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Error message encountered with mlr3 parametric learner #96

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Lee-xli opened this issue Sep 19, 2024 · 0 comments
Open

Error message encountered with mlr3 parametric learner #96

Lee-xli opened this issue Sep 19, 2024 · 0 comments

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@Lee-xli
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Lee-xli commented Sep 19, 2024

Hi survex team,

I encountered the following error message "Error in vecdist$wrappedModels()[[i]]: wrong arguments for subsetting an environment" when applying model_survshap function with aft_weibull model from mlr3. This has not been a problem with other models/learners from mlr3 in my experience.

Any insight and suggestion on how this may be debugged would be very much appreciated!

library(mlr3)
library(mlr3extralearners)
library(mlr3pipelines)
library('mlr3proba') 
library(survival)
library(survex)

lung = tsk('lung')$data()

aft=lrn('surv.parametric')
aft$train(tsk('lung'))

class(aft) = c(class(aft), 'LearnerSurv')

aft_exp_lung = explain(aft,
                       data= lung[, -c(1,2)],
                       y=Surv(lung$time, lung$status),
                       label = 'aft')
#> Preparation of a new explainer is initiated 
#>   -> model label       :  aft 
#>   -> data              :  168  rows  7  cols 
#>   -> target variable   :  168  values ( 121 events and 47 censored ) 
#>   -> times             :  50 unique time points , min = 8 , median survival time = 320 , max = 918 
#>   -> times             :  (  generated from y as uniformly distributed survival quantiles based on Kaplan-Meier estimator  ) 
#>   -> predict function  :  predict_newdata()$crank will be used ( �[33m default �[39m ) 
#>   -> predict survival function  :  predict_newdata()$distr$survival will be used ( �[33m default �[39m ) 
#>   -> predict cumulative hazard function  :  predict_newdata()$distr$cumHazard will be used ( �[33m default �[39m ) 
#>   -> model_info        :  package mlr3proba , ver. 0.6.3 , task survival ( �[33m default �[39m ) 
#>   A new explainer has been created!
kernelSHAP_aft_lung = model_survshap(explainer = aft_exp_lung,
                                     calculation_method = 'kernelshap',
                                     aggregation_method = 'integral',  
                                     output_type = 'risk')
#> Error in vecdist$wrappedModels()[[i]]: wrong arguments for subsetting an environment

Created on 2024-09-19 by the reprex package (v2.0.1)

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
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#>  os       macOS Big Sur 10.16         
#>  system   x86_64, darwin17.0          
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       Australia/Adelaide          
#>  date     2024-09-19                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version    date       lib
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#>  patchwork           1.2.0      2024-01-08 [1]
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#>  R6                  2.5.1      2021-08-19 [1]
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#>  survivalmodels      0.1.19     2024-06-26 [1]
#>  tibble              3.2.1      2023-03-20 [1]
#>  tidyselect          1.2.0      2022-10-10 [1]
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#>  vctrs               0.6.5      2023-12-01 [1]
#>  withr               3.0.0      2024-01-16 [1]
#>  xfun                0.25       2021-08-06 [2]
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#> 
#> [1] /Users/Lee/Library/R/x86_64/4.1/library
#> [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
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