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glance method for gam fails: no 'nobs' method is available #737

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IndrajeetPatil opened this issue Aug 10, 2019 · 7 comments
Closed

glance method for gam fails: no 'nobs' method is available #737

IndrajeetPatil opened this issue Aug 10, 2019 · 7 comments
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beginner-friendly bug an unexpected problem or unintended behavior

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@IndrajeetPatil
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# setup
library(gamm4)
#> Loading required package: Matrix
#> Loading required package: lme4
#> Loading required package: mgcv
#> Loading required package: nlme
#> 
#> Attaching package: 'nlme'
#> The following object is masked from 'package:lme4':
#> 
#>     lmList
#> This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
#> This is gamm4 0.2-5
set.seed(123)

# data
dat <- gamSim(1, n = 400, scale = 2)
#> Gu & Wahba 4 term additive model

# now add 20 level random effect `fac'...
dat$fac <- fac <- as.factor(sample(1:20, 400, replace = TRUE))
dat$y <- dat$y + model.matrix(~ fac - 1) %*% rnorm(20) * .5

# model object
br <- gamm4::gamm4(
  formula = y ~ s(x0) + x1 + s(x2),
  data = dat,
  random = ~ (1 | fac)
)

# checking class
class(br$gam)
#> [1] "gam"

# checking gam component
broom::tidy(br$gam)
#> # A tibble: 2 x 5
#>   term    edf ref.df statistic   p.value
#>   <chr> <dbl>  <dbl>     <dbl>     <dbl>
#> 1 s(x0)  3.64   3.64      11.6 3.65e-  8
#> 2 s(x2)  8.20   8.20      72.9 4.52e-104

# model summary
broom::glance(br$gam)
#> Error in nobs.default(x): no 'nobs' method is available

Traceback:

8. stop("no 'nobs' method is available") 
7. nobs.default(x) 
6. stats::nobs(x) 
5. eval_tidy(xs[[i]], unique_output) 
4. lst_quos(xs, transform = expand_lst) 
3. tibble(df = sum(x$edf), logLik = as.numeric(stats::logLik(x)), 
    AIC = stats::AIC(x), BIC = stats::BIC(x), deviance = stats::deviance(x), 
    df.residual = stats::df.residual(x), nobs = stats::nobs(x)) at mgcv-tidiers.R#91
2. glance.gam(br$gam) 
1. broom::glance(br$gam)

Created on 2019-08-10 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     2019-08-10                  
#> 
#> - Packages --------------------------------------------------------------
#>  package     * version     date       lib
#>  assertthat    0.2.1       2019-03-21 [1]
#>  backports     1.1.4       2019-04-10 [1]
#>  boot          1.3-23      2019-07-05 [1]
#>  broom         0.5.2.9002  2019-08-08 [1]
#>  callr         3.3.1       2019-07-18 [1]
#>  cli           1.1.0       2019-03-19 [1]
#>  crayon        1.3.4       2017-09-16 [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]
#>  fs            1.3.1       2019-05-06 [1]
#>  gamm4       * 0.2-5       2017-07-25 [1]
#>  generics      0.0.2       2019-03-05 [1]
#>  glue          1.3.1       2019-03-12 [1]
#>  highr         0.8         2019-03-20 [1]
#>  htmltools     0.3.6       2017-04-28 [1]
#>  knitr         1.24        2019-08-08 [1]
#>  lattice       0.20-38     2018-11-04 [2]
#>  lifecycle     0.1.0       2019-08-01 [1]
#>  lme4        * 1.1-21      2019-03-05 [1]
#>  magrittr      1.5         2014-11-22 [1]
#>  MASS          7.3-51.4    2019-03-31 [1]
#>  Matrix      * 1.2-17      2019-03-22 [1]
#>  memoise       1.1.0       2017-04-21 [1]
#>  mgcv        * 1.8-28      2019-03-21 [1]
#>  minqa         1.2.4       2014-10-09 [1]
#>  nlme        * 3.1-140     2019-05-12 [2]
#>  nloptr        1.2.1       2018-10-03 [1]
#>  pillar        1.4.2       2019-06-29 [1]
#>  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]
#>  remotes       2.1.0       2019-06-24 [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         0.8.99.9000 2019-08-10 [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]
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#>  Github (brodieG/fansi@ab11e9c)    
#>  CRAN (R 3.6.0)                    
#>  CRAN (R 3.6.0)                    
#>  Github (r-lib/generics@c15ac43)   
#>  CRAN (R 3.6.0)                    
#>  CRAN (R 3.6.0)                    
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#> 
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#> [2] C:/Program Files/R/R-3.6.1/library
@alexpghayes alexpghayes added beginner-friendly bug an unexpected problem or unintended behavior labels Aug 10, 2019
@alexpghayes
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This might be a collation issue? Might need something like #' @include nobs.R to take advantage of nobs() methods from #597.

