Report Templates and Helper Functions for Applied Epidemiology.

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"