MuMIn package news:
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).
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).
Version: 1.10.3 (2014-06-27)
(fixed) dredge: no longer drops random term in 'glmmadmb' models (spotted by
Carlos León)
Version: 1.10.2
mystery update
Version: 1.10.1 (2014-05-19)
dredge: more meaningful warning message about misspecified 'fixed' argument
pdredge: synchronized code with 'dredge'
documentation: improved formatting
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.
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).
Version: 1.9.25 (2014-03-13)
(added) methods for 'cpglm' and 'cpglmm' (from package 'cplm') (suggested by
Andrew Cooper)
Version: 1.9.24 (2014-02-26)
(fixed) 'getAllTerms.unmarkedFit' gave error when 'alpha' was estimated in
pcount model (when else?) (reported by Lindsey Garner)
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.
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.
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.
Version: 1.9.20 (2014-02-12)
(added) methods for 'phylolm' (suggestion by Rafael Maia)
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)
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)
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
Version: 1.9.16 (2013-11-24)
model.sel: now accepts arguments 'extra' and 'beta', like 'dredge' (requested by
D. Duro on R-Forge).
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.
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).
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)
Version: 1.9.12 (2013-10-21)
further adjustments to deal with unavailability of 'lme4' on CRAN
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.
Version: 1.9.10 (2013-08-27)
pdredge: removed global assignments (within cluster nodes).
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)
Version: 1.9.8 (2013-05-02)
(fixed) handling bar in formulas for 'hurdle' class of models (reported by
Jean-Yves Barnagaud)
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 '...').
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).
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.
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".
Version: 1.9.3 (2013-02-21)
(fixed) method registration for 'getAllTerms.gam' was missing (reported by
Steven Delean).
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).
Version: 1.9.1 (2013-01-24)
(fixed) bugs with 'MCMCglmm' models and 'varying' lists in 'dredge'.
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".
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".
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'.
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'.
Version: 1.7.12 (2012-11-11)
tests/classes.R: fixed compatibility spdep-0.5.53. (spdep::spautolm now uses
method = "eigen", was "full")
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.
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).
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).
Version: 1.7.8 (2012-04-01)
(fixed) 'coef.model.selection' returns now proper coefficients
Version: 1.7.7 (2012-04-01)
(fixed) dependencies in tests
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").
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.
Version: 1.7.3 (2012-02-01)
(added) methods for 'glimML' class from package 'aod'
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.
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.
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').
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)
Version: 1.6.5 (2011-11-28)
pdredge example changed to use SOCK cluster type (portability issue).
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'.
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.
Version: 1.6.2 (2011-11-13)
pdredge: new function, a parallel version of dredge (experimental).
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.
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')
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).
Version: 1.5.1 (2011-10-20)
compatibility with R prior to 2.13.0: added workarounds for missing generic
function 'nobs'.
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.
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').
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.
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)
Version: 1.4.1 (2011-10-10)
A few changes to vignette 'gamm'
Version: 1.4.0 (2011-10-05)
importance: new function
mod.sel: added method for a 'model.selection' object
Version: 1.3.10 (2011-09-23)
Reverted changes made in previous version (package dependencies) to succesfully
pass checks.
Version: 1.3.9 (2011-09-17)
removed *.lmer *.glmer methods, added dependency on lme4 >= 0.999375-16
tTable.mer: minor change
Version: 1.3.8 (2011-09-17)
Restored compatibility with R 2.12.2
getAllTerms: new attribute 'intercept'
Version: 1.3.7 (2011-09-16)
handling double intercept (phi(Int) and p(Int)) in 'unmarked'
Version: 1.3.6 (2011-09-12)
changes in the documentation and vignette
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'
Version: 1.3.4 (2011-08-03)
Added vignette document on model selection with 'gamm' and 'gamm4'
(thanks to Graham MacDonald for an incentive)
Version: 1.3.3 (2011-08-01)
dredge: small improvements, no longer dependent on 'bitops'
Polished the documentation
Version: 1.3.2 (2011-08-01)
nobs: updated methods
Version: 1.3.1 (2011-07-31)
dredge: bugs fixed
Version: 1.3.0 (2011-07-29)
model.avg: now may be used directly with 'model.selection' object
summary.averaging: gives now more information
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
Version: 1.2.3 (2011-04-07)
fixed some REML/ML issues, AICc rewritten (based on the new AIC code in stats)
Version: 1.2.2 (2011-04-06)
nobs: corrected methods for mixed models, added documentation page
Version: 1.2.1 (2011-04-05)
.GetLogLik - hidden helper function (returns the proper logLik to use)
Version: 1.2.0 (2011-04-04)
AICc has new argument REML used with mixed models. Thanks to Benjamin Augustine
for suggestion.
Version: 1.1.2 (2011-03-19)
removed arguments 'alpha' and 'level' from model.avg. 'confint' is used instead
to obtain CI
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.
Version: 1.1.0 (2011-03-10)
added z-statistic, p-values (with significance stars) to model.avg output
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
Version: 0.14.2 (2011-02-05)
dredge: small changes, slightly faster
manual corrected
Version: 0.14.1 (2011-02-04)
vcov.averaging, logLik.averaging: new methods,
revised formula for unconditional variance
manual reworked
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
Version: 0.13.21 (2011-01-16)
dredge: handling of update'd lmer models improved
QAICc: new function
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
Version: 0.13.19 (2011-01-15)
model.avg: fixed wrong ordering of model names (thanks to Dennis Jonason for
noticing this)
Version: 0.13.18 (2010-10-16)
Support for coxph (package survival)
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
Version: 0.13.16 (2010-09-07)
dredge, model.avg: broken support for several types of models was fixed
Version: 0.13.15 (2010-09-06)
support for 'MASS::multinom'
Version: 0.13.14 (2010-09-03)
print.model.selection: empty columns are not printed now
Version: 0.13.13 (2010-09-02)
dredge: handling of models with no intercept, added "call" attribute
update.model.selection: new function
Version: 0.13.12 (2010-08-29)
dredge, getAllTerms, dredge.Rd: small modifications
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.
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.
Version: 0.13.9 (2010-08-24)
dredge: fixed bugs introduced in the previous version
Version: 0.13.8 (2010-08-03)
QAIC: examples expanded
Version: 0.13.7 (2010-08-02)
dredge: prints errors generated by models as warnings (previously these were
skipped silently)
Version: 0.13.6 (2010-08-01)
print.model.selection: improved column abbreviation.
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.
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
Version: 0.13.3 (2010-07-15)
Bug fixed in print.averaging
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.
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.
Version: 0.12.13 (2010-07-09)
'recalc.weights' argument added to "subset.model.selection".
Small bug fixed in dredge.
Version: 0.12.12 (2010-07-08)
New in "dredge": Subsetting models a priori according to a formula
Version: 0.12.11 (2010-07-07)
Subset/extract methods for 'model.selection' object
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')
Version: 0.12.9 (2010-07-03)
Finally fixed problems with variable exporting and hidden methods
Version: 0.12.7-8 (2010-07-02)
Small changes in namespace and documentation
Version: 0.12.6 (2010-06-26)
Tidying up the code, small changes.
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.
Version: 0.12.2 (2009-06-14)
fixed: 'alpha' in "model.avg" was not passed to "par.avg"
Version: 0.12.1 (2009-04-20)
fixed: method="NA" in model.avg, par.avg now accepts NA's in 'weight'
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.
Version 0.1.1 (2009-03-22)
Modified: dredge: added "fixed" and "m.max" arguments.
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
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).