figS1_mosquito_overview.Rmd

---
title: "Mosquito overview"
author: "Zena Lapp"
date: "2023-10-29"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
library(tidyverse)
library(ggpubr)
library(lubridate)

# set plotting theme
theme_set(theme_bw() + 
            theme(text = element_text(size = 15),
                  strip.background = element_rect(fill = 'white', color = 'white')))

f_anoph <- read_csv('analysis/clean_data/data/female_anopheles.csv') |> 
  mutate(species = paste0('*', species, '*'),
         species = gsub('SS', 's.s.', species))
```
## Summaries

```{r}
nrow(f_anoph)
f_anoph |> group_by(species) |> tally() |> 
  ungroup() |> 
  filter(species != '*Undetermined*') |> 
  mutate(tot = sum(n),
         prop = n/tot)
f_anoph |> group_by(reared) |> tally() |> ungroup() |> mutate(prop = n/sum(n))
f_anoph |> 
  group_by(year(collection_date), month(collection_date)) |> 
  tally() |> 
  mutate(high_trans_2021 = `year(collection_date)` == 2021 & `month(collection_date)` %in% 3:8) |> 
  group_by(high_trans_2021) |> 
  summarize(n = sum(n)) |> 
  ungroup() |> 
  mutate(tot = sum(n),
         prop = n/tot)
```

## Plots

```{r, fig.width = 6.5, fig.height = 3.5}
(moz_overview <- ggarrange(f_anoph |> 
  mutate(species = factor(ifelse(species %in% c('*An. gambiae s.s.*', '*An. funestus*'), species, 'Other')),
         species = factor(species, levels = rev(levels(species))),
         reared = ifelse(reared == 'yes', 'Reared', 'Immediately processed')) |> 
  ggplot(aes(x = collection_date, fill = species)) +
  facet_grid(reared~., scales = 'free', space = 'free') +
  geom_histogram(binwidth = 14) +
  scale_fill_grey(start = 0.8, end = 0.2) +
  scale_x_date(date_breaks = "6 months", date_labels =  "%b %Y") +
  labs(x = 'Collection date', y = 'Number of female<br>*Anopheles* collected', fill = 'Species') +
  theme(legend.text = element_markdown(),
        axis.title.y = element_markdown()),

f_anoph |> 
  mutate(species = factor(ifelse(species %in% c('*An. gambiae s.s.*', '*An. funestus*'), species, 'Other')),
         species = factor(species, levels = rev(levels(species))),
         reared = ifelse(reared == 'yes', 'Reared', 'Immediately processed')) |> 
  ggplot(aes(x = village, fill = species)) +
  geom_bar() +
  scale_fill_grey(start = 0.8, end = 0.2) +
  labs(x = 'Village', y = 'Number of female<br>*Anopheles* collected', fill = 'Species') +
  theme(legend.text = element_markdown(),
        axis.title.y = element_markdown()), 
common.legend = TRUE, labels = 'AUTO'))

ggsave(plot = moz_overview, filename = 'analysis/manuscript_figures/figures/mosquito_overview.png',
       width = 6.5, height = 3.5) 
```