---
title: "Predicted values"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Predicted values}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
warning = FALSE,
message = FALSE
)
```
This vignette demonstrates the versatility and utility of the `predict.modeler()`
function when applied to a fitted model. This function is designed to handle
models of class `modeler` and provides several prediction types, outlined as follows:
- **"point"**: Computes the value of the fitted function \(\hat{f}(x)\) for a
given vector of \(x\) values.
- **"auc"**: Calculates the area under the fitted curve (AUC) over a specified
interval by approximating the integral using the trapezoidal rule.
- **"fd"**: Provides the first derivative \(\hat{f}'(x)\) for a given vector of
\(x\) values using numerical approximation.
- **"sd"**: Computes the second derivative \(\hat{f}''(x)\) for a given vector
of \(x\) values using numerical approximation.
- **"formula"**: Evaluates a user-defined function of the model parameters,
returning both the predicted value and its standard error.
Each type of prediction includes corresponding standard errors, which are
calculated using the delta method.
```{r setup}
library(flexFitR)
library(dplyr)
library(kableExtra)
library(ggpubr)
library(purrr)
data(dt_potato)
head(dt_potato) |> kable()
```
## 0. Model fitting
To illustrate the functionality of `predict()`, we use a potato dataset to fit
logistic models of the form:
$$f(t) = \frac{L}{1 + e^{-k(t - t_0)}}$$
```{r}
fun_logistic <- function(t, L, k, t0) L / (1 + exp(-k * (t - t0)))
```
For simplicity, we’ll focus on just two plots from the dataset
(plot 40 and plot 166) out of the total 196 plots available. After fitting the
model, we’ll take a closer look at the parameter estimates, visualize the fitted
curves, and start making predictions.
```{r}
plots <- c(40, 166)
```
```{r}
mod_1 <- dt_potato |>
modeler(
x = DAP,
y = Canopy,
grp = Plot,
fn = "fun_logistic",
parameters = c(L = 100, k = 4, t0 = 40),
subset = plots
)
```
```{r}
print(mod_1)
```
```{r, fig.width= 8, fig.height=4, fig.alt="plot fit"}
plot(mod_1, id = plots)
```
## 1. Point prediction
To make point predictions, we use the `predict()` function and specify the \(x\)
value(s) for which we want to compute \(\hat{f}(x)\). By default, the prediction
type is set to `"point"`, so it is unnecessary to explicitly include
`type = "point"`.
```{r, fig.alt="plot fit 2", fig.width= 8}
points <- predict(mod_1, x = 55, type = "point", se_interval = "confidence")
points |> kable()
```
A great way to visualize this is by plotting the fitted curve and overlaying the
predicted points.
```{r, fig.alt="plot fit 2", fig.width= 8}
mod_1 |>
plot(id = plots, type = 3) +
color_palette(palette = "jco") +
geom_point(data = points, aes(x = x_new, y = predicted.value), shape = 8)
```
You’ll also notice that predictions come with standard errors,
which can be adjusted using the `se_interval` argument to choose between
`"confidence"` or `"prediction"` intervals, depending on the type of intervals you
want to generate (sometimes referred to as narrow vs. wide intervals).
```{r}
points <- predict(mod_1, x = 55, type = "point", se_interval = "prediction")
points |> kable()
```
## 2. Integral of the function (area under the curve)
The area under the fitted curve is another common calculation, especially when
trying to summarize the overall behavior of a function over a specific range. To
compute the AUC, set `type = "auc"` and provide the interval of interest in the
`x` argument. You can also specify the number of subintervals for the trapezoidal
rule approximation using `n_points` (e.g., `n_points = 500` provides a
high-resolution approximation here).
$$ \text{Area} = \int_{0}^{T} \frac{L}{1 + e^{-k(t - t_0)}} \, dt $$
```{r}
predict(mod_1, x = c(0, 108), type = "auc", n_points = 500) |> kable()
```
## 3. Function of the parameters
In many cases, interest lies not in the parameters themselves but in functions
of these parameters. By using the `formula` argument, we can compute
user-defined functions of the estimated parameters along with their standard
errors. No additional arguments are required for this functionality.
```{r}
predict(mod_1, formula = ~ k / L * 100) |> kable()
```
```{r}
predict(mod_1, formula = ~ (k * L) / 4) |> kable()
```
## 4. Derivatives
For those interested in the derivatives of the fitted function,
`predict.modeler()` provides tools to compute both the first (\(f'(x)\)) and
second order (\(f''(x)\)) derivatives at specified points or over intervals.
