maximize_gam_metric {cutpointr}  R Documentation 
Optimize a metric function in binary classification after smoothing via generalized additive models
Description
Given a function for computing a metric in metric_func
, these functions
smooth the function of metric value per cutpoint using generalized additive
models (as implemented in mgcv), then
maximize or minimize the metric by selecting an optimal cutpoint. For further details
on the GAM smoothing see ?mgcv::gam
.
The metric
function should accept the following inputs:

tp
: vector of number of true positives 
fp
: vector of number of false positives 
tn
: vector of number of true negatives 
fn
: vector of number of false negatives
Usage
maximize_gam_metric(
data,
x,
class,
metric_func = youden,
pos_class = NULL,
neg_class = NULL,
direction,
formula = m ~ s(x.sorted),
optimizer = c("outer", "newton"),
tol_metric,
use_midpoints,
...
)
minimize_gam_metric(
data,
x,
class,
metric_func = youden,
pos_class = NULL,
neg_class = NULL,
direction,
formula = m ~ s(x.sorted),
optimizer = c("outer", "newton"),
tol_metric,
use_midpoints,
...
)
Arguments
data 
A data frame or tibble in which the columns that are given in x and class can be found. 
x 
(character) The variable name to be used for classification, e.g. predictions or test values. 
class 
(character) The variable name indicating class membership. 
metric_func 
(function) A function that computes a metric to be maximized. See description. 
pos_class 
The value of class that indicates the positive class. 
neg_class 
The value of class that indicates the negative class. 
direction 
(character) Use ">=" or "<=" to select whether an x value >= or <= the cutoff predicts the positive class. 
formula 
A GAM formula. See 
optimizer 
An array specifying the numerical optimization method to
use to optimize the smoothing parameter estimation criterion (given by method).
See 
tol_metric 
All cutpoints will be returned that lead to a metric value in the interval [m_max  tol_metric, m_max + tol_metric] where m_max is the maximum achievable metric value. This can be used to return multiple decent cutpoints and to avoid floatingpoint problems. 
use_midpoints 
(logical) If TRUE (default FALSE) the returned optimal cutpoint will be the mean of the optimal cutpoint and the next highest observation (for direction = ">") or the next lowest observation (for direction = "<") which avoids biasing the optimal cutpoint. 
... 
Further arguments that will be passed to metric_func or the GAM smoother. 
Details
The above inputs are arrived at by using all unique values in x
, Inf, and
Inf as possible cutpoints for classifying the variable in class.
Value
A tibble with the columns optimal_cutpoint
, the corresponding metric
value and roc_curve
, a nested tibble that includes all possible cutoffs
and the corresponding numbers of true and false positives / negatives and
all corresponding metric values.
See Also
Other method functions:
maximize_boot_metric()
,
maximize_loess_metric()
,
maximize_metric()
,
maximize_spline_metric()
,
oc_manual()
,
oc_mean()
,
oc_median()
,
oc_youden_kernel()
,
oc_youden_normal()
Examples
oc < cutpointr(suicide, dsi, suicide, gender, method = maximize_gam_metric,
metric = accuracy)
plot_metric(oc)
oc < cutpointr(suicide, dsi, suicide, gender, method = minimize_gam_metric,
metric = abs_d_sens_spec)
plot_metric(oc)