Introduction to broom.mixed

Ben Bolker

2021-07-05

Introduction

UNDER CONSTRUCTION

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

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.

Mixed-model-specific issues

Terminology

Time-consuming computations

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.

Capabilities

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 ? ? ?