While derivatives for logistic functions are straightforward to compute
analytically, this is not true for many other functions. To address this,
`predict()` employs a numerical approximation using the "Richardson" method.
For the logistic function, the first derivative has the following form:
$$ f'(t) = \frac{k L e^{-k(t - t_0)}}{\left(1 + e^{-k(t - t_0)}\right)^2} $$
And the second derivative the following:
$$f''(t) = \frac{k^2 L e^{-k(t - t_0)} \left(1 - e^{-k(t - t_0)}\right)}{\left(1 + e^{-k(t - t_0)}\right)^3}$$
Here the first derivative tells us the growth rate, while the second derivative
reveals how the growth rate is accelerating or decelerating.
### 4.1. First derivative
To compute the first derivative, set `type = "fd"` in the `predict()` function
and provide points or intervals in the `x` argument.
In case we just want to visualize the first derivative we can use the `plot()`
function.
```{r, fig.width= 8, fig.height=4, fig.alt="plot 1 deriv"}
plot(mod_1, id = plots, type = 5, color = "blue", add_ci = FALSE)
```
The \(x\)-coordinate where the maximum occurs can be found
programmatically, and the corresponding value of \(\hat{f}(x)\) can be
computed using point predictions as follows:
```{r}
interval <- seq(0, 100, by = 0.1)
points_fd <- mod_1 |>
predict(x = interval, type = "fd") |>
group_by(uid) |>
summarise(
max_fd = max(predicted.value),
argmax_fd = x_new[which.max(predicted.value)]
)
points_fd |> kable()
```
```{r, fig.alt="plot deriv" , fig.width= 8}
mod_1 |>
plot(id = plots, type = 3) +
color_palette(palette = "jco") +
geom_vline(data = points_fd, aes(xintercept = argmax_fd), linetype = 2) +
geom_label(data = points_fd, aes(x = argmax_fd, y = 0, label = argmax_fd)) +
facet_wrap(~uid) +
theme(legend.position = "none")
```
```{r}
points_fd$y_hat <- sapply(
X = plots,
FUN = \(i) {
mod_1 |>
predict(x = points_fd[points_fd$uid == i, "argmax_fd"], id = i) |>
pull(predicted.value)
}
)
points_fd |> kable()
```
```{r, fig.alt="plot points" , fig.width= 8}
mod_1 |>
plot(id = plots, type = 3) +
color_palette(palette = "jco") +
geom_point(data = points_fd, aes(x = argmax_fd, y = y_hat), shape = 8)
```
### 4.2. Second derivative
Similarly, the second derivative can be calculated by setting `type = "sd"`.
This derivative shows how the growth rate itself is changing, helping to determine
when growth starts to slow down or speed up.
```{r, fig.width= 8, fig.height=4, fig.alt="plot 2 deriv"}
plot(mod_1, id = plots, type = 6, color = "blue", add_ci = FALSE)
```
We can also identify where the second derivative reaches its maximum and minimum
values, and plot these changes for a deeper understanding of the growth dynamics.
```{r}
points_sd <- mod_1 |>
predict(x = interval, type = "sd") |>
group_by(uid) |>
summarise(
max_sd = max(predicted.value),
argmax_sd = x_new[which.max(predicted.value)],
min_sd = min(predicted.value),
argmin_sd = x_new[which.min(predicted.value)]
)
points_sd |> kable()
```
```{r, fig.alt="plot deriv 2" , fig.width= 8}
mod_1 |>
plot(id = plots, type = 3) +
color_palette(palette = "jco") +
geom_vline(data = points_sd, aes(xintercept = argmax_sd), linetype = 2) +
geom_vline(data = points_sd, aes(xintercept = argmin_sd), linetype = 2) +
facet_wrap(~uid) +
theme(legend.position = "none")
```
## 5. Conclusions
The `predict.modeler()` function, as part of the modeling toolkit, offers a
range of useful predictions that can be tailored to various needs—whether it's
making point estimates, exploring the area under a curve, or analyzing derivatives.
While the examples presented here showcase the flexibility and power of the
function, they are just the beginning. Every dataset and research question
brings its own unique challenges, and we hope this vignette demonstrates how
`predict.modeler()` can help address those.