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.

Detailed information about the project and the templates can be found at https://r4epis.netlify.com. An online manual for the functions in {sitrep} can be found at https://r4epi.github.io/sitrep.

Installation

You can install the released version of sitrep from CRAN with:

And the development version from GitHub with:

Available templates

Sitrep has four outbreak templates and three 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 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"

# generate the measles outbreak template in the output directory
check_sitrep_templates("measles_outbreak", path = output_dir)
#> [1] "/tmp/RtmpkK0upp/sitrep_example"

# view the contents
list.files(output_dir, recursive = TRUE)
#>  [1] "measles_outbreak_files/figure-docx/age_pyramid-1.png"              
#>  [2] "measles_outbreak_files/figure-docx/bar_attack_rate_by_region-1.png"
#>  [3] "measles_outbreak_files/figure-docx/biweekly_epicurve-1.png"        
#>  [4] "measles_outbreak_files/figure-docx/choropleth_maps-1.png"          
#>  [5] "measles_outbreak_files/figure-docx/epicurve_ar_cfr-1.png"          
#>  [6] "measles_outbreak_files/figure-docx/epicurve-1.png"                 
#>  [7] "measles_outbreak_files/figure-docx/incidence_by_case_def-1.png"    
#>  [8] "measles_outbreak_files/figure-docx/incidence_by_gender-1.png"      
#>  [9] "measles_outbreak_files/figure-docx/incidence_by_sex_facility-1.png"
#> [10] "measles_outbreak_files/figure-docx/incidence_by_vax_status-1.png"  
#> [11] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-1.png"     
#> [12] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-10.png"    
#> [13] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-11.png"    
#> [14] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-12.png"    
#> [15] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-13.png"    
#> [16] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-14.png"    
#> [17] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-15.png"    
#> [18] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-16.png"    
#> [19] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-17.png"    
#> [20] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-18.png"    
#> [21] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-19.png"    
#> [22] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-2.png"     
#> [23] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-20.png"    
#> [24] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-3.png"     
#> [25] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-4.png"     
#> [26] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-5.png"     
#> [27] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-6.png"     
#> [28] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-7.png"     
#> [29] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-8.png"     
#> [30] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-9.png"     
#> [31] "measles_outbreak.md"                                               
#> [32] "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.