memory.core/Figure9.Rmd at main · dd-harp/memory.core · GitHub

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---
title: "Figure 9"
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
---

***

[Home](Memory.html) |
[Fig 3](Figure3.html) |
[Fig 4](Figure4.html) |
[Fig 5](Figure5.html) |
[Fig 6](Figure6.html) |
[Fig 7](Figure7.html) |
[Fig 8](Figure8.html) |
[Fig 10](Figure10.html)

***
# {.tabset}

## $\odot$

![Figure 9a](Figure9a.png)

![Figure 9b](Figure9b.png)

## Setup

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

```{r}
clrs8d = viridis(8)
```

## Fig 9a

```{r}

Figure9a = function(xl=0, xh=13){

  xl = 0
  xh = 13
  meshX=seq(xl,xh,by=0.1)

  DD <- d_detect(meshX, bvm=13, pars=par_nb(s=6))
  CB <- t(sapply(meshX, d_nz_counts_log_binned, bins=c(1:5, 13), pars=par_nb(s=6)))

  plot(meshX, CB[,1], type = "n", xlab =expression(log[10](B)), ylab = "Proportion", ylim = c(0,1), col = "white", xlim = c(xl, xh), xaxt = "n")

  cbi = 1-DD
  polygon(c(xl, meshX,13), 1-c(0, cbi,0), col = clrs8d[8], border=clrs8d[8])

  cb0 = cbi
  cbi = CB[,1]
  polygon(c(meshX, rev(meshX)), 1-c(cbi, rev(cb0)), col = clrs8d[7], border=clrs8d[7])

  for(i in 2:6){
    cb0 = cbi
    cbi = rowSums(CB[,1:i])
    polygon(c(meshX, rev(meshX)), 1-c(cbi, rev(cb0)), col = clrs8d[8-i], border=clrs8d[8-i])
  }

  #cbi = 1-DD
  #polygon(c(xl, meshX), 1-c(0, cbi), col = "red", border=clrs8d[8])

  ssrt=62
  ccx=1.2
  text(4.5, 0.8, "Parasites not Detected", cex=ccx)

  text(7.3, .25, expression(1-10), col = "white", cex=ccx, srt = ssrt)
  text(8.4, .25, expression(10-10^2), col = "white", cex=ccx, srt = ssrt)
  text(9.4, .25, expression(10^2-10^3), col = "white", cex=ccx, srt = ssrt)
  text(10.4, 0.25, expression(10^3-10^4), col = "white", cex=ccx, srt = ssrt)
  text(11.4, .25, expression(10^4-10^5), col = "white", cex=ccx, srt = ssrt)
  text(12.1, 0.2, expression(10^5-infinity), col = "white", cex=ccx, srt=ssrt)
  axis(1, 1:12, 1:12)
  mtext("a) Probability of Detection", 3, 1, at=1)
}
Figure9a()
```
```{r}
png("Figure9a.png", height= 360, width = 720)
Figure9a()
invisible(dev.off(dev.cur()))
```

## Figure 9b

```{r}
Figure9b = function(){
  pp = par_nb(s=7)
  b2c = d_nz_counts_log_binned(1, bins = c(1:5, 13), pars=pp)
  b2d = 1-d_detect(1,pars=pp)
  b2cl = c(b2d, b2c*(1-b2d))
  plot(3-0.05+c(-3:3)/10, b2cl, type = "h", lwd=5, col = rev(clrs8d)[-2], xlim = c(2.5,11.5), xaxt = "n", xlab = expression(log[10](B)), ylab="Proportion")
  for(i in c(4:11)){
    b2c = d_nz_counts_log_binned(i,bins = c(1:5, 13), pars=pp)
    b2d = 1-d_detect(i,pars=pp)
    b2cl = c(b2d, b2c*(1-b2d))
    lines(i -0.05 + c(-3:3)/10, b2cl, type = "h", lwd=5, col = rev(clrs8d)[-2])
    axis(1, 3:11, 3:11)
  }
  mtext("b) Parasite Counts", 3, 1, at=2.9)
}
Figure9b()
```

```{r}
png("Figure9b.png", height= 360, width = 720)
Figure9b()
invisible(dev.off(dev.cur()))
```

## Remake


To remake Figure 9, first run this purl script to make `Figure9.R`

```{r, purl=F, eval=F}
purl("Figure9.Rmd", "Figure9.R")
```

then source `Figure9.R`

```{r, purl=F, eval=F}
source("Figure9.R")
```