Package 'sitrep'

Title: Report templates and helper functions for applied epidemiology
Description: Report templates and helper functions for applied epidemiology
Authors: Alexander Spina [aut, cre] , Zhian N. Kamvar [aut] , Dirk Schumacher [aut], Kate Doyle [aut], Chris Jarvis [aut], Lukas Richter [aut], Annick Lenglet [cph], Neale Batra [ctb]
Maintainer: Alexander Spina <[email protected]>
License: GPL-3
Version: 0.2.3
Built: 2024-08-26 02:48:42 UTC
Source: https://github.com/r4epi/sitrep

Help Index

Functions re-exported from apyramid

Description

Functions re-exported from apyramid

Usage

age_pyramid

Format

An object of class function of length 1.

See Also

apyramid functions:

Example outbreak data for Hepatatis E virus or Acute Jaundice Syndrome (AJS)

Description

Data from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the Chadian town of Am Timan between October 2016 and April 2017. The Chadian Ministry of Health (MoH) has approved the use of this data for training purposes. Please note, that some data has been adapted in order to best achieve training objectives. Also, the GPS coordinates included in the dataset do not correspond to real cases identified during this outbreak. They have been generated exclusively for training purposes.

Usage

data(AJS_linelist_internal)

Format

An object of class "cross"; see read.cross.

Source

Article

References

None (PLoS)

Examples

data(AJS_linelist_internal)
head(AJS_linelist_internal)

Example population data for Hepatatis E virus or Acute Jaundice Syndrome (AJS)

Description

Population data from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the Chadian town of Am Timan between October 2016 and April 2017. The Chadian Ministry of Health (MoH) has approved the use of this data for training purposes. Please note, that some data has been adapted in order to best achieve training objectives. Also, the GPS coordinates included in the dataset do not correspond to real cases identified during this outbreak. They have been generated exclusively for training purposes.

Usage

data(AJS_pop_internal)

Format

An object of class "cross"; see read.cross.

Source

Article

References

None (PLoS)

Examples

data(AJS_pop_internal)
head(AJS_pop_internal)

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)

Access kobo data dictionary

Description

Access kobo data dictionary

Usage

download_kobo(path = rstudioapi::selectDirectory())

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string

Access AJS outbreak linelist

Description

Access AJS outbreak linelist

Usage

download_outbreak_linelist(path = rstudioapi::selectDirectory())

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string

Access AJS outbreak population data

Description

Access AJS outbreak population data

Usage

download_outbreak_pop(path = rstudioapi::selectDirectory())

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string

Access Am Timan blocks shapefile

Description

Access Am Timan blocks shapefile

Usage

download_shape_block(path = rstudioapi::selectDirectory())

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string

Access Am Timan quartier shapefile

Description

Access Am Timan quartier shapefile

Usage

download_shape_quartier(path = rstudioapi::selectDirectory())

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string

Access fake mortality survey data

Description

Access fake mortality survey data

Usage

download_survey(path = rstudioapi::selectDirectory())

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string

Internal function (not exported - i.e. not userfacing) to reduce code duplication

Description

Internal function (not exported - i.e. not userfacing) to reduce code duplication

Usage

generic_download(path = rstudioapi::selectDirectory(), dataset)

Arguments

path

Run with no arguments to pick a directory interactively. Path on your computer where the file(s) should be saved to string
dataset

The name of the file to save

Quartier shapefile for example outbreak Hepatatis E virus or Acute Jaundice Syndrome (AJS)

Description

Shapefile for blocks (polygons) from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the Chadian town of Am Timan between October 2016 and April 2017. The Chadian Ministry of Health (MoH) has approved the use of this data for training purposes. Please note, that some data has been adapted in order to best achieve training objectives. Also, the GPS coordinates included in the dataset do not correspond to real cases identified during this outbreak. They have been generated exclusively for training purposes.

Usage

data(shape_block_internal)

Format

An object of class "cross"; see read.cross.

Source

Article

References

None (PLoS)

Examples

data(shape_block_internal)
head(shape_block_internal)

Quartier shapefile for example outbreak Hepatatis E virus or Acute Jaundice Syndrome (AJS)

Description

Shapefile for quartier (polygons) from a real outbreak of Hepatitis E virus (HEV) infection which occurred in the Chadian town of Am Timan between October 2016 and April 2017. The Chadian Ministry of Health (MoH) has approved the use of this data for training purposes. Please note, that some data has been adapted in order to best achieve training objectives. Also, the GPS coordinates included in the dataset do not correspond to real cases identified during this outbreak. They have been generated exclusively for training purposes.

Usage

data(shape_quartier_internal)

Format

An object of class "cross"; see read.cross.

Source

Article

References

None (PLoS)

Examples

data(shape_quartier_internal)
head(shape_quartier_internal)