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working.Rmd
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---
title: "Tracking a deadly infectious disease: the case of canine rabies on Pemba Island"
author: "Malavika Rajeev"
date: "5/26/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(here) # wrap all paths in here() so that file paths stay relative to project root
library(rchie) # requires system dependency V8!
library(visNetwork)
library(networkD3)
library(treerabid)
library(readr)
# set up our google doc copy
library(googledrive)
library(googlesheets4)
googlesheets4::gs4_deauth() # for knitting without having to reauthorize (otherwise will hang!)
gdata <- from_aml(as_id("1NZQ27a-3-CEMkO6rpZfNhO_tvEVSbZWTOah-nsq-mTs"))
# pemba data
pemba_dt <- read_csv(here("src/assets/data/rabies_cases_anonymized.csv"))
```
`r gdata$rabies_primer$lede`
`r gdata$rabies_primer$pepvax`
<iframe width="100%" height="300" src="//jsfiddle.net/LaurieLBaker/dq38pbm6/20/embedded/" allowfullscreen="allowfullscreen" allowpaymentrequest frameborder="0"></iframe>
[photos of pep vax or pep vax poster]
`r gdata$rabies_primer$dogvax`
[photos of dog vax | map of countries that have elim/close to elim/endemic]
`r gdata$rabies_primer$elimination`
[links to zeroby30 etc.]
`r gdata$pemba$lede`
[map of Pemba]
`r gdata$pemba$story`
`r gdata$pemba$background`
`r gdata$pemba$tracing_lede`
`r gdata$tracing_case_rabid$step1`
[follow Kennedy's travel path]
`r gdata$tracing_case_rabid$step2`
[zoom in to location of a clinic]
`r gdata$tracing_case_rabid$step3`
[zoom in to Selem & show the four dogs Killa, Polisi, Hatari, Simba]
`r gdata$tracing_case_rabid$transitionCT`
[show the network of transmission with four dogs]
`r gdata$tracing_case_rabid$step4`
[add in the human exposures]
`r gdata$tracing_case_rabid$normal`
[link to how to avoid animal bites]
`r gdata$tracing_case_rabid$sample`
[video with gore warning]
`r gdata$tracing_case_rabid$sequence`
[add in visualisation of sequences alongside tree]
`r gdata$tracing_segway`
[circle pack showing all cases traced, probable rabies cases, confirmed, and sequenced,
& also link each circle to stories here]