Report Templates and Helper Functions for Applied Epidemiology

A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including 'epitabulate' (for epidemiological tables), 'epidict' (for data dictionaries), 'epikit' (for epidemiological utilities), and 'apyramid' (for age-sex pyramids). Simply load 'sitrep' to access all functions from the ecosystem.

Sitrep

The goal of {sitrep} is provide report templates for common epidemiological surveys and outbreak reports. The package further contains helper function that standardize certain analyses.

While templates are primarily for Medecins Sans Frontieres analyses - they have been setup to be as generic as possible for use by the general applied epidemiology community.

Detailed information about the project, the templates and functions in {sitrep} can be found at https://r4epi.github.io/sitrep/.

{sitrep} includes a number of other R packages which facilitate specific analysis:
{epitabulate}: Tables for epidemiological analysis
{epidict}: Epidemiology data dictionaries and random data generators
{epikit}: Miscellaneous helper tools for epidemiologists
{apyramid}: Age pyramid construction and plotting

Installation

You can install {sitrep} from CRAN:

install.packages("sitrep")

# install.packages("remotes")
remotes::install_github("R4EPI/sitrep") 

## Available templates

Sitrep has outbreak templates and survey templates available. These templates 
will generate the following:

1. A word document with the situation report
2. A plain text markdown document (for conversion to other formats such as HTML or PDF)
3. A directory with all of the figures produced

You can access the list of templates in *R Studio* by clicking (see example below): 
file > New file > R Markdown... > From Template

You can generate an example template by using the `check_sitrep_templates()`
function:


``` r
library("sitrep")
output_dir <- file.path(tempdir(), "sitrep_example")
dir.create(output_dir)

# view the available templates, categorized by type
available_sitrep_templates(categorise = TRUE)
#> $outbreak
#>  [1] "ajs_intersectional_outbreak"        "ajs_outbreak"                      
#>  [3] "ajs_outbreak_recode"                "cholera_intersectional_outbreak"   
#>  [5] "cholera_outbreak"                   "cholera_outbreak_recode"           
#>  [7] "diphtheria_intersectional_outbreak" "intersectional_outbreak_recode"    
#>  [9] "measles_intersectional_outbreak"    "measles_outbreak"                  
#> [11] "measles_outbreak_recode"            "meningitis_intersectional_outbreak"
#> [13] "meningitis_outbreak"                "meningitis_outbreak_recode"        
#> 
#> $survey
#> [1] "ebs"                      "mortality"               
#> [3] "mortality_recode"         "nutrition"               
#> [5] "nutrition_recode"         "vaccination_long"        
#> [7] "vaccination_long_recode"  "vaccination_short"       
#> [9] "vaccination_short_recode"

# generate the measles outbreak template in the output directory
check_sitrep_templates("measles_outbreak", path = output_dir)
#> [1] "C:\\Users\\spina\\AppData\\Local\\Temp\\RtmpMfBkNj/sitrep_example"

# view the contents
list.files(output_dir, recursive = TRUE)
#> [1] "measles_outbreak.Rmd"