library(yardstick)yardstick already includes a large number of metrics, but there’s obviously a chance that you might have a custom metric that hasn’t been implemented yet. In that case, you can use a few of the tools yardstick exposes to create custom metrics.
Why create custom metrics? With the infrastructure yardstick provides, you get:
NA handlingmetric_set()The implementation metrics differ slightly depending on whether you are implementing a numeric, class or class probability metric. Examples for numeric and classification metrics are given below. I would encourage you to look into the implementation of roc_auc() after reading this vignette if you want to work on a class probability metric.
Mean squared error (from here on, mse()) is a numeric metric that measures the average of the squared errors. Numeric metrics are generally the simplest to create with yardstick, as they do not have multiclass implementations. The formula for mse() is:
\[ MSE = \frac{1}{N} \sum_{i=1}^{N} (truth_i - estimate_i) ^ 2 = mean( (truth - estimate) ^ 2) \]
All metrics should have a data frame version, and a vector version. The data frame version here will be named mse(), and the vector version will be mse_vec().
To start, create the vector version. Generally, all metrics have the same arguments unless the metric requires an extra parameter (such as beta in f_meas()). To create the vector function, you need to do two things:
mse_impl().metric_vec_template().Below, mse_impl() contains the actual implementation of the metric, and takes truth and estimate as arguments along with any metric specific arguments.
metric_vec_template() is a yardstick function that accepts the implementation function along with the other arguments to mse_vec() and actually executes mse_impl(). Additionally, it has a cls argument to specify the allowed class type of truth and estimate. If the classes are the same, a single character class can be passed, and if they are different a character vector of length 2 can be supplied.
The metric_vec_template() helper handles the removal of NA values in your metric, so your implementation function does not have to worry about them. It performs type checking using cls and also checks that the estimator is valid, the second of which is covered in the classification example. This way, all you have to worry about is the core implementation.
mse_vec <- function(truth, estimate, na_rm = TRUE, ...) {
mse_impl <- function(truth, estimate) {
mean((truth - estimate) ^ 2)
}
metric_vec_template(
metric_impl = mse_impl,
truth = truth,
estimate = estimate,
na_rm = na_rm,
cls = "numeric",
...
)
}At this point, you’ve created the vector version of the mean squared error metric.
data("solubility_test")
mse_vec(
truth = solubility_test$solubility,
estimate = solubility_test$prediction
)
#> [1] 0.5214438Intelligent error handling is immediately available.
mse_vec(truth = "apple", estimate = 1)
#> Error: `truth` should be a numeric but a character was supplied.
mse_vec(truth = 1, estimate = factor("xyz"))
#> Error: `estimate` should be a numeric but a factor was supplied.NA values are removed if na_rm = TRUE (the default). If na_rm = FALSE and any NA values are detected, then the metric automatically returns NA.
# NA values removed
mse_vec(truth = c(NA, .5, .4), estimate = c(1, .6, .5))
#> [1] 0.01
# NA returned
mse_vec(truth = c(NA, .5, .4), estimate = c(1, .6, .5), na_rm = FALSE)
#> [1] NAThe data frame version of the metric should be fairly simple. It is a generic function with a data.frame method that calls the yardstick helper, metric_summarizer(), and passes along the mse_vec() function to it along with versions of truth and estimate that have been wrapped in rlang::enquo() and then unquoted with !! so that non-standard evaluation can be supported. Additionally, the generic itself has been wrapped in new_numeric_metric() to formalize it as a numeric metric function. This allows the metric to work with metric_set() and the tune package.
library(rlang)
mse <- function(data, ...) {
UseMethod("mse")
}
mse <- new_numeric_metric(mse, direction = "minimize")
mse.data.frame <- function(data, truth, estimate, na_rm = TRUE, ...) {
metric_summarizer(
metric_nm = "mse",
metric_fn = mse_vec,
data = data,
truth = !! enquo(truth),
estimate = !! enquo(estimate),
na_rm = na_rm,
...
)
}And that’s it. yardstick handles the rest with an internal call to summarise().
mse(solubility_test, truth = solubility, estimate = prediction)
#> # A tibble: 1 × 3
#> .metric .estimator .estimate
#> <chr> <chr> <dbl>
#> 1 mse standard 0.521
# Error handling
mse(solubility_test, truth = solubility, estimate = factor("xyz"))
#> Error: Problem with `summarise()` column `.estimate`.
