All the templates are written in RMarkdown according to the template
structure section of the RMarkdown book. In the sitrep package, that contains
these templates, the teplates all live in
inst/rmarkdown/<NAME>/skeleton/skeleton.Rmd. This is what the current template
structure looks like:
inst
└── rmarkdown
└── templates
├── ajs_outbreak
│ ├── skeleton
│ │ └── skeleton.Rmd
│ └── template.yaml
├── cholera_outbreak
│ ├── skeleton
│ │ └── skeleton.Rmd
│ └── template.yaml
├── measles_outbreak
│ ├── skeleton
│ │ └── skeleton.Rmd
│ └── template.yaml
├── meningitis_outbreak
│ ├── skeleton
│ │ └── skeleton.Rmd
│ └── template.yaml
├── mortality
│ ├── skeleton
│ │ └── skeleton.Rmd
│ └── template.yaml
├── nutrition
│ ├── skeleton
│ │ └── skeleton.Rmd
│ └── template.yaml
└── vaccination
├── skeleton
│ └── skeleton.Rmd
└── template.yaml
All templates start with a minimal yaml header and have the following main sections:
---
title: "AJS outbreak report"
output:
word_document:
keep_md: true
---
# Data Import
```{r import_data}
# If you have standard DHIS2 data, then follow these instructions...
dat <- rio::import("mydata.xlsx", sheet = 1)
```
# Data Cleaning
# Descriptive analysis
The first two sections will be heavily commented to instruct the user on how to set up their data. The idea is that the pain of setting up the data analysis is front-loaded when the field epi is starting their analysis, and automated after that.
This setup will create a word document report, keeping both the word and markdown version. The markdown version is kept so that the figures from the template are exported to PNG format instead of simply embedded in the document.
If you use RStudio, you can use
usethis::create_from_github('R4EPI/sitrep', fork = TRUE) to create a fork of
the project to your account and clone it to your computer. After that, create a
new branch using RStudio, make your changes, push it to your account and then
create a pull request.