Figure3.Rmd

---
title: "Figure 3"
subtitle: "A Probabilistic Synthesis of Malaria Epidemiology: Exposure, Infection, Parasite Densities, and Detection"
date: "`r format(Sys.time(), '%B %d, %Y')`"
author: John M. Henry, Austin R. Carter, Sean L. Wu, and David L. Smith
output:
  html_document 
---

`Figure3.Rmd` 

***

[Home](Memory.html) | 
[Fig 4](Figure4.html) |
[Fig 5](Figure5.html) |
[Fig 6](Figure6.html) |
[Fig 7](Figure7.html) |
[Fig 8](Figure8.html) |
[Fig 9](Figure9.html) |
[Fig 10](Figure10.html) 

*** 

# {.tabset}

## $\odot$ 

![Figure3.png](Figure3.png)

## Setup

```{r}
library(ramp.falciparum)
library(viridisLite)
```

## Fig3a 

```{r}
clrs = plasma(8)


par_t2 = par_type2Age() 

a20yearsBy10days=seq(0, 7300, by=10)
wt1 = ageFoI(a20yearsBy10days, par_type2Age())
wt2 = ageFoI(a20yearsBy10days, par_flatAge())
```


```{r}
plot(a20yearsBy10days/365, wt1, type = "l", xlab = "Age in Years", ylab = expression(omega(a)), col = clrs[1])
lines(a20yearsBy10days/365, wt2, col = clrs[5])
```

## Fig3b 

```{r}
p1 = par_expSeason(phase=-90, pwr=3.5, lift=0) 
p2 = par_sinSeason(lift=-0.85, pwr=4, phase=0)
p3 = par_sinSeason(lift=0, pwr=4, phase=-90)
p4 = par_sinSeason(phase=-90)
p5 = par_flatSeason()
```


```{r}
oneYear = c(0:365)
plot(oneYear,  seasonalFoI(oneYear, p1), type = "l", ylab = expression(S(t) - paste("Seasonal Pattern")), xlab = "Day of Year", col = clrs[1]) 
lines(oneYear, seasonalFoI(oneYear, p2), col = clrs[3], lwd=1.5) 
lines(oneYear, seasonalFoI(oneYear, p3), col = clrs[5], lwd=1.5) 
lines(oneYear, seasonalFoI(oneYear, p4), col = clrs[6], lwd=2) 
lines(oneYear, seasonalFoI(oneYear, p5), col = grey(0.5), lwd=1.5)
```

## Remake 

```{r, purl=F, eval=FALSE} 
print("Making Figure 3")
purl("Figure3.Rmd", "Figure3.R")
png("Figure3.png", height= 320, width = 720)
par(mfrow = c(1,2))
source("Figure3.R")
invisible(dev.off(dev.cur()))
```