#> ℹ `.estimate = metric_fn(truth = solubility, estimate = factor("xyz"), na_rm = na_rm)`.
#> x `estimate` should be a numeric but a factor was supplied.Let’s test it out on a grouped data frame.
library(dplyr)
set.seed(1234)
size <- 100
times <- 10
# create 10 resamples
solubility_resampled <- bind_rows(
replicate(
n = times,
expr = sample_n(solubility_test, size, replace = TRUE),
simplify = FALSE
),
.id = "resample"
)
solubility_resampled %>%
group_by(resample) %>%
mse(solubility, prediction)
#> # A tibble: 10 × 4
#> resample .metric .estimator .estimate
#> <chr> <chr> <chr> <dbl>
#> 1 1 mse standard 0.512
#> 2 10 mse standard 0.454
#> 3 2 mse standard 0.513
#> 4 3 mse standard 0.414
#> 5 4 mse standard 0.543
#> 6 5 mse standard 0.456
#> 7 6 mse standard 0.652
#> 8 7 mse standard 0.642
#> 9 8 mse standard 0.404
#> 10 9 mse standard 0.479Miss rate is another name for the False Negative Rate, and is a classification metric in the same family as sens() and spec(). It follows the formula:
\[ miss\_rate = \frac{FN}{FN + TP} \]
This metric, like other classification metrics, is more easily computed when expressed as a confusion matrix. As you will see in the example, you can achieve this with a call to base::table(estimate, truth) which correctly puts the “correct” result in the columns of the confusion matrix.
Classification metrics are more complicated than numeric ones because you have to think about extensions to the multiclass case. For now, let’s start with the binary case.
The vector implementation for classification metrics initially has the same setup as numeric metrics, but has two additional arguments.
estimator determines the type of estimator to use (binary or some kind of multiclass implementation or averaging). This argument is auto-selected for the user, so default it to NULL. Additionally, pass it along to metric_vec_template() so that it can check the provided estimator against the classes of truth and estimate to see if they are allowed.
event_level determines which level of truth should be considered the “event” when truth is a binary factor. The two options are "first", and "second", but you should default it to "first".
# Logic for `event_level`
event_col <- function(xtab, event_level) {
if (identical(event_level, "first")) {
colnames(xtab)[[1]]
} else {
colnames(xtab)[[2]]
}
}
miss_rate_vec <- function(truth,
estimate,
estimator = NULL,
na_rm = TRUE,
event_level = "first",
...) {
estimator <- finalize_estimator(truth, estimator)
miss_rate_impl <- function(truth, estimate) {
# Create
xtab <- table(estimate, truth)
col <- event_col(xtab, event_level)
col2 <- setdiff(colnames(xtab), col)
tp <- xtab[col, col]
fn <- xtab[col2, col]
fn / (fn + tp)
}
metric_vec_template(
metric_impl = miss_rate_impl,
truth = truth,
estimate = estimate,
na_rm = na_rm,
cls = "factor",
estimator = estimator,
...
)
}Another change from the numeric metric is that a call to finalize_estimator() is made. This is the infrastructure that auto-selects the type of estimator to use.
data("two_class_example")
miss_rate_vec(two_class_example$truth, two_class_example$predicted)
#> [1] 0.120155What happens if you try and pass in a multiclass result?
data("hpc_cv")
fold1 <- filter(hpc_cv, Resample == "Fold01")
miss_rate_vec(fold1$obs, fold1$pred)
#> F M L
#> 0.06214689 0.00000000 0.00000000This isn’t great, as currently multiclass miss_rate() isn’t supported and it would have been better to throw an error if the estimator was not "binary". Currently, finalize_estimator() uses its default implementation which selected "macro" as the estimator since truth was a factor with more than 2 classes. When we implement multiclass averaging, this is what you want, but if your metric only works with a binary implementation (or has other specialized multiclass versions), you might want to guard against this.
To fix this, a generic counterpart to finalize_estimator(), called finalize_estimator_internal(), exists that helps you restrict the input types. If you provide a method to finalize_estimator_internal() where the method name is the same as your metric name, and then set the metric_class argument in finalize_estimator() to be the same thing, you can control how the auto-selection of the estimator is handled.
