case weights about proc

[xrobin]

I agree this would be cool. Do you have a reference on how this is implemented in the context of ROC curves?

[topepo]

The curve would be based on the weighted versions of sensitivity and specificity.

library(tidymodels)
#> Registered S3 method overwritten by 'tune':
#>   method                   from   
#>   required_pkgs.model_spec parsnip

data(pathology)
str(pathology)
#> 'data.frame':    344 obs. of  2 variables:
#>  $ pathology: Factor w/ 2 levels "abnorm","norm": 1 1 1 1 1 1 1 1 1 1 ...
#>  $ scan     : Factor w/ 2 levels "abnorm","norm": 1 1 1 1 1 1 1 1 1 1 ...

set.seed(1)
pathology$weights <- runif(nrow(pathology))

event <- "abnorm"

unweighted <- 
  sum(pathology$pathology == event & pathology$scan == event) /
  sum(pathology$pathology == event)
unweighted
#> [1] 0.8953488

# via yardstick:
sensitivity(pathology, pathology, scan)
#> # A tibble: 1 × 3
#>   .metric .estimator .estimate
#>   <chr>   <chr>          <dbl>
#> 1 sens    binary         0.895

weighted <- 
  sum( pathology$weights * (pathology$pathology == event & pathology$scan == event) ) /
  sum( pathology$weights * (pathology$pathology == event) )

weighted
#> [1] 0.9013333

^{Created on 2021-09-13 by the reprex package (v2.0.0)}

@DavisVaughan has the start of changes that we will be making to yardstick here

[xrobin]

I think I see. The easiest would be to directly update the roc.utils.perfs.all.fast to calculate TP/FP taking the weights into account:

  tp <- cumsum(response.sorted==1 * weights.sorted)
  fp <- cumsum(response.sorted==0 * weights.sorted)

A few thought on the implementation:

• The number of cases and controls might become fractional because of this change. I'm not sure what side-effects this could have.
• There's a C++ algorithm that will need to be updated too. It's a loop so it should be quite straightforward. Alternatively it could be a good time to get rid of alternative algorithms and simplify the code.
• It will be necessary to modify the roc objects and store the weights there, so that bootstrap functions re-use the weights appropriately.
• At this point I'm not sure how much changes will be required in those bootstrapping functions. They've needed major refactoring for a long time but I never found the time to do so.
• Issue #70 will get in the way. There's quite a lot of redundancy as pROC has several functions that build ROC curves under the hood (ie auc, ci, etc), which will have to be updated.