Calculates the type 1 recalibrated predictions — calculate_predictions_recalibrated_type

Using the function get_recalibrate_param_type_1_cox() calculates the recalibration parameters in each of the imputed datasets stored in data. With all the parameters estimated aggregates them and calculates the recalibrated predictions with these aggregated parameters and the aggregated predictions.

Usage

# S3 method for class 'cox'
calculate_predictions_recalibrated_type_1(model, data, .progress = FALSE)

Arguments

model: Model generated with mv_model_cox(). Needs the prediction_agg and predictions_imp parameters of the model, to generate it, the function calculate_predictions() must be executed over the model.
data: External validation data. Multiple imputation dataset in long format.
.progress: TRUE to render the progress bar FALSE otherwise.

Value

A model with the parameter prediction_type_1 added to predictions_agg and the parameter alpha stored in recal_parameters

predictions_agg: stores now a new variable prediction_type_1
alpha: stored in recal_parameters and contains the \(\alpha\) recalibration parameter.

Examples

set.seed(123)

model <- mv_model_cox(
  formula = event ~ 0.5 * (x - 1) + 0.3 * (z - 2),
  S0 = 0.98765
)

data <- data.frame(
  .imp = c(1, 1, 1, 2, 2, 2, 3, 3, 3),
  id = c(1, 2, 3, 1, 2, 3, 1, 2, 3),
  x = rnorm(9, 1, 0.25),
  z = rnorm(9, 2, 0.75),
  event = survival::Surv(rpois(9, 5), rbinom(n = 9, size = 1, prob = 0.5))
)

model |>
  calculate_predictions(data) |>
  calculate_predictions_recalibrated_type_1(data)
#> 
#> ── <MiceExtVal/cox> ────────────────────────────────────────────────────────────
#> 
#> ── formula ──
#> 
#> event ~ 0.5 * (x - 1) + 0.3 * (z - 2)
#> 
#> ── S0 ──
#> 
#> 0.98765
#> 
#> ── predictions_imp ──
#> 
#> # A tibble: 5 × 4
#>    .imp    id   betax prediction
#>   <dbl> <dbl>   <dbl>      <dbl>
#> 1     1     1 -0.170      0.0104
#> 2     1     2  0.247      0.0158
#> 3     1     3  0.276      0.0162
#> 4     2     1  0.0990     0.0136
#> 5     2     2  0.0411     0.0129
#> ── predictions_agg ──
#> 
#> # A tibble: 3 × 4
#>      id   betax prediction prediction_type_1
#>   <dbl>   <dbl>      <dbl>             <dbl>
#> 1     1  0.129      0.0145                 0
#> 2     2  0.0805     0.0135                 0
#> 3     3 -0.0544     0.0123                 0
#> ── recal_parameters ──
#> 
#> # A tibble: 1 × 2
#>   param value
#>   <chr> <dbl>
#> 1 alpha  -Inf