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vgam objects are not consistently supported across easystats packages #49

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IndrajeetPatil opened this issue Nov 22, 2019 · 2 comments
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@IndrajeetPatil
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library(VGAM)
#> Loading required package: stats4
#> Loading required package: splines

# Nonparametric proportional odds model
pneumo <- transform(pneumo, let = log(exposure.time))
fit <- vgam(
  formula = cbind(normal, mild, severe) ~ s(let),
  cumulative(parallel = TRUE),
  data = pneumo,
  trace = FALSE
)

insight::get_parameters(fit)
#>       Parameter  Estimate    Component
#> 1 (Intercept):1  9.117550  conditional
#> 2 (Intercept):2 10.019252  conditional
#> 3        s(let) -2.439717 smooth_terms

parameters::ci(fit)
#> Error in standard_error.vglm(model, component = component): no slot of name "coef3" for this object of class "summary.vgam"

parameters::model_parameters(fit)
#> Error in cs[, 3]: incorrect number of dimensions

performance::model_performance(fit)
#> Can't extract residuals from model.
#> Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : arguments imply differing number of rows: 0, 1

Created on 2019-11-22 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       Europe/Berlin               
#>  date     2019-11-22                  
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version    date       lib source                               
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                       
#>  backports     1.1.5      2019-10-02 [1] CRAN (R 3.6.1)                       
#>  bayestestR    0.4.0      2019-10-20 [1] CRAN (R 3.6.1)                       
#>  callr         3.3.2      2019-09-22 [1] CRAN (R 3.6.1)                       
#>  cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                       
#>  crayon        1.3.4      2017-09-16 [1] CRAN (R 3.5.1)                       
#>  desc          1.2.0      2019-11-11 [1] Github (r-lib/desc@61205f6)          
#>  devtools      2.2.1      2019-09-24 [1] CRAN (R 3.6.1)                       
#>  digest        0.6.22     2019-10-21 [1] CRAN (R 3.6.1)                       
#>  ellipsis      0.3.0      2019-09-20 [1] CRAN (R 3.6.1)                       
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                       
#>  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                       
#>  glue          1.3.1      2019-03-12 [1] CRAN (R 3.6.0)                       
#>  highr         0.8        2019-03-20 [1] CRAN (R 3.6.0)                       
#>  htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.1)                       
#>  insight       0.7.0      2019-11-20 [1] local                                
#>  knitr         1.26       2019-11-12 [1] CRAN (R 3.6.1)                       
#>  magrittr      1.5        2014-11-22 [1] CRAN (R 3.5.1)                       
#>  memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                       
#>  parameters    0.3.0      2019-11-19 [1] Github (easystats/parameters@155a843)
#>  performance   0.4.0.1    2019-11-19 [1] local                                
#>  pkgbuild      1.0.6      2019-10-09 [1] CRAN (R 3.6.1)                       
#>  pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                       
#>  prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.5.1)                       
#>  processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.1)                       
#>  ps            1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                       
#>  R6            2.4.1      2019-11-12 [1] CRAN (R 3.6.1)                       
#>  Rcpp          1.0.3      2019-11-08 [1] CRAN (R 3.6.1)                       
#>  remotes       2.1.0      2019-06-24 [1] CRAN (R 3.6.0)                       
#>  rlang         0.4.1      2019-10-24 [1] Github (r-lib/rlang@30feeac)         
#>  rmarkdown     1.17       2019-11-13 [1] CRAN (R 3.6.1)                       
#>  rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.5.1)                       
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                       
#>  stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                       
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                       
#>  testthat      2.3.0      2019-11-05 [1] CRAN (R 3.6.1)                       
#>  usethis       1.5.1.9000 2019-11-13 [1] Github (r-lib/usethis@c5f1e7f)       
#>  VGAM        * 1.1-2      2019-11-21 [1] CRAN (R 3.6.1)                       
#>  withr         2.1.2      2018-03-15 [1] CRAN (R 3.5.1)                       
#>  xfun          0.11       2019-11-12 [1] CRAN (R 3.6.1)                       
#>  yaml          2.2.0      2018-07-25 [1] CRAN (R 3.5.1)                       
#> 
#> [1] C:/Users/inp099/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.1/library
strengejacke added a commit to easystats/parameters that referenced this issue Nov 22, 2019
@strengejacke
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should work now in insight and parameters. Will look at performance.

strengejacke added a commit to easystats/performance that referenced this issue Nov 24, 2019
@strengejacke
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hm, r2() for vgam models looks quite suspicious...

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