readme.Rmd

---
output: github_document
---

<!-- readme.md is generated from README.Rmd. Please edit that file -->

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(readr)
library(dplyr)
library(here)
case_dt <- read_csv(here("src/assets/data/rabies_cases_anonymized.csv"))
```

## Rabies data from Pemba

[rabies_cases_anonymized.csv](src/assets/data/rabes_cases_anonymized.csv) are `r nrow(case_dt)` suspected rabid animal cases on Pemba Island, Tanzania between `r min(case_dt$date_symptoms)` - `r max(case_dt$date_symptoms)`. The case-infector links have been reconstructed using methods described in 
[Hampson et al. 2009](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000053).

### Metadata for columns
```{r}
knitr::kable(
  data.frame(
    Column = names(case_dt), 
    Description = c("The unique id of the case.", 
                    "The unique id of the infector identified through a combination of contact tracing and transmission tree reconstruction.", 
                    "The unique id of the infector for a subset of animals for which contact tracing data is available.", 
                    "The phylogenetic lineage which the case belongs to identified through transmission tree reconstruction. All cases will have a non-zero value.", 
                    "The phylogenetic lineage assigned to a sampled case, if zero that means this case was unsampled.", 
                    "The x-coordinate location (in UTM coordinates) randomly jittered by 500 - 1000 meters to preserve anonymity.", 
                    "The y-coordinate location (in UTM coordinates) randomly jittered by 500 - 1000 meters to preserve anonymity.", 
                    "The species of animal.", 
                    "The date at which the animal began showing symptoms.")))
```

All case locations have been anonymized spatially. Please contact the Rabies Research team to request access to the non-anoymized coordinates.