prevalence function

Prevalence

preval estimates the prevalence of positive cases for a nominal/categorical predicted-observed dataset.

preval_t estimates the prevalence threshold for a binary predicted-observed dataset.

preval(
  data = NULL,
  obs,
  pred,
  atom = FALSE,
  pos_level = 2,
  tidy = FALSE,
  na.rm = TRUE
)

preval_t(
  data = NULL,
  obs,
  pred,
  atom = FALSE,
  pos_level = 2,
  tidy = FALSE,
  na.rm = TRUE
)

Arguments

• data: (Optional) argument to call an existing data frame containing the data.
• obs: Vector with observed values (character | factor).
• pred: Vector with predicted values (character | factor).
• atom: Logical operator (TRUE/FALSE) to decide if the estimate is made for each class (atom = TRUE) or at a global level (atom = FALSE); Default : FALSE.
• pos_level: Integer, for binary cases, indicating the order (1|2) of the level corresponding to the positive. Generally, the positive level is the second (2) since following an alpha-numeric order, the most common pairs are (Negative | Positive), (0 | 1), (FALSE | TRUE). Default : 2.
• tidy: Logical operator (TRUE/FALSE) to decide the type of return. TRUE returns a data.frame, FALSE returns a list; Default : FALSE.
• na.rm: Logic argument to remove rows with missing values (NA). Default is na.rm = TRUE.

Returns

an object of class numeric within a list (if tidy = FALSE) or within a data frame (if tidy = TRUE).

Details

The prevalence measures the overall proportion of actual positives with respect to the total number of observations. Currently, it is defined for binary cases only.

The general formula is:

$preval = \frac{positive}{positive + negative}$

The prevalence threshold represents an point on the ROC curve (function of sensitivity (recall) and specificity) below which the precision (or PPV) dramatically drops.

$preval_t = \frac{\sqrt{TPR * FPR} - FPR}{TPR - FPR}$

It is bounded between 0 and 1. The closer to 1 the better. Values towards zero indicate low performance. For the formula and more details, see online-documentation

Examples

set.seed(123)
# Two-class
binomial_case <- data.frame(labels = sample(c("True","False"), 100, replace = TRUE), 
predictions = sample(c("True","False"), 100, replace = TRUE))
# Multi-class
multinomial_case <- data.frame(labels = sample(c("Red","Blue", "Green"), 100, replace = TRUE),
predictions = sample(c("Red","Blue", "Green"), 100, replace = TRUE)    )

# Get prevalence estimate for two-class case
preval(data = binomial_case, obs = labels, pred = predictions, tidy = TRUE)

# Get prevalence estimate for each class for the multi-class case
preval(data = multinomial_case, obs = labels, pred = predictions, atom = TRUE)

References

Freeman, E.A., Moisen, G.G. (2008). A comparison of the performance of threshold criteria for binary classification in terms of predicted prevalence and kappa. . Ecol. Modell. 217(1-2): 45-58. tools:::Rd_expr_doi("10.1016/j.ecolmodel.2008.05.015")

Balayla, J. (2020). Prevalence threshold and the geometry of screening curves. _Plos one, 15(10):e0240215, _ tools:::Rd_expr_doi("10.1371/journal.pone.0240215")