broom.mixed
broom.mixed
is a spinoff of the broom package. The
goal of broom
is to bring the modeling process into a
“tidy”(TM) workflow, in particular by providing standardized verbs that
provide information on
tidy
: estimates, standard errors, confidence intervals,
etc.augment
: residuals, fitted values, influence measures,
etc.glance
: whole-model summaries: AIC, R-squared,
etc.broom.mixed
aims to provide these methods for as many
packages and model types in the R ecosystem as possible. These methods
have been separated from those in the main broom
package
because there are issues that need to be dealt with for these models
(e.g. different types of parameters: fixed, random-effects parameters,
conditional modes/BLUPs of random effects, etc.) that are not especially
relevant to the broader universe of models that broom
deals
with.
ran_pars
in the effects
argument when
tidying)ran_vals
in the
effects
argument when tidying)fixed
in the effects
argument
when tidying)group
column in tidy()
output)level
column in tidy()
output)term
column in
tidy()
output); note that unlike in base
broom
, the term column may have duplicated
values, because the same term may enter multiple model
components (e.g. zero-inflated and conditional models; models for more
than one response; fixed effects and random effects)Some kinds of computations needed for mixed model summaries are
computationally expensive, e.g. likelihood profiles or parametric
bootstrapping. In this case broom.mixed
may offer an option
for passing a pre-computed object to tidy()
, eg. the
profile
argument in the tidy.merMod
(lmer
/glmer
) method.
Automatically retrieve table of available methods:
## # A tibble: 24 × 4
## class tidy glance augment
## <chr> <lgl> <lgl> <lgl>
## 1 MCMCglmm TRUE FALSE FALSE
## 2 MixMod TRUE FALSE FALSE
## 3 TMB TRUE FALSE FALSE
## 4 allFit TRUE TRUE FALSE
## 5 brmsfit TRUE TRUE TRUE
## 6 gamlss TRUE TRUE FALSE
## 7 gamm4 TRUE TRUE TRUE
## 8 glmmTMB TRUE TRUE TRUE
## 9 glmmadmb TRUE TRUE TRUE
## 10 gls TRUE TRUE TRUE
## # ℹ 14 more rows
Manually compiled list of capabilities (possibly out of date):
package | object | tidy | glance | augment | effects.fixed | effects.ran_vals | effects.ran_pars | effects.ran_coefs | confint…Ww.ald. | confint..profile. | confint..boot. | component.zi | component.disp | covstruct |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
lme4 | glmer | y | y | y | y | y | y | y | NA | y | NA | NA | NA | ? |
lme4 | lmer | y | y | y | y | y | y | y | NA | y | NA | NA | NA | ? |
nlme | lme | y | y | y | y | y | y | y | NA | n | NA | NA | ? | ? |
nlme | gls | y | y | y | y | NA | NA | NA | NA | n | NA | NA | ? | ? |
nlme | nlme | y | y | y | y | y | n | y | NA | n | NA | NA | ? | ? |
glmmTMB | glmmTMB | y | y | y | y | y | y | n | NA | NA | y | y | ? | |
glmmADMB | glmmadmb | y | y | y | y | y | y | n | NA | NA | y | ? | ? | |
brms | brmsfit | y | y | y | y | y | y | n | NA | NA | y | ? | ? | |
rstanarm | stanreg | y | y | y | y | y | y | n | NA | NA | NA | NA | ? | |
MCMCglmm | MCMCglmm | y | y | y | y | y | y | n | NA | NA | ? | ? | ? | |
TMB | TMB | y | n | n | n | n | n | n | NA | NA | NA | NA | ? | |
INLA | n | n | n | n | n | n | n | NA | NA | ? | ? | ? |