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bbolker / broom.mixed

tidy methods for mixed models in R
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adding no. of observations to `glance` summaries? #71

Open IndrajeetPatil opened 5 years ago

IndrajeetPatil commented 5 years ago

Maybe adding no. of observations nobs column to glance methods in broom.mixed will be a nice addition? I certaintly find this information useful to have.

# setup
set.seed(123)
library(tidyverse, warn.conflicts = FALSE)
library(tidymodels, warn.conflicts = FALSE)
library(ordinal)

# model
mod <- lme4::glmer(
  formula = Survived ~ Sex + Age + (Sex + Age | Class),
  # select 20% of the sample to reduce the time of execution
  data = dplyr::sample_frac(tbl = ggstatsplot::Titanic_full, size = 0.2),
  family = stats::binomial(link = "logit"),
  control = lme4::glmerControl(
    optimizer = "Nelder_Mead",
    calc.derivs = FALSE,
    boundary.tol = 1e-7
  )
)
# summary provided by `broom.mixed` package
broom.mixed::glance(mod)
#> # A tibble: 1 x 6
#>   sigma logLik   AIC   BIC deviance df.residual
#>   <dbl>  <dbl> <dbl> <dbl>    <dbl>       <int>
#> 1     1  -209.  436.  473.     400.         431
nobs(mod)
#> [1] 440

broom has recently started including this information in the glance summaries-

# summary provided by `broom` for linear model
# example-1
mod <- lm(mpg ~ wt + qsec, data = mtcars)
broom::glance(mod)
#> # A tibble: 1 x 12
#>   r.squared adj.r.squared sigma statistic  p.value    df logLik   AIC   BIC
#>       <dbl>         <dbl> <dbl>     <dbl>    <dbl> <dbl>  <dbl> <dbl> <dbl>
#> 1     0.826         0.814  2.60      69.0 9.39e-12     2  -74.4  157.  163.
#> # ... with 3 more variables: deviance <dbl>, df.residual <int>, nobs <int>

# example-2
fit <- ordinal::clm(rating ~ temp * contact, data = wine)
broom::glance(fit)
#> # A tibble: 1 x 6
#>     edf   AIC   BIC logLik df.residual  nobs
#>   <int> <dbl> <dbl>  <dbl>       <dbl> <dbl>
#> 1     7  187.  203.  -86.4          65    72

Created on 2019-05-27 by the reprex package (v0.3.0)

Session info ``` r devtools::session_info() #> - Session info ---------------------------------------------------------- #> setting value #> version R version 3.6.0 alpha (2019-03-29 r76300) #> os Windows 10 x64 #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.1252 #> ctype English_United States.1252 #> tz America/New_York #> date 2019-05-27 #> #> - Packages -------------------------------------------------------------- #> package * version date lib #> abind 1.4-5 2016-07-21 [1] #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.4 2019-04-10 [1] #> base64enc 0.1-3 2015-07-28 [1] #> BayesFactor 0.9.12-4.2 2018-05-19 [1] #> bayesplot 1.7.0 2019-05-23 [1] #> boot 1.3-21 2019-03-01 [2] #> broom * 0.5.2.9001 2019-04-09 [1] #> broom.mixed 0.2.4.9000 2019-03-14 [1] #> broomExtra 0.0.3.9000 2019-05-20 [1] #> callr 3.2.0 2019-03-15 [1] #> car 3.0-3 2019-05-27 [1] #> carData 3.0-2 2018-09-30 [1] #> cellranger 1.1.0 2016-07-27 [1] #> class 7.3-15 2019-01-01 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corybrunson commented 2 years ago

This is implemented for some classes (stanreg, gamlss) but not others (merMod). This last case would require an extra line in the internal helper finish_glance(). I don't know why that function is flagged for fixing, but lme4 does include a nobs.merMod method that could be used there. I'd be glad to give it a try (if there's no a priori reason it shouldn't work) and submit a PR (if indeed it works).

bbolker commented 2 years ago

Definitely no reason it shouldn't work. I think finish_glance() might be a leftover function from broom (possibly even deprecated there now?) that tries to create a "generic" glance object by trying all of the widely implemented methods (AIC, R2, nobs, etc etc). Could probably be refactored, but a quick-and-dirty fix would also be welcome. (Could look at broom to see how it's done there now ...)

corybrunson commented 2 years ago

Note: I'm pressed for time right now but would be glad to come back in a month or two to see about removing finish_glance() and making the lme4 tidiers standalone!