Create table summaries of predictNMBscreen objects.

Create table summaries of predictNMBscreen objects.

Usage

# S3 method for predictNMBscreen
summary(
  object,
  what = c("nmb", "inb", "cutpoints"),
  inb_ref_col = NULL,
  agg_functions = list(median = function(x) {
     round(stats::median(x), digits = 2)

    }, `95% CI` = function(x) {
     paste0(round(stats::quantile(x, probs = c(0.025,
    0.975)), digits = 1), collapse = " to ")
 }),
  rename_vector,
  show_full_inputs = FALSE,
  ...
)

Arguments

object

A predictNMBscreen object.

what

What to summarise: one of "nmb", "inb" or "cutpoints". Defaults to "nmb".

inb_ref_col

Which cutpoint method to use as the reference strategy when calculating the incremental net monetary benefit. See do_nmb_sim for more information.

agg_functions

A named list of functions to use to aggregate the selected values. Defaults to the median and 95% interval.

rename_vector

A named vector for renaming the methods in the summary. The values of the vector are the default names and the names given are the desired names in the output.

show_full_inputs

A logical. Whether or not to include the inputs used for simulation alongside aggregations.

...

Additional, ignored arguments.

Value

Returns a tibble.

Details

Table summaries will be based on the what argument. Using "nmb" returns the simulated values for NMB, with no reference group; "inb" returns the difference between simulated values for NMB and a set strategy defined by inb_ref_col; "cutpoints" returns the cutpoints selected (0, 1).

Examples

# perform screen with increasing values of model discimination (sim_auc)
# \donttest{
get_nmb <- function() c("TP" = -3, "TN" = 0, "FP" = -1, "FN" = -4)
sim_screen_obj <- screen_simulation_inputs(
  n_sims = 50, n_valid = 10000, sim_auc = seq(0.7, 0.9, 0.1),
  event_rate = 0.1, fx_nmb_training = get_nmb, fx_nmb_evaluation = get_nmb,
  cutpoint_methods = c("all", "none", "youden", "value_optimising")
)
summary(
  sim_screen_obj,
  rename_vector = c(
    "Value_Optimising" = "value_optimising",
    "Treat_None" = "none",
    "Treat_All" = "all",
    "Youden_Index" = "youden"
  )
)
#> # A tibble: 3 × 9
#>   sim_auc Treat_All_median `Treat_All_95% CI` Treat_None_median
#>     <dbl>            <dbl> <chr>                          <dbl>
#> 1     0.7             -1.2 -1.2 to -1.2                    -0.4
#> 2     0.8             -1.2 -1.2 to -1.2                    -0.4
#> 3     0.9             -1.2 -1.2 to -1.2                    -0.4
#> # ℹ 5 more variables: `Treat_None_95% CI` <chr>, Youden_Index_median <dbl>,
#> #   `Youden_Index_95% CI` <chr>, Value_Optimising_median <dbl>,
#> #   `Value_Optimising_95% CI` <chr>
# }