Specificity

These functions calculate the spec() (specificity) of a measurement system compared to a reference result (the "truth" or gold standard). Highly related functions are sens(), ppv(), and npv().

Usage

spec(data, ...)

# S3 method for data.frame
spec(
  data,
  truth,
  estimate,
  estimator = NULL,
  na_rm = TRUE,
  case_weights = NULL,
  event_level = yardstick_event_level(),
  ...
)

spec_vec(
  truth,
  estimate,
  estimator = NULL,
  na_rm = TRUE,
  case_weights = NULL,
  event_level = yardstick_event_level(),
  ...
)

specificity(data, ...)

# S3 method for data.frame
specificity(
  data,
  truth,
  estimate,
  estimator = NULL,
  na_rm = TRUE,
  case_weights = NULL,
  event_level = yardstick_event_level(),
  ...
)

specificity_vec(
  truth,
  estimate,
  estimator = NULL,
  na_rm = TRUE,
  case_weights = NULL,
  event_level = yardstick_event_level(),
  ...
)

Arguments

data: Either a data.frame containing the columns specified by the truth and estimate arguments, or a table/matrix where the true class results should be in the columns of the table.
...: Not currently used.
truth: The column identifier for the true class results (that is a factor). This should be an unquoted column name although this argument is passed by expression and supports quasiquotation (you can unquote column names). For _vec() functions, a factor vector.
estimate: The column identifier for the predicted class results (that is also factor). As with truth this can be specified different ways but the primary method is to use an unquoted variable name. For _vec() functions, a factor vector.
estimator: One of: "binary", "macro", "macro_weighted", or "micro" to specify the type of averaging to be done. "binary" is only relevant for the two class case. The other three are general methods for calculating multiclass metrics. The default will automatically choose "binary" or "macro" based on estimate.
na_rm: A logical value indicating whether NA values should be stripped before the computation proceeds.
case_weights: The optional column identifier for case weights. This should be an unquoted column name that evaluates to a numeric column in data. For _vec() functions, a numeric vector, hardhat::importance_weights(), or hardhat::frequency_weights().
event_level: A single string. Either "first" or "second" to specify which level of truth to consider as the "event". This argument is only applicable when estimator = "binary". The default uses an internal helper that defaults to "first".

Value

A tibble with columns .metric, .estimator, and .estimate and 1 row of values.

For grouped data frames, the number of rows returned will be the same as the number of groups.

For spec_vec(), a single numeric value (or NA).

Details

The specificity measures the proportion of negatives that are correctly identified as negatives.

When the denominator of the calculation is 0, specificity is undefined. This happens when both # true_negative = 0 and # false_positive = 0 are true, which mean that there were no true negatives. When computing binary specificity, a NA value will be returned with a warning. When computing multiclass specificity, the individual NA values will be removed, and the computation will procede, with a warning.

Relevant Level

There is no common convention on which factor level should automatically be considered the "event" or "positive" result when computing binary classification metrics. In yardstick, the default is to use the first level. To alter this, change the argument event_level to "second" to consider the last level of the factor the level of interest. For multiclass extensions involving one-vs-all comparisons (such as macro averaging), this option is ignored and the "one" level is always the relevant result.

Multiclass

Macro, micro, and macro-weighted averaging is available for this metric. The default is to select macro averaging if a truth factor with more than 2 levels is provided. Otherwise, a standard binary calculation is done. See vignette("multiclass", "yardstick") for more information.

Implementation

Suppose a 2x2 table with notation:

	Reference
Predicted	Positive	Negative
Positive	A	B
Negative	C	D

The formulas used here are:

$$Sensitivity = A/(A+C)$$ $$Specificity = D/(B+D)$$ $$Prevalence = (A+C)/(A+B+C+D)$$ $$PPV = (Sensitivity * Prevalence) / ((Sensitivity * Prevalence) + ((1-Specificity) * (1-Prevalence)))$$ $$NPV = (Specificity * (1-Prevalence)) / (((1-Sensitivity) * Prevalence) + ((Specificity) * (1-Prevalence)))$$

See the references for discussions of the statistics.

References

Altman, D.G., Bland, J.M. (1994) ``Diagnostic tests 1: sensitivity and specificity,'' British Medical Journal, vol 308, 1552.

Author

Max Kuhn

Examples

# Two class
data("two_class_example")
spec(two_class_example, truth, predicted)
#> # A tibble: 1 × 3
#>   .metric .estimator .estimate
#>   <chr>   <chr>          <dbl>
#> 1 spec    binary         0.793

# Multiclass
library(dplyr)
data(hpc_cv)

hpc_cv %>%
  filter(Resample == "Fold01") %>%
  spec(obs, pred)
#> # A tibble: 1 × 3
#>   .metric .estimator .estimate
#>   <chr>   <chr>          <dbl>
#> 1 spec    macro          0.886

# Groups are respected
hpc_cv %>%
  group_by(Resample) %>%
  spec(obs, pred)
#> # A tibble: 10 × 4
#>    Resample .metric .estimator .estimate
#>    <chr>    <chr>   <chr>          <dbl>
#>  1 Fold01   spec    macro          0.886
#>  2 Fold02   spec    macro          0.882
#>  3 Fold03   spec    macro          0.899
#>  4 Fold04   spec    macro          0.879
#>  5 Fold05   spec    macro          0.881
#>  6 Fold06   spec    macro          0.873
#>  7 Fold07   spec    macro          0.866
#>  8 Fold08   spec    macro          0.884
#>  9 Fold09   spec    macro          0.867
#> 10 Fold10   spec    macro          0.875

# Weighted macro averaging
hpc_cv %>%
  group_by(Resample) %>%
  spec(obs, pred, estimator = "macro_weighted")
#> # A tibble: 10 × 4
#>    Resample .metric .estimator     .estimate
#>    <chr>    <chr>   <chr>              <dbl>
#>  1 Fold01   spec    macro_weighted     0.816
#>  2 Fold02   spec    macro_weighted     0.815
#>  3 Fold03   spec    macro_weighted     0.839
#>  4 Fold04   spec    macro_weighted     0.803
#>  5 Fold05   spec    macro_weighted     0.812
#>  6 Fold06   spec    macro_weighted     0.795
#>  7 Fold07   spec    macro_weighted     0.790
#>  8 Fold08   spec    macro_weighted     0.814
#>  9 Fold09   spec    macro_weighted     0.795
#> 10 Fold10   spec    macro_weighted     0.801

# Vector version
spec_vec(
  two_class_example$truth,
  two_class_example$predicted
)
#> [1] 0.7933884

# Making Class2 the "relevant" level
spec_vec(
  two_class_example$truth,
  two_class_example$predicted,
  event_level = "second"
)
#> [1] 0.879845