R/lists/dataset-list.R
In epiforecasts/covid-rt-estimates: Forecasting and nowcasting Covid-19 related metrics Globally and Subnationally.
#' Requirements
if (!exists("Region", mode = "function")) source(here::here("R", "entities/region.R"))
if (!exists("SuperRegion", mode = "function")) source(here::here("R", "entities/super-region.R"))
if (!exists("add_uk", mode = "function")) source(here::here("R", "case-manipulation-utils.R"))
#' List of datasets (Regions / Super regions
#' Order is defined as follows:
#' 1. Priority
#' 2. ABC
#'
DATASETS <- list(
"united-kingdom" = Region$new(name = "united-kingdom", # leaving this as the default UK for historic purposes
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United Kingdom. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "United Kingdom"),
covid_regional_data_identifier = "UK",
reporting_delay = readRDS(here::here("data", "uk_onset_to_case.rds")),
case_modifier = function(cases) {
cases <- add_uk(cases)
return(cases) },
data_args = list(nhsregions = TRUE),
truncation = 4),
"united-kingdom-deaths" = Region$new(name = "united-kingdom-deaths",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United Kingdom.",
breakdown = "region",
country = "United Kingdom"),
covid_regional_data_identifier = "UK",
folder_name = "united-kingdom",
dataset_folder_name = "deaths",
reporting_delay = readRDS(here::here("data", "cocin_onset_to_death_delay.rds")),
case_modifier = function(deaths) {
deaths <- deaths[, cases_new := deaths_new]
deaths <- add_uk(deaths)
return(deaths) },
data_args = list(nhsregions = TRUE),
truncation = 4),
"united-kingdom-admissions" = Region$new(name = "united-kingdom-admissions",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Hospital Admissions",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United Kingdom.",
breakdown = "region",
country = "United Kingdom"),
covid_regional_data_identifier = "UK",
folder_name = "united-kingdom",
dataset_folder_name = "admissions",
case_modifier = function(admissions) {
admissions <- admissions[, cases_new := hosp_new]
admissions <- add_uk(admissions)
admissions <- admissions[!is.na(cases_new)]
return(admissions)
},
data_args = list(nhsregions = TRUE)),
"united-kingdom-local" = Region$new(name = "united-kingdom-local",
publication_metadata = PublicationMetadata$new(
title = "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting at the local authority level in the United Kingdom. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "authority",
country = "United Kingdom"),
cases_subregion_source = "level_2_region",
covid_regional_data_identifier = "UK",
reporting_delay = readRDS(here::here("data", "uk_onset_to_case.rds")),
data_args = list(level = "2"),
truncation = 4),
"united-kingdom-local-deaths" = Region$new(name = "united-kingdom-local-deaths",
publication_metadata = PublicationMetadata$new(
title = "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting at the local authority level in the United Kingdom.",
breakdown = "authority",
country = "United Kingdom"),
cases_subregion_source = "level_2_region",
covid_regional_data_identifier = "UK",
data_args = list(level = "2"),
folder_name = "united-kingdom-local",
dataset_folder_name = "deaths",
reporting_delay = readRDS(here::here("data", "cocin_onset_to_death_delay.rds")),
case_modifier = function(deaths) {
deaths <- deaths[, cases_new := deaths_new]
return(deaths) },
truncation = 4),
"united-kingdom-local-admissions" = Region$new(name = "united-kingdom-local-admissions",
publication_metadata = PublicationMetadata$new(
title = "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting at the local authority level in the United Kingdom.",
breakdown = "authority",
country = "United Kingdom"),
folder_name = "united-kingdom-local",
dataset_folder_name = "admissions",
cases_subregion_source = "level_2_region",
data = function() {
admissions <- covid19.nhs.data::get_admissions(level = "utla")
admissions <- data.table::setDT(admissions)
admissions <- admissions[, .(level_2_region = geo_name, date, cases_new = admissions)]
admissions <- admissions[!is.na(level_2_region)]
return(admissions)
}),
"united-states" = Region$new(name = "united-states",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United States of America. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "United States"),
covid_regional_data_identifier = "USA",
region_scale = "State"),
"regional-cases" = SuperRegion$new(name = "regional-cases",
publication_metadata = PublicationMetadata$new(
title = "Continent Summary Reproduction Number (R) Based on Reported Cases",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "continent"),
region_scale = "Region",
folder_name = "cases",
case_modifier = function(regional_cases) {
regional_cases <- regional_cases[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date", "un_region")][, region := un_region]
global_cases <- data.table::copy(regional_cases)[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date")][, region := "Global"]
regional_cases <- data.table::rbindlist(list(regional_cases, global_cases),
fill = TRUE, use.names = TRUE)
}),
"regional-deaths" = SuperRegion$new(name = "regional-deaths",
publication_metadata = PublicationMetadata$new(
title = "Continent Summary Reproduction Number (R) Based on Reported Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "continent"),
region_scale = "Region",
folder_name = "deaths",
case_modifier = function(regional_deaths) {
regional_deaths <- regional_deaths[country != "Cases_on_an_international_conveyance_Japan"]
regional_deaths <- regional_deaths[, cases_new := deaths_new]
regional_deaths <- regional_deaths[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date", "un_region")][, region := un_region]
global_deaths <- data.table::copy(regional_deaths)[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date")][, region := "Global"]
regional_deaths <- data.table::rbindlist(list(regional_deaths, global_deaths),
fill = TRUE, use.names = TRUE)
}),
"cases" = SuperRegion$new(name = "cases",
publication_metadata = PublicationMetadata$new(
title = "National Reproduction Number (R) Based on Reported Cases",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "country"),
case_modifier = function(cases) {
cases <- cases[, region := country]
}),
"deaths" = SuperRegion$new(name = "deaths",
publication_metadata = PublicationMetadata$new(
title = "National Reproduction Number (R) Estimates Based on Reported Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "country"),
case_modifier = function(deaths) {
deaths <- deaths[country != "Cases_on_an_international_conveyance_Japan"]
deaths <- deaths[, cases_new := deaths_new]
deaths <- deaths[, region := country]
}),
"belgium" = Region$new(name = "belgium",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Belgium Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Belgium. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "Belgium")),
"brazil" = Region$new(name = "brazil",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Brazil Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Brazil. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Brazil")),
"canada" = Region$new(name = "canada",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Canada Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Canada. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Canada")),
"colombia" = Region$new(name = "colombia",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Colombia Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Colombia. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "Colombia")),
"germany" = Region$new(name = "germany",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Germany Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Germany. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Germany")),
"india" = Region$new(name = "india",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for India Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in India. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "India"),
case_modifier = function(cases) {
cases <- cases[!(level_1_region %in% "Unknown")]
return(cases)
}),
"italy" = Region$new(name = "italy",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Italy Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Italy. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Italy")),
"south-africa" = Region$new(name = "south-africa",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in South Africa. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "South Africa"),
covid_regional_data_identifier = "South Africa",
case_modifier = function(cases) {
cases <- cases[!is.na(level_1_region)]
return(cases) }),
"south-africa-deaths" = Region$new(name = "south-africa-deaths",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in South Africa.",
breakdown = "state",
country = "South Africa"),
covid_regional_data_identifier = "South Africa",
folder_name = "south-africa",
dataset_folder_name = "deaths",
reporting_delay = readRDS(here::here("data", "cocin_onset_to_death_delay.rds")),
case_modifier = function(deaths) {
deaths <