Don’t worry about the metric_dispatcher argument. This is handled for you and just exists as a dummy argument to dispatch off of.
It is also good practice to call validate_estimator() which handles the case where a user passed in the estimator themselves. This validates that the supplied estimator is one of the allowed types and error otherwise.
finalize_estimator_internal.miss_rate <- function(metric_dispatcher, x, estimator) {
validate_estimator(estimator, estimator_override = "binary")
if(!is.null(estimator)) {
return(estimator)
}
lvls <- levels(x)
if(length(lvls) > 2) {
stop("A multiclass `truth` input was provided, but only `binary` is supported.")
}
"binary"
}
miss_rate_vec <- function(truth,
estimate,
estimator = NULL,
na_rm = TRUE,
event_level = "first",
...) {
# calls finalize_estimator_internal() internally
estimator <- finalize_estimator(truth, estimator, metric_class = "miss_rate")
miss_rate_impl <- function(truth, estimate) {
# Create
xtab <- table(estimate, truth)
col <- event_col(xtab, event_level)
col2 <- setdiff(colnames(xtab), col)
tp <- xtab[col, col]
fn <- xtab[col2, col]
fn / (fn + tp)
}
metric_vec_template(
metric_impl = miss_rate_impl,
truth = truth,
estimate = estimate,
na_rm = na_rm,
cls = "factor",
estimator = estimator,
...
)
}
# Error thrown by our custom handler
miss_rate_vec(fold1$obs, fold1$pred)
#> Error in finalize_estimator_internal.miss_rate(metric_dispatcher, x, estimator): A multiclass `truth` input was provided, but only `binary` is supported.
# Error thrown by validate_estimator()
miss_rate_vec(fold1$obs, fold1$pred, estimator = "macro")
#> Error: `estimator` must be one of: "binary". Not "macro".Like many other classification metrics such as precision() or recall(), miss rate does not have a natural multiclass extension, but one can be created using methods such as macro, weighted macro, and micro averaging. If you have not, I encourage you to read vignette("multiclass", "yardstick") for more information about how these methods work.
Generally, they require more effort to get right than the binary case, especially if you want to have a performant version. Luckily, a somewhat standard template is used in yardstick and can be used here as well.
Let’s first remove the “binary” restriction we created earlier.
rm(finalize_estimator_internal.miss_rate)The main changes below are:
The binary implementation is moved to miss_rate_binary().
miss_rate_estimator_impl() is a helper function for switching between binary and multiclass implementations. It also applies the weighting required for multiclass estimators. It is called from miss_rate_impl() and also accepts the estimator argument using R’s function scoping rules.
miss_rate_multiclass() provides the implementation for the multiclass case. It calculates the true positive and false negative values as vectors with one value per class. For the macro case, it returns a vector of miss rate calculations, and for micro, it first sums the individual pieces and returns a single miss rate calculation. In the macro case, the vector is then weighted appropriately in miss_rate_estimator_impl() depending on whether or not it was macro or weighted macro.
miss_rate_vec <- function(truth,
estimate,
estimator = NULL,
na_rm = TRUE,
event_level = "first",
...) {
# calls finalize_estimator_internal() internally
estimator <- finalize_estimator(truth, estimator, metric_class = "miss_rate")
miss_rate_impl <- function(truth, estimate) {
xtab <- table(estimate, truth)
# Rather than implement the actual method here, we rely on
# an *_estimator_impl() function that can handle binary
# and multiclass cases
miss_rate_estimator_impl(xtab, estimator, event_level)
}
metric_vec_template(
metric_impl = miss_rate_impl,
truth = truth,
estimate = estimate,
na_rm = na_rm,
cls = "factor",
estimator = estimator,
...
