---
title: "Robust cutpoint estimation"
author: "Christian Thiele"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Robust cutpoint estimation}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(fig.width = 6, fig.height = 5, fig.align = "center")
options(rmarkdown.html_vignette.check_title = FALSE)
load("vignettedata/vignettedata.Rdata")
```


# More robust cutpoint estimation methods

## Bootstrapped cutpoints

It has been shown that bagging can substantially improve performance of a wide range of types of models in regression as well as in classification tasks. This method is available for cutpoint estimation via the `maximize_boot_metric` and `minimize_boot_metric` functions. If one of these functions is used as `method`, `boot_cut` bootstrap samples are drawn, the cutpoint optimization is carried out in each one and a summary (e.g. the mean) of the resulting optimal cutpoints on the bootstrap samples is returned as the optimal cutpoint in `cutpointr`. Note that if bootstrap validation is run, i.e. if `boot_runs` is larger zero, an outer bootstrap will be executed. In the bootstrap validation routine `boot_runs` bootstrap samples are generated and each one is again bootstrapped `boot_cut` times. This may lead to long run times, so activating the built-in parallelization may be advisable. 

The advantages of bootstrapping the optimal cutpoint are that the procedure doesn't possess parameters that have to be tuned, unlike the LOESS smoothing, that it doesn't rely on assumptions, unlike the Normal method, and that it is applicable to any metric that can be used with `minimize_metric` or `maximize_metric`, unlike the Kernel method. Furthermore, like Random Forests cannot be overfit by increasing the number of trees, the bootstrapped cutpoints cannot be overfit by running an excessive amount of `boot_cut` repetitions. 

```{r, cache=TRUE}
library(cutpointr)
set.seed(100)
cutpointr(suicide, dsi, suicide, gender, 
          method = maximize_boot_metric,
          boot_cut = 200, summary_func = mean,
          metric = accuracy, silent = TRUE)
```


## LOESS smoothing for selecting a cutpoint

When using `maximize_metric` and `minimize_metric` the optimal cutpoint is 
selected by searching the maximum or minimum of the metric function. For 
example, we may want to minimize the misclassification cost. Since false 
negatives (a suicide attempt was not anticipated) can be regarded as much more 
severe than false positives we can set the cost of a false negative `cost_fn`
for example to ten times the cost of a false positive.

```{r}
opt_cut <- cutpointr(suicide, dsi, suicide, gender, method = minimize_metric,
                     metric = misclassification_cost, cost_fp = 1, cost_fn = 10)
```

```{r}
plot_metric(opt_cut)
```

As this "optimal" cutpoint may depend on minor differences between the 
possible cutoffs, smoothing of the function of metric values by
cutpoint value might be desirable, especially in small samples. The
`minimize_loess_metric` and `maximize_loess_metric` functions can be used
to smooth the function so that the optimal cutpoint is selected based on the
smoothed metric values. Options to modify the smoothing, which is implemented using
`loess.as` from the **fANCOVA** package, include:

- `criterion`: the criterion for automatic smoothing parameter selection: "aicc" denotes bias-corrected AIC criterion, "gcv" denotes generalized cross-validation.
- `degree`: the degree of the local polynomials to be used. It can be 0, 1 or 2.
- `family`: if "gaussian" fitting is by least-squares, and if "symmetric" a re-descending M estimator is used with Tukey's biweight function.
- `user.span`: the user-defined parameter which controls the degree of smoothing.

Using parameters for the LOESS smoothing of `criterion = "aicc"`, `degree = 2`, 
`family = "symmetric"`, and `user.span = 0.7` we get the following smoothed
versions of the above metrics:

```{r, message = FALSE}
opt_cut <- cutpointr(suicide, dsi, suicide, gender, 
                     method = minimize_loess_metric,
                     criterion = "aicc", family = "symmetric", 
                     degree = 2, user.span = 0.7,
                     metric = misclassification_cost, cost_fp = 1, cost_fn = 10)
```

```{r}
plot_metric(opt_cut)
```


The optimal cutpoint for the female subgroup changes to 3. Note, though, that there 
are no reliable rules for selecting the "best" smoothing parameters. Notably,
the LOESS smoothing is sensitive to the number of unique cutpoints. A large 
number of unique cutpoints generally leads to a more volatile curve of 
metric values by cutpoint value, even after smoothing. Thus, the curve
tends to be undersmoothed in that scenario. The unsmoothed metric
values are returned in `opt_cut$roc_curve` in the column
`m_unsmoothed`.


## Smoothing via Generalized Additive Models for selecting a cutpoint

In a similar fashion, the function of metric values per cutpoint can be smoothed 
using Generalized Additive Models with smooth terms. Internally, `mgcv::gam` 
carries out the smoothing which can be customized via the arguments
`formula` and `optimizer`, see `help("gam", package = "mgcv")`. Most importantly,
the GAM can be specified by altering the default formula, for example the 
smoothing function could be configured to apply cubic regression splines (`"cr"`)
as the smooth term. As the `suicide` data has only very few unique cutpoints,
it is not very suitable for showcasing the GAM smoothing, so we will use two 
classes of the `iris` data here. In this case, the purely empirical method and
the GAM smoothing lead to identical cutpoints, but in practice the GAM smoothing
tends to be more robust, especially with larger data. An attractive feature of
the GAM smoothing is that the default values tend to work quite well and
usually require no tuning, eliminating researcher degrees of freedom. 

