Title: | Report templates and helper functions for applied epidemiology |
---|---|
Description: | Report templates and helper functions for applied epidemiology |
Authors: | Alexander Spina [aut, cre] |
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 |
Functions re-exported from apyramid
age_pyramid
age_pyramid
An object of class function
of length 1.
apyramid functions:
apyramid::age_pyramid()
: Plot a population pyramid (age-sex) from a dataframe
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.
data(AJS_linelist_internal)
data(AJS_linelist_internal)
An object of class "cross"
; see read.cross
.
None (PLoS)
data(AJS_linelist_internal) head(AJS_linelist_internal)
data(AJS_linelist_internal) head(AJS_linelist_internal)
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.
data(AJS_pop_internal)
data(AJS_pop_internal)
An object of class "cross"
; see read.cross
.
None (PLoS)
data(AJS_pop_internal) head(AJS_pop_internal)
data(AJS_pop_internal) head(AJS_pop_internal)
Display the available sitrep templates
available_sitrep_templates(categorise = FALSE, ...)
available_sitrep_templates(categorise = FALSE, ...)
categorise |
if |
... |
options to pass on to dir |
a vector of available templates in the sitrep package
available_sitrep_templates(categorise = TRUE) available_sitrep_templates(categorise = TRUE, full.names = TRUE)
available_sitrep_templates(categorise = TRUE) available_sitrep_templates(categorise = TRUE, full.names = TRUE)
Access kobo data dictionary
download_kobo(path = rstudioapi::selectDirectory())
download_kobo(path = rstudioapi::selectDirectory())
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
download_outbreak_linelist(path = rstudioapi::selectDirectory())
download_outbreak_linelist(path = rstudioapi::selectDirectory())
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
download_outbreak_pop(path = rstudioapi::selectDirectory())
download_outbreak_pop(path = rstudioapi::selectDirectory())
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
download_shape_block(path = rstudioapi::selectDirectory())
download_shape_block(path = rstudioapi::selectDirectory())
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
download_shape_quartier(path = rstudioapi::selectDirectory())
download_shape_quartier(path = rstudioapi::selectDirectory())
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
download_survey(path = rstudioapi::selectDirectory())
download_survey(path = rstudioapi::selectDirectory())
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
generic_download(path = rstudioapi::selectDirectory(), dataset)
generic_download(path = rstudioapi::selectDirectory(), dataset)
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 |
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.
data(shape_block_internal)
data(shape_block_internal)
An object of class "cross"
; see read.cross
.
None (PLoS)
data(shape_block_internal) head(shape_block_internal)
data(shape_block_internal) head(shape_block_internal)
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.
data(shape_quartier_internal)
data(shape_quartier_internal)
An object of class "cross"
; see read.cross
.
None (PLoS)
data(shape_quartier_internal) head(shape_quartier_internal)
data(shape_quartier_internal) head(shape_quartier_internal)