---
title: "Model visualization"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Model visualization}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

```{r setup, output=FALSE}
library(serosv)
```

## Visualize model

To visualize the model, user can simply use function `plot`

```{r}
hav <- hav_be_1993_1994
model <- fp_model(
  hav$age, hav$pos, hav$tot,
  p=c(1.5, 1.6), link="cloglog")
plot(model)
```

If implementation for confidence interval calculation is not yet available, `plot` function would simply visualize seroprevalence line

```{r, warning=FALSE}
rubella <- rubella_uk_1986_1987

farrington_md <- farrington_model(
   rubella$age, pos = rubella$pos, tot = rubella$tot,
   start=list(alpha=0.07,beta=0.1,gamma=0.03)
   )
plot(farrington_md)
```

## Customize the plot

Function `set_plot_style()` is provided to customize some attributes of the plot.

Current modifiable attributes include color, linetype for seroprevalence, foi and fill color for confidence interval

```{r}
a <- hav_bg_1964
pos <- a$pos
age <- a$age
tot <- a$tot
gf_model <- polynomial_model(age, pos = pos, tot = tot, type = "Griffith")

# customize plot
plot(gf_model) +
  set_plot_style(
    sero = "#3de071",
    foi = "#2f22e0",
    ci = "#aaf2b2",
    foi_line = "dotted", 
    sero_line = "dotdash"
  )
```