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 MSF analyses - they have been setup to be as generic as possible for use by the general applied epidemiology community.

Detailed information about the project and the templates can be found at
A reference website for the functions in {sitrep} can be found at

{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


The {sitrep} package, is currently stored in a GitHub repository. Therefore, the procedure to install these packages have one extra step required.

To install sitrep from GitHub you must first install the remotes package.

# install.packages("remotes")

If you are getting errors, check the frequently asked questions.

Available templates

Sitrep has four outbreak templates and four 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

Example of how to open and save the cholera template

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

output_dir <- file.path(tempdir(), "sitrep_example")

# view the available templates, categorized by type
available_sitrep_templates(categorise = TRUE)
#> $outbreak
#> [1] "ajs_outbreak"        "cholera_outbreak"    "measles_outbreak"   
#> [4] "meningitis_outbreak"
#> $survey
#> [1] "mortality"         "nutrition"         "vaccination_long" 
#> [4] "vaccination_short"

# generate the measles outbreak template in the output directory
check_sitrep_templates("measles_outbreak", path = output_dir)
#> [1] "C:\\Users\\alexf\\AppData\\Local\\Temp\\Rtmpcv1H8d/sitrep_example"

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

Please note that the ‘sitrep’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.