)
}
# This function switches between binary and multiclass implementations
miss_rate_estimator_impl <- function(data, estimator, event_level) {
if(estimator == "binary") {
miss_rate_binary(data, event_level)
} else {
# Encapsulates the macro, macro weighted, and micro cases
wt <- get_weights(data, estimator)
res <- miss_rate_multiclass(data, estimator)
weighted.mean(res, wt)
}
}
miss_rate_binary <- function(data, event_level) {
col <- event_col(data, event_level)
col2 <- setdiff(colnames(data), col)
tp <- data[col, col]
fn <- data[col2, col]
fn / (fn + tp)
}
miss_rate_multiclass <- function(data, estimator) {
# We need tp and fn for all classes individually
# we can get this by taking advantage of the fact
# that tp + fn = colSums(data)
tp <- diag(data)
tpfn <- colSums(data)
fn <- tpfn - tp
# If using a micro estimator, we sum the individual
# pieces before performing the miss rate calculation
if(estimator == "micro") {
tp <- sum(tp)
fn <- sum(fn)
}
# return the vector
tp / (tp + fn)
}For the macro case, this separation of weighting from the core implementation might seem strange, but there is good reason for it. Some metrics are combinations of other metrics, and it is nice to be able to reuse code when calculating more complex metrics. For example, f_meas() is a combination of recall() and precision(). When calculating a macro averaged f_meas(), the weighting must be applied 1 time, at the very end of the calculation. recall_multiclass() and precision_multiclass() are defined similarly to how miss_rate_multiclass() is defined and returns the unweighted vector of calculations. This means we can directly use this in f_meas(), and then weight everything once at the end of that calculation.
Let’s try it out now:
# two class
miss_rate_vec(two_class_example$truth, two_class_example$predicted)
#> [1] 0.120155
# multiclass
miss_rate_vec(fold1$obs, fold1$pred)
#> [1] 0.5483506Luckily, the data frame implementation is as simple as the numeric case, we just need to add an extra estimator argument and pass that through. We’ll also use new_class_metric() to formalize miss_rate() as a class metric.
miss_rate <- function(data, ...) {
UseMethod("miss_rate")
}
miss_rate <- new_class_metric(miss_rate, direction = "minimize")
miss_rate.data.frame <- function(data,
truth,
estimate,
estimator = NULL,
na_rm = TRUE,
event_level = "first",
...) {
metric_summarizer(
metric_nm = "miss_rate",
metric_fn = miss_rate_vec,
data = data,
truth = !! enquo(truth),
estimate = !! enquo(estimate),
estimator = estimator,
na_rm = na_rm,
event_level = event_level,
...
)
}# Macro weighted automatically selected
fold1 %>%
miss_rate(obs, pred)
#> # A tibble: 1 × 3
#> .metric .estimator .estimate
#> <chr> <chr> <dbl>
#> 1 miss_rate macro 0.548
# Switch to micro
fold1 %>%
miss_rate(obs, pred, estimator = "micro")
#> # A tibble: 1 × 3
#> .metric .estimator .estimate
#> <chr> <chr> <dbl>
#> 1 miss_rate micro 0.726
# Macro weighted by resample
hpc_cv %>%
group_by(Resample) %>%
miss_rate(obs, pred, estimator = "macro_weighted")
#> # A tibble: 10 × 4
#> Resample .metric .estimator .estimate
#> <chr> <chr> <chr> <dbl>
#> 1 Fold01 miss_rate macro_weighted 0.726
#> 2 Fold02 miss_rate macro_weighted 0.712
#> 3 Fold03 miss_rate macro_weighted 0.758
#> 4 Fold04 miss_rate macro_weighted 0.712
#> 5 Fold05 miss_rate macro_weighted 0.712
#> 6 Fold06 miss_rate macro_weighted 0.697
#> 7 Fold07 miss_rate macro_weighted 0.675
#> 8 Fold08 miss_rate macro_weighted 0.721
#> 9 Fold09 miss_rate macro_weighted 0.673
#> 10 Fold10 miss_rate macro_weighted 0.699
# Error handling
miss_rate(hpc_cv, obs, VF)
#> Error: Problem with `summarise()` column `.estimate`.
#> ℹ `.estimate = metric_fn(truth = obs, estimate = VF, na_rm = na_rm, event_level = "first")`.
#> x `estimate` should be a factor but a numeric was supplied.metric_set()metric_set() validates that all metric functions are of the same metric type by checking the class of the function. If any metrics are not of the right class, metric_set() fails. By using new_numeric_metric() and new_class_metric() in the above custom metrics, they work out of the box without any additional adjustments.
numeric_mets <- metric_set(mse, rmse)
numeric_mets(solubility_test, solubility, prediction)
#> # A tibble: 2 × 3
#> .metric .estimator .estimate
#> <chr> <chr> <dbl>
#> 1 mse standard 0.521
#> 2 rmse standard 0.722