---
title: "Ecotypes"
author: "Joe Thorley and Ayla Pearson"
date: "`r Sys.Date()`"
bibliography: bibliography.bib
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Ecotypes}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

## Ecotypes

In the `ypr` package a population is considered to be group of interbreeding fish that are indistinguishable to anglers. 
Ecotypes are groups of individuals with a population that have different life-history strategies.
Consequently, ecotypes must share key fishery (`pi`, `Llo`, `Lup`, `Nc`, `rho`, `Hm` and `q`) and stock recruitment (`BH`, `RK`, `tR` and `Rmax`) parameters.y 
To use a yield-per-recruit approach it is also necessary to assume that the relative proportion of recruits (`RPR`) adopting each life-history strategy is independent of the size and composition of the parental stock.

## Two Ecotypes

Consider a population with a smaller ecotype and a second larger ecotype that delays maturation in order to achieve sufficient size to switch to piscivory which allows it to grow much larger.

```{r}
library(ypr)
library(ggplot2) # for plotting

ecotypes <- ypr_ecotypes(
  Linf2 = 200,
  L2 = c(100, 50),
  Ls = c(50, 75), 
  pi = 0.05,
  names = c("small", "large"),
  RPR = c(0.8, 0.2))

ypr_plot_schedule(ecotypes) + scale_color_manual(values = c("black", "blue"))
ypr_plot_schedule(ecotypes, x = "Age", y  = "Spawning") + scale_color_manual(values = c("black", "blue"))
```

### Fish

```{r, fig.width=6, fig.height=4}
ypr_plot_fish(ecotypes, color = "white") + scale_fill_manual(values = c("black", "blue"))
ypr_plot_fish(ecotypes, x = "Length", y = "Caught", color = "white", binwidth = 15) + scale_fill_manual(values = c("black", "blue"))
```

### Stock-Recruitment

```{r, fig.width=6, fig.height=4}
ypr_plot_sr(ecotypes, biomass = TRUE)
ypr_tabulate_sr(ecotypes, biomass = TRUE)
```

### Yield

```{r, fig.width=6, fig.height=4}
ypr_tabulate_yield(ecotypes, biomass = TRUE)
ypr_plot_yield(ecotypes, biomass = TRUE)
```