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Sitrep

Lifecycle: maturing CRAN status Codecov test coverage R build status

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 https://r4epis.netlify.com.
A reference website for the 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

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")
remotes::install_github("r4epi/sitrep")

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:

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_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.