@PirateGrunt
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I actually get a different error:

library(gamm4)
#> Loading required package: Matrix
#> Loading required package: lme4
#> Loading required package: mgcv
#> Loading required package: nlme
#> 
#> Attaching package: 'nlme'
#> The following object is masked from 'package:lme4':
#> 
#>     lmList
#> This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
#> This is gamm4 0.2-5
set.seed(123)

dat <- gamSim(1, n = 400, scale = 2)
#> Gu & Wahba 4 term additive model

dat$fac <- fac <- as.factor(sample(1:20, 400, replace = TRUE))
dat$y <- dat$y + model.matrix(~ fac - 1) %*% rnorm(20) * .5

br <- gamm4::gamm4(
  formula = y ~ s(x0) + x1 + s(x2),
  data = dat,
  random = ~ (1 | fac)
)

class(br$gam)
#> [1] "gam"

broom::tidy(br$gam)
#> # A tibble: 2 x 5
#>   term    edf ref.df statistic   p.value
#>   <chr> <dbl>  <dbl>     <dbl>     <dbl>
#> 1 s(x0)  3.64   3.64      11.6 3.65e-  8
#> 2 s(x2)  8.20   8.20      72.9 4.52e-104
broom::glance(br$gam)
#> Error in `$<-.data.frame`(`*tmp*`, "logLik", value = numeric(0)): replacement has 0 rows, data has 1

Created on 2019-09-12 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       Ubuntu 19.04                
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2019-09-12                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version  date       lib source        
#>  assertthat    0.2.1    2019-03-21 [1] CRAN (R 3.6.1)
#>  backports     1.1.4    2019-04-10 [1] CRAN (R 3.6.1)
#>  boot          1.3-23   2019-07-05 [5] CRAN (R 3.6.1)
#>  broom         0.5.2    2019-04-07 [1] CRAN (R 3.6.1)
#>  callr         3.3.1    2019-07-18 [1] CRAN (R 3.6.1)
#>  cli           1.1.0    2019-03-19 [1] CRAN (R 3.6.1)
#>  crayon        1.3.4    2017-09-16 [1] CRAN (R 3.6.1)
#>  desc          1.2.0    2018-05-01 [1] CRAN (R 3.6.1)
#>  devtools      2.1.0    2019-07-06 [1] CRAN (R 3.6.1)
#>  digest        0.6.20   2019-07-04 [1] CRAN (R 3.6.1)
#>  dplyr         0.8.3    2019-07-04 [1] CRAN (R 3.6.1)
#>  evaluate      0.14     2019-05-28 [1] CRAN (R 3.6.1)
#>  fansi         0.4.0    2018-10-05 [1] CRAN (R 3.6.1)
#>  fs            1.3.1    2019-05-06 [1] CRAN (R 3.6.1)
#>  gamm4       * 0.2-5    2017-07-25 [1] CRAN (R 3.6.1)
#>  generics      0.0.2    2018-11-29 [1] CRAN (R 3.6.1)
#>  glue          1.3.1    2019-03-12 [1] CRAN (R 3.6.1)
#>  highr         0.8      2019-03-20 [1] CRAN (R 3.6.1)
#>  htmltools     0.3.6    2017-04-28 [1] CRAN (R 3.6.1)
#>  knitr         1.24     2019-08-08 [1] CRAN (R 3.6.1)
#>  lattice       0.20-38  2018-11-04 [1] CRAN (R 3.6.1)
#>  lme4        * 1.1-21   2019-03-05 [1] CRAN (R 3.6.1)
#>  magrittr      1.5      2014-11-22 [1] CRAN (R 3.6.1)
#>  MASS          7.3-51.1 2018-11-01 [1] CRAN (R 3.6.1)
#>  Matrix      * 1.2-17   2019-03-22 [1] CRAN (R 3.6.1)
#>  memoise       1.1.0    2017-04-21 [1] CRAN (R 3.6.1)
#>  mgcv        * 1.8-28   2019-03-21 [1] CRAN (R 3.6.1)
#>  minqa         1.2.4    2014-10-09 [1] CRAN (R 3.6.1)
#>  nlme        * 3.1-140  2019-05-12 [1] CRAN (R 3.6.1)
#>  nloptr        1.2.1    2018-10-03 [1] CRAN (R 3.6.1)
#>  pillar        1.4.2    2019-06-29 [1] CRAN (R 3.6.1)
#>  pkgbuild      1.0.3    2019-03-20 [1] CRAN (R 3.6.1)
#>  pkgconfig     2.0.2    2018-08-16 [1] CRAN (R 3.6.1)
#>  pkgload       1.0.2    2018-10-29 [1] CRAN (R 3.6.1)
#>  plyr          1.8.4    2016-06-08 [1] CRAN (R 3.6.1)
#>  prettyunits   1.0.2    2015-07-13 [1] CRAN (R 3.6.1)
#>  processx      3.4.1    2019-07-18 [1] CRAN (R 3.6.1)
#>  ps            1.3.0    2018-12-21 [1] CRAN (R 3.6.1)
#>  purrr         0.3.2    2019-03-15 [1] CRAN (R 3.6.1)
#>  R6            2.4.0    2019-02-14 [1] CRAN (R 3.6.1)
#>  Rcpp          1.0.2    2019-07-25 [1] CRAN (R 3.6.1)
#>  remotes       2.1.0    2019-06-24 [1] CRAN (R 3.6.1)
#>  rlang         0.4.0    2019-06-25 [1] CRAN (R 3.6.1)
#>  rmarkdown     1.14     2019-07-12 [1] CRAN (R 3.6.1)
#>  rprojroot     1.3-2    2018-01-03 [1] CRAN (R 3.6.1)
#>  sessioninfo   1.1.1    2018-11-05 [1] CRAN (R 3.6.1)
#>  stringi       1.4.3    2019-03-12 [1] CRAN (R 3.6.1)
#>  stringr       1.4.0    2019-02-10 [1] CRAN (R 3.6.1)
#>  testthat      2.1.1    2019-04-23 [1] CRAN (R 3.6.1)
#>  tibble        2.1.3    2019-06-06 [1] CRAN (R 3.6.1)
#>  tidyr         0.8.3    2019-03-01 [1] CRAN (R 3.6.1)
#>  tidyselect    0.2.5    2018-10-11 [1] CRAN (R 3.6.1)
#>  usethis       1.5.1    2019-07-04 [1] CRAN (R 3.6.1)
#>  utf8          1.1.4    2018-05-24 [1] CRAN (R 3.6.1)
#>  vctrs         0.2.0    2019-07-05 [1] CRAN (R 3.6.1)
#>  withr         2.1.2    2018-03-15 [1] CRAN (R 3.6.1)
#>  xfun          0.8      2019-06-25 [1] CRAN (R 3.6.1)
#>  yaml          2.2.0    2018-07-25 [1] CRAN (R 3.6.1)
#>  zeallot       0.1.0    2018-01-28 [1] CRAN (R 3.6.1)
#> 
#> [1] /home/brian/Rlibs
#> [2] /home/brian/R/x86_64-pc-linux-gnu-library/3.6
#> [3] /usr/local/lib/R/site-library
#> [4] /usr/lib/R/site-library
#> [5] /usr/lib/R/library

