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
You can install {sitrep} from CRAN:
install.packages("sitrep")Click here for alternative installation options
You can also install the in-development version from GitHub using the {remotes} package (but there’s no guarantee that it will be stable):
# 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"