Calculating only the ROC curve
When running cutpointr, a ROC curve is by default returned in the column roc_curve. This ROC curve can be plotted using plot_roc. Alternatively, if only the ROC curve is desired and no cutpoint needs to be calculated, the ROC curve can be created using roc() and plotted using plot_cutpointr. The roc function, unlike cutpointr, does not determine direction, pos_class or neg_class automatically.
library(cutpointr)
roc_curve <- roc(data = suicide, x = dsi, class = suicide,
pos_class = "yes", neg_class = "no", direction = ">=")
auc(roc_curve)
## [1] 0.9237791
## # A tibble: 6 x 9
## x.sorted tp fp tn fn tpr tnr fpr fnr
## <dbl> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl>
## 1 Inf 0 0 496 36 0 1 0 1
## 2 11 1 0 496 35 0.0278 1 0 0.972
## 3 10 2 1 495 34 0.0556 0.998 0.00202 0.944
## 4 9 3 1 495 33 0.0833 0.998 0.00202 0.917
## 5 8 4 1 495 32 0.111 0.998 0.00202 0.889
## 6 7 7 1 495 29 0.194 0.998 0.00202 0.806
ROC curve and optimal cutpoint for multiple variables
Alternatively, we can map the standard evaluation version cutpointr to the column names. If direction and / or pos_class and neg_class are unspecified, these parameters will automatically be determined by cutpointr so that the AUC values for all variables will be \(> 0.5\).
We could do this manually, e.g. using purrr::map, but to make this task more convenient multi_cutpointr can be used to achieve the same result. It maps multiple predictor columns to cutpointr, by default all numeric columns except for the class column.
mcp <- multi_cutpointr(suicide, class = suicide, pos_class = "yes",
use_midpoints = TRUE, silent = TRUE)
summary(mcp)
## Method: maximize_metric
## Predictor: age, dsi
## Outcome: suicide
##
## Predictor: age
## --------------------------------------------------------------------------------
## direction AUC n n_pos n_neg
## <= 0.5257 532 36 496
##
## optimal_cutpoint sum_sens_spec acc sensitivity specificity tp fn fp tn
## 55.5 1.1154 0.1992 0.9722 0.1431 35 1 425 71
##
## Predictor summary:
## Data Min. 5% 1st Qu. Median Mean 3rd Qu. 95% Max. SD NAs
## Overall 18 19 24 28.0 34.1259 41.25 65.00 83 15.0542 0
## no 18 19 24 28.0 34.2218 41.25 65.50 83 15.1857 0
## yes 18 18 22 27.5 32.8056 41.25 54.25 69 13.2273 0
##
## Predictor: dsi
## --------------------------------------------------------------------------------
## direction AUC n n_pos n_neg
## >= 0.9238 532 36 496
##
## optimal_cutpoint sum_sens_spec acc sensitivity specificity tp fn fp tn
## 1.5 1.7518 0.8647 0.8889 0.8629 32 4 68 428
##
## Predictor summary:
## Data Min. 5% 1st Qu. Median Mean 3rd Qu. 95% Max. SD NAs
## Overall 0 0.00 0 0 0.9211 1 5.00 11 1.8527 0
## no 0 0.00 0 0 0.6331 0 4.00 10 1.4122 0
## yes 0 0.75 4 5 4.8889 6 9.25 11 2.5498 0
Accessing data, roc_curve, and boot
The object returned by cutpointr is of the classes cutpointr, tbl_df, tbl, and data.frame. Thus, it can be handled like a usual data frame. The columns data, roc_curve, and boot consist of nested data frames, which means that these are list columns whose elements are data frames. They can either be accessed using [ or by using functions from the tidyverse. If subgroups were given, the output contains one row per subgroup and the function that accesses the data should be mapped to every row or the data should be grouped by subgroup.
set.seed(123)
opt_cut_b_g <- cutpointr(suicide, dsi, suicide, gender, boot_runs = 500)
library(dplyr)
library(tidyr)
opt_cut_b_g |>
group_by(subgroup) |>
select(subgroup, boot) |>
unnest(cols = boot) |>
summarise(sd_oc_boot = sd(optimal_cutpoint),
m_oc_boot = mean(optimal_cutpoint),
m_acc_oob = mean(acc_oob))
## # A tibble: 2 x 4
## subgroup sd_oc_boot m_oc_boot m_acc_oob
## <chr> <dbl> <dbl> <dbl>
## 1 female 0.766 2.17 0.880
## 2 male 1.51 2.92 0.806
Adding metrics to the result of cutpointr() or roc()
By default, the output of cutpointr includes the optimized metric and several other metrics. The add_metric function adds further metrics. Here, we’re adding the negative predictive value (NPV) and the positive predictive value (PPV) at the optimal cutpoint per subgroup:
cutpointr(suicide, dsi, suicide, gender, metric = youden, silent = TRUE) |>
add_metric(list(ppv, npv)) |>
select(subgroup, optimal_cutpoint, youden, ppv, npv)
## # A tibble: 2 x 5
## subgroup optimal_cutpoint youden ppv npv
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 female 2 0.808118 0.367647 0.993827
## 2 male 3 0.625106 0.259259 0.982301
In the same fashion, additional metric columns can be added to a roc_cutpointr object:
roc(data = suicide, x = dsi, class = suicide, pos_class = "yes",
neg_class = "no", direction = ">=") |>
add_metric(list(cohens_kappa, F1_score)) |>
select(x.sorted, tp, fp, tn, fn, cohens_kappa, F1_score) |>
head()
## # A tibble: 6 x 7
## x.sorted tp fp tn fn cohens_kappa F1_score
## <dbl> <dbl> <dbl> <int> <int> <dbl> <dbl>
## 1 Inf 0 0 496 36 0 0
## 2 11 1 0 496 35 0.0506 0.0541
## 3 10 2 1 495 34 0.0931 0.103
## 4 9 3 1 495 33 0.138 0.15
## 5 8 4 1 495 32 0.182 0.195
## 6 7 7 1 495 29 0.301 0.318