@IndrajeetPatil
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Maybe because you are using broom 0.5.2 , while I am using the development version (broom 0.5.2.9002)?

@PirateGrunt
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D'oh! Forgot I was running the CRAN version. Updating to dev now. Sorry!

@PirateGrunt
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There is no nobs.gam() method. I checked nobs.R in the package source and don't see one. One is not needed for mgcv::gam(), because those objects also have class lm and glm.

@vincentarelbundock
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vincentarelbundock commented Jun 12, 2020 •
edited

I think this issue should be closed. As @PirateGrunt noted, glance works perfectly fine for objects produced by mgcv::gam, which is the package that broom officially supports in mgcv-tidiers.R. The package gamm4 is not supported (yet?), and it confusingly produces objects with the same class name as mgcv.

If you want to add nobs, I recommend you define a new method as such, but note that this will still leave you without LogLik, AIC, etc.

library(gamm4)
library(mgcv)
library(broom)

dat <- gamSim(1, n = 400, scale = 2)
dat$fac <- fac <- as.factor(sample(1:20, 400, replace = TRUE))
dat$y <- dat$y + model.matrix(~ fac - 1) %*% rnorm(20) * .5

f1 <- y ~ s(x0) + x1 + s(x2)
f2 <- ~ (1 | fac)
mod1 <- mgcv::gam(formula = f1, data = dat, random = f2)
mod2 <- gamm4::gamm4(formula = f1, data = dat, random = f2)$gam

nobs.gam <- function(object) length(object$y)
glance(mod1)
#> # A tibble: 1 x 7
#>      df logLik   AIC   BIC deviance df.residual  nobs
#>   <dbl>  <dbl> <dbl> <dbl>    <dbl>       <dbl> <int>
#> 1  12.6  -872. 1772. 1826.    1836.        387.   400
glance(mod2)
#> # A tibble: 1 x 7
#>      df logLik   AIC   BIC deviance df.residual  nobs
#>   <dbl>  <dbl> <dbl> <dbl>    <dbl>       <dbl> <int>
#> 1  13.3     NA    NA    NA       NA        387.   400

Created on 2020-06-12 by the reprex package (v0.3.0)

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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.

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@vincentarelbundock @PirateGrunt @IndrajeetPatil @alexpghayes