---
title: "ECDF and Mahalanobis Distance for Theoretical Niche Modeling"
author: "Luíz Fernando Esser"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{ecdfniche}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 7,
fig.height = 4
)
```

## Introduction

This vignette shows how to use the **ECDFniche** package to reproduce the simulations from the original `ECDF_MahalDist.R` script, comparing Mahalanobis distance-based suitability transformations using the chi-squared distribution and the empirical cumulative distribution function (ECDF).

```{r}
library(ECDFniche)
```

## Core simulation: `ecdf_theoretical_niche()`

The function `ecdf_theoretical_niche()` simulates a multivariate normal "environmental space", computes Mahalanobis distances for a sample of points, and then maps those distances to suitability using:

- \(1 - F_{\chi^2}(D^2)\) (theoretical chi-squared transformation)
- \(1 - \text{ECDF}(D^2)\) (empirical transformation)

```{r}
set.seed(3)
res1 <- ecdf_theoretical_niche(n = 2)
res1$corplot
```

The returned list contains:

- `corplot`: correlation vs sample size between the “true” niche and both suitability transformations
- `sample_data`: matrix with the last sample of environmental predictors
- `sample_niche`, `chisq_suits`, `ecdf_suits`: suitability values
- `mahal_dists`: Mahalanobis distances for the last sample 

You can directly plot the correlation object:

```{r}
res1$corplot
```


## Reproducing the full analysis

The convenience function `run_ecdf_mahal_analysis()` wraps the original workflow: it runs `ecdf_theoretical_niche()` for several dimensions (by default 1 to 5) and produces three figures analogous to those in the script.

```{r}
set.seed(3)
full_res <- run_ecdf_mahal_analysis(dims = 1:5)
```


### Figure 1: Spatial visualization (2D)

Figure 1 shows the 2D environmental space (two predictor variables) with color representing different suitability definitions: the simulated "true" niche, the chi-squared-based suitability, and the ECDF-based suitability.

```{r}
full_res$figure1 |> plot()
```


### Figure 2: Correlation vs sample size

Figure 2 presents, for each dimensionality, how the correlation between the true niche and each distance-to-suitability transformation changes with sample size.

```{r}
full_res$figure2 |> plot()
```


### Figure 3: Distance–suitability relationships

Figure 3 plots Mahalanobis distance on the x-axis and suitability on the y-axis, showing how niche records, chi-squared suitability, and ECDF suitability relate across different numbers of predictor variables.

```{r}
full_res$figure3 |> plot()
```


## Customizing simulations

You can customize key aspects of the simulation by passing arguments to
`ecdf_theoretical_niche()`:

```{r}
res_custom <- ecdf_theoretical_niche(
n = 3,
n_population = 20000,
sample_sizes = seq(50, 1000, 50),
seed = 123
)

res_custom$corplot
```

These arguments control the dimensionality, the size of the
environmental "background", and the grid of sample sizes used to compute
correlations.

