plot_SummaryReport.Rmd

---
title: "plot_SummaryReport"
author: "Anne Stahlfeld"
date: "5/18/2023"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(data.table)
```

```{r}
root <- "/projects/b1139/FE-2023-examples/experiments/aew2948/simulation_outputs"
subfolder <- "week2_outputs"
filename <- "PfPR_ClinicalIncidence_monthly.csv"
df <- fread(paste(root,subfolder,filename,sep='/'))
colnames(df) <- make.names(colnames(df))
lineT = c("dotted","solid","dashed")

df %>%
  group_by(agebin,month,Year) %>%
  summarise_all(mean) %>%
  relocate(month, Year, agebin) %>%
  pivot_longer(-c(month,Year, agebin), names_to = "variable", values_to = "value") %>%
  ggplot(aes(x=month,y=value)) +
  facet_wrap(~variable, scales="free_y", ncol=2) +
  geom_path(aes(color=variable, linetype=as.factor(agebin))) +
  scale_linetype_manual(name="Agebin", values = lineT) +
  ylab("") + xlab("Month") +
  theme_minimal(base_size=14) +
  guides(color="none")

ggsave('SummaryReport_sample_plots.png',path = paste(root,subfolder,sep='/'), height = 10)
ggsave('SummaryReport_sample_plots.pdf',path = paste(root,subfolder,sep='/'), height = 10)

```