06-21)
- added: "predict.averaging" and "coef.averaging", 'averaging' object contains
- additional elements, so that several default methods work with it.
Changes in version 0.12.2 (2009-06-14)
- fixed: 'alpha' in "model.avg" was not passed to "par.avg"
Changes in version 0.12.1 (2009-04-20)
- fixed: method="NA" in model.avg, par.avg now accepts NA's in 'weight'
Changes in version 0.12.0 (2009-03-24)
- Change in version number only. Had to make this jump in numbering, as there was
a typo in DESCRIPTION file of an early version, (0.11.2 instead of 0.1.0), and
since then R-forge mechanism seemed to ignore actual newer versions, as they had
lower number.
Changes in version 0.1.1 (2009-03-22)
- Modified: dredge: added "fixed" and "m.max" arguments.
Changes in version 0.1.1 (2009-03-17)
- Fixed: par.avg: Variance estimate corrected (previous estimate was square root
of variance). Thanks to Mick Wu.
- Fixed: dredge: Apparently "expand.grid" cannot handle too many combinations, so
now dredge stops with a more explanatory message
Changes in version 0.1.0
- dRedging (0.11.2) moved to R-Forge.
- Since model averaging is now the main focus of the package, its name changed
to MuMIn (from MUlti Model INference).