```{r}
library(ggplot2)
exdat <- iris
exdat <- exdat[exdat$Species != "setosa", ]
opt_cut <- cutpointr(exdat, Petal.Length, Species,
                     method = minimize_gam_metric,
                     formula = m ~ s(x.sorted, bs = "cr"),
                     metric = abs_d_sens_spec)
plot_metric(opt_cut)
```


## Spline smoothing for selecting a cutpoint

Again in the same fashion the function of metric values per cutpoint can be smoothed 
using smoothing splines. By default, the number of knots is automatically 
chosen using the `cutpoint_knots` function. That function uses `stats::.nknots.smspl`,
which is the default in `stats::smooth.spline` to pick the number of knots. 

Alternatively, the number of knots
can be set manually and also the other smoothing parameters of `stats::smooth.spline`
can be set as desired. For details see `?maximize_spline_metric`. 

```{r}
opt_cut <- cutpointr(suicide, dsi, suicide, gender, 
                     method = minimize_spline_metric, spar = 0.4,
                     metric = misclassification_cost, cost_fp = 1, cost_fn = 10)
plot_metric(opt_cut)
```

### Parametric method assuming normality

The Normal method in `oc_youden_normal` is a parametric method for maximizing the Youden-Index or equivalently the sum of $Se$ and $Sp$. It relies on the assumption that the predictor for both the negative and positive observations is normally distributed. In that case it can be shown that

$$c^* = \frac{(\mu_P \sigma_N^2 - \mu_N \sigma_P^2) - \sigma_N \sigma_P \sqrt{(\mu_N - \mu_P)^2 + (\sigma_N^2 - \sigma_P^2) log(\sigma_N^2 / \sigma_P^2)}}{\sigma_N^2 - \sigma_P^2}$$

where the negative class is normally distributed with $\sim N(\mu_N, \sigma_N^2)$ and the positive class independently normally distributed with $\sim N(\mu_P, \sigma_P^2)$ provides the optimal cutpoint $c^*$ that maximizes the Youden-Index. If $\sigma_N$ and $\sigma_P$ are equal, the expression can be simplified to $c^* = \frac{\mu_N + \mu_P}{2}$. However, the `oc_youden_normal` method in cutpointr always assumes unequal standard deviations. Since this method does not select a cutpoint from the observed predictor values, it is questionable which values for $Se$ and $Sp$ should be reported. Here, the Youden-Index can be calculated as 

$$J = \Phi(\frac{c^* - \mu_N}{\sigma_N}) - \Phi(\frac{c^* - \mu_P}{\sigma_P})$$

if the assumption of normality holds. However, since there exist several methods that do not select cutpoints from the available observations and to unify the reporting of metrics for these methods, **cutpointr** reports all metrics, e.g. $Se$ and $Sp$, based on the empirical observations. 


```{r}
cutpointr(suicide, dsi, suicide, gender, method = oc_youden_normal)
```

### Nonparametric kernel method

A nonparametric alternative is the Kernel method [@fluss_estimation_2005]. Here, the empirical distribution functions are smoothed using the Gaussian kernel functions $\hat{F}_N(t) = \frac{1}{n} \sum^n_{i=1} \Phi(\frac{t - y_i}{h_y})$ and $\hat{G}_P(t) = \frac{1}{m} \sum^m_{i=1} \Phi(\frac{t - x_i}{h_x})$ for the negative and positive classes respectively. Following Silverman's plug-in "rule of thumb" the bandwidths are selected as $h_y = 0.9 * min\{s_y, iqr_y/1.34\} * n^{-0.2}$ and $h_x = 0.9 * min\{s_x, iqr_x/1.34\} * m^{-0.2}$ where $s$ is the sample standard deviation and $iqr$ is the inter quartile range. It has been demonstrated that AUC estimation is rather insensitive to the choice of the bandwidth procedure [@faraggi_estimation_2002] and thus the plug-in bandwidth estimator has also been recommended for cutpoint estimation. The `oc_youden_kernel` function in **cutpointr** uses a Gaussian kernel and the direct plug-in method for selecting the bandwidths. The kernel smoothing is done via the `bkde` function from the **KernSmooth** package [@wand_kernsmooth:_2013]. 

Again, there is a way to calculate the Youden-Index from the results of this method [@fluss_estimation_2005] which is

$$\hat{J} = max_c \{\hat{F}_N(c) - \hat{G}_N(c) \}$$

but as before we prefer to report all metrics based on applying the cutpoint that was estimated using the Kernel method to the empirical observations. 

```{r}
cutpointr(suicide, dsi, suicide, gender, method = oc_youden_kernel)
```