Type: Package
Title: Report Templates and Helper Functions for Applied Epidemiology
Version: 0.2.3
Description: A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including 'epitabulate' (for epidemiological tables), 'epidict' (for data dictionaries), 'epikit' (for epidemiological utilities), and 'apyramid' (for age-sex pyramids). Simply load 'sitrep' to access all functions from the ecosystem.
License: GPL-3
URL: https://github.com/R4EPI/sitrep/, https://r4epi.github.io/sitrep/
BugReports: https://github.com/R4EPI/sitrep/issues/
Depends: R (≥ 3.2)
Imports: apyramid (≥ 0.1.0), epidict (≥ 0.1.0), epikit, epitabulate (≥ 0.1.0), utils
Suggests: anthro, binom, broom, clipr, covr, dplyr (≥ 0.8.0), flextable, forcats, ggalluvial, ggplot2 (≥ 3.0.0), ggspatial, glue, gtsummary (≥ 2.0.0), here, janitor, knitr, labelled, lubridate, matchmaker, pacman, parsedate, patchwork, purrr, rio, rlang (≥ 0.4.0), rmarkdown, scales, sessioninfo, sf, slider, srvyr, stats, stringr, summarytools, survey, testthat (≥ 2.1.0), tibble, tidyr (≥ 1.0.0), tidyselect, tsibble, vdiffr
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.3
Collate: 'sitrep-package.R' 'check_templates.R' 'metapackage_functions.R'
NeedsCompilation: no
Packaged: 2025-12-18 06:54:23 UTC; spina
Author: Alexander Spina ORCID iD [aut, cre], Zhian N. Kamvar ORCID iD [aut], Dirk Schumacher [aut], Kate Doyle [aut], Chris Jarvis [aut], Lukas Richter [aut], Paula Blomquist [aut], Annick Lenglet [ctb], Neale Batra [ctb], Applied Epi Incorporated [cph], Medecins Sans Frontieres Operational Centre Amsterdam [fnd]
Maintainer: Alexander Spina <aspina@appliedepi.org>
Repository: CRAN
Date/Publication: 2025-12-22 19:40:02 UTC

sitrep: Report Templates and Helper Functions for Applied Epidemiology

Description

logo

A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including 'epitabulate' (for epidemiological tables), 'epidict' (for data dictionaries), 'epikit' (for epidemiological utilities), and 'apyramid' (for age-sex pyramids). Simply load 'sitrep' to access all functions from the ecosystem.

Author(s)

Maintainer: Alexander Spina aspina@appliedepi.org (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Display the available sitrep templates

Description

Display the available sitrep templates

Usage

available_sitrep_templates(categorise = FALSE, ...)

Arguments

categorise

if TRUE, the results are split into a list of outbreak and survey categories. Defaults to FALSE.

...

options to pass on to dir

Value

a vector of available templates in the sitrep package

Examples

available_sitrep_templates(categorise = TRUE)
available_sitrep_templates(categorise = TRUE, full.names = TRUE)

Run the templates found in the sitrep package.

Description

Run the templates found in the sitrep package.

Usage

check_sitrep_templates(
  templates = available_sitrep_templates(),
  path = tempdir(),
  quiet = FALSE,
  progress = FALSE,
  mustwork = FALSE,
  output_format = NULL,
  clean = TRUE
)

Arguments

templates

a vector of templates to create and render

path

a directory in which to store the templates

quiet

if FALSE (default), a message will be printed for every template.

progress

if TRUE, then the progress of the template is printed to screen (passed to the quiet argument of rmarkdown::render()). Defaults to FALSE

mustwork

if TRUE, then the templates must work for the function to succeed. Defaults to FALSE, which will simply print the errors.

output_format

a character defining the output formats to use for the template files. Defaults to the output_format defined in the templates (which is word_document), but can be modified to html_document for cross-platform cromulence checking.

clean

if TRUE (default), this will remove the previous output file before rendering.

Value

the path where the templates were built.

Examples


check_sitrep_templates("mortality")

Check if all sitrep dependencies are available

Description

Checks if all packages needed for the sitrep ecosystem are installed and loads properly. Useful for verifying offline readiness.

Usage

sitrep_check_deps(quiet = FALSE)

Arguments

quiet

Should output be suppressed? Default is FALSE

Value

Named logical vector indicating which packages are available. Names are package names, values are TRUE if available, FALSE otherwise.

Examples


# Check what's missing before going offline
sitrep_check_deps()

Check for function conflicts in sitrep ecosystem

Description

This function identifies any naming conflicts between functions in the sitrep ecosystem packages.

Usage

sitrep_conflicts()

Value

NULL (invisibly). Prints messages about conflicts to console.

List all functions in sitrep ecosystem

Description

Shows all available functions across the sitrep ecosystem packages.

Usage

sitrep_functions(pattern = NULL)

Arguments

pattern

Optional regex pattern to filter function names

Value

A data frame with columns 'package' and 'function_name', sorted by package and function name.

Install all sitrep ecosystem dependencies for offline use

Description

This function provides code to install all packages needed for the complete sitrep ecosystem, ensuring you have everything needed for working without internet connection.

Usage

sitrep_install_deps(
  upgrade = "ask",
  dependencies = TRUE,
  repos = getOption("repos"),
  quiet = FALSE,
  force = FALSE
)

Arguments

upgrade

Should packages be upgraded? Options: "ask", "always", "never". Default is "ask"

dependencies

Should dependencies be installed? Default is TRUE

repos

Repository to use. Default uses getOption("repos")

quiet

Should installation be quiet? Default is FALSE

force

Should installation proceed without prompts? Default is FALSE

Details

This function reads the sitrep DESCRIPTION file and provides code to install all packages listed in Depends, Imports, and Suggests fields. This ensures complete functionality in offline environments.

Value

Character vector of all dependency package names (invisibly).

Examples


# Install everything for offline field work (with prompts)
sitrep_install_deps()

# Install without prompts
sitrep_install_deps(force = TRUE)

# Install quietly without prompts or upgrades
sitrep_install_deps(upgrade = "never", quiet = TRUE, force = TRUE)