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inconsistent behavior with mclogit objects #736

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IndrajeetPatil opened this issue Aug 9, 2019 · 3 comments · Fixed by #887
Closed

inconsistent behavior with mclogit objects #736

IndrajeetPatil opened this issue Aug 9, 2019 · 3 comments · Fixed by #887
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beginner-friendly new-tidiers

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@IndrajeetPatil
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broom currently doesn't support mclogit objects. But because these objects also inherit lm, the tidier seems to work.

# setup
set.seed(123)
library(mclogit)
#> Loading required package: Matrix
data(electors)

# model
mod <- mclogit::mclogit(
  formula = cbind(Freq, interaction(time, class)) ~ econ.left / class + welfare / class + auth / class,
  random = ~ 1 | party.time,
  data = within(electors, party.time <- interaction(party, time))
)
#> Fitting plain conditional logit to obtain starting values
#> Iteration 1 - Deviance = 7377.939
#> Iteration 2 - Deviance = 4589.544
#> Iteration 3 - Deviance = 4293.485
#> Iteration 4 - Deviance = 4277.887
#> Iteration 5 - Deviance = 4277.808
#> Iteration 6 - Deviance = 4277.808
#> converged
#> Fitting random effects/random coefficients model
#> Iteration 1 - Deviance = 1876.788
#> Iteration 2 - Deviance = 1212.004
#> Iteration 3 - Deviance = 1009.8
#> Iteration 4 - Deviance = 958.7431
#> Iteration 5 - Deviance = 949.4332
#> Iteration 6 - Deviance = 948.1453
#> Iteration 7 - Deviance = 947.9013
#> Iteration 8 - Deviance = 947.8442
#> Iteration 9 - Deviance = 947.8329
#> Iteration 10 - Deviance = 947.8308
#> Iteration 11 - Deviance = 947.8305
#> Iteration 12 - Deviance = 947.8304
#> Iteration 13 - Deviance = 947.8304
#> Iteration 14 - Deviance = 947.8304
#> converged

# class of objects
class(mod)
#> [1] "mmclogit" "mclogit"  "lm"

# tidier?
broom::tidy(mod)
#> # A tibble: 9 x 5
#>   term                      estimate std.error statistic   p.value
#>   <chr>                        <dbl>     <dbl>     <dbl>     <dbl>
#> 1 econ.left                  -0.172     0.138     -1.25  2.12e-  1
#> 2 welfare                     2.05      0.214      9.58  9.71e- 22
#> 3 auth                        0.0817    0.118      0.691 4.89e-  1
#> 4 econ.left:classnew.middle  -1.67      0.0880   -19.0   3.61e- 80
#> 5 econ.left:classold.middle  -2.97      0.149    -19.9   4.56e- 88
#> 6 classnew.middle:welfare    -0.989     0.0609   -16.2   2.30e- 59
#> 7 classold.middle:welfare    -1.62      0.129    -12.6   3.82e- 36
#> 8 classnew.middle:auth       -1.39      0.0468   -29.8   1.64e-194
#> 9 classold.middle:auth        1.46      0.0582    25.0   2.05e-138

But it has trouble computing confidence intervals because the underlying method from stats fails:

# confidence intervals?
broom::tidy(mod, conf.int = TRUE)
#> Error in qt(a, object$df.residual): Non-numeric argument to mathematical function

# is there even a method for this?
confint(mod)
#> Error in qt(a, object$df.residual): Non-numeric argument to mathematical function

The glance and augment methods also fail:

# glance?
broom::glance(mod)
#> Error in eval_tidy(xs[[i]], unique_output): object 'r.squared' not found

# augment?
broom::augment(mod, data = electors)
#> Error: Can't augment data with observation level measures.
#> Did you provide `data` with the exact data used for model fitting?

Created on 2019-08-09 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
#> - Session info ----------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.1 (2019-07-05)
#>  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     2019-08-09                  
#> 
#> - 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]
#>  broom         0.5.2.9002 2019-08-08 [1]
#>  callr         3.3.1      2019-07-18 [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]
#>  cli           1.1.0      2019-03-19 [1]
#>  crayon        1.3.4      2017-09-16 [1]
#>  curl          4.0        2019-07-22 [1]
#>  data.table    1.12.2     2019-04-07 [1]
#>  desc          1.2.0      2019-04-03 [1]
#>  devtools      2.1.0      2019-07-06 [1]
#>  digest        0.6.20     2019-07-04 [1]
#>  dplyr         0.8.3      2019-07-04 [1]
#>  evaluate      0.14       2019-05-28 [1]
#>  fansi         0.4.0      2018-11-05 [1]
#>  forcats       0.4.0      2019-02-17 [1]
#>  foreign       0.8-71     2018-07-20 [2]
#>  fs            1.3.1      2019-05-06 [1]
#>  generics      0.0.2      2019-03-05 [1]
#>  glue          1.3.1      2019-03-12 [1]
#>  haven         2.1.1      2019-07-04 [1]
#>  highr         0.8        2019-03-20 [1]
#>  hms           0.5.0      2019-07-09 [1]
#>  htmltools     0.3.6      2017-04-28 [1]
#>  jsonlite      1.6        2018-12-07 [1]
#>  knitr         1.24       2019-08-08 [1]
#>  lattice       0.20-38    2018-11-04 [2]
#>  magrittr      1.5        2014-11-22 [1]
#>  MASS          7.3-51.4   2019-03-31 [1]
#>  Matrix      * 1.2-17     2019-03-22 [1]
#>  mclogit     * 0.6.1      2018-09-27 [1]
#>  memisc        0.99.17.2  2019-04-24 [1]
#>  memoise       1.1.0      2017-04-21 [1]
#>  openxlsx      4.1.0.1    2019-05-28 [1]
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#>  pkgbuild      1.0.4      2019-08-05 [1]
#>  pkgconfig     2.0.2      2018-08-16 [1]
#>  pkgload       1.0.2      2018-10-29 [1]
#>  prettyunits   1.0.2      2015-07-13 [1]
#>  processx      3.4.1      2019-07-18 [1]
#>  ps            1.3.0      2018-12-21 [1]
#>  purrr         0.3.2      2019-03-15 [1]
#>  R6            2.4.0      2019-02-14 [1]
#>  Rcpp          1.0.2      2019-07-25 [1]
#>  readxl        1.3.1      2019-03-13 [1]
#>  remotes       2.1.0      2019-06-24 [1]
#>  repr          1.0.1      2019-05-14 [1]
#>  rio           0.5.16     2018-11-26 [1]
#>  rlang         0.4.0      2019-06-25 [1]
#>  rmarkdown     1.14.3     2019-08-02 [1]
#>  rprojroot     1.3-2      2018-01-03 [1]
#>  sessioninfo   1.1.1      2018-11-05 [1]
#>  stringi       1.4.3      2019-03-12 [1]
#>  stringr       1.4.0      2019-02-10 [1]
#>  testthat      2.2.1      2019-07-25 [1]
#>  tibble        2.1.3      2019-06-06 [1]
#>  tidyr         0.8.3      2019-03-01 [1]
#>  tidyselect    0.2.5      2018-10-11 [1]
#>  usethis       1.5.1.9000 2019-07-27 [1]
#>  utf8          1.1.4      2018-05-24 [1]
#>  vctrs         0.2.0      2019-07-05 [1]
#>  withr         2.1.2      2018-03-15 [1]
#>  xfun          0.8        2019-06-25 [1]
#>  yaml          2.2.0      2018-07-25 [1]
#>  zeallot       0.1.0      2018-01-28 [1]
#>  zip           2.0.3      2019-07-03 [1]
#>  source                            
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#>  Github (r-lib/desc@c860e7b)       
#>  CRAN (R 3.6.1)                    
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#>  Github (brodieG/fansi@ab11e9c)    
#>  CRAN (R 3.5.2)                    
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#>  CRAN (R 3.6.0)                    
#>  Github (r-lib/generics@c15ac43)   
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#>  Github (rstudio/rmarkdown@37bcb8f)
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#>  Github (r-lib/usethis@b241420)    
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#>  CRAN (R 3.6.0)                    
#> 
#> [1] C:/Users/inp099/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.1/library
@alexpghayes
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alexpghayes commented Aug 10, 2019 •
edited

Another case where the short term solution is

#' @export
tidy.mclogit <- tidy.default

...

and the long term solution is new tidiers. GAH WHY DOES EVERYONE SUBCLASS LM.

alexpghayes added a commit that referenced this issue Aug 13, 2019
@alexpghayes
Block lm tidiers for mclogit objects. Fixes #736.
c07371e
@IndrajeetPatil IndrajeetPatil mentioned this issue Dec 2, 2019
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@IndrajeetPatil
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Closing following #795 (comment)

@gregmacfarlane gregmacfarlane mentioned this issue Jul 2, 2020
Merged
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github-actions bot commented Mar 8, 2021

This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue.

@github-actions github-actions bot locked and limited conversation to collaborators Mar 8, 2021
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Add tidy, augment, and glance methods for mlogit objects gregmacfarlane/broom
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@IndrajeetPatil @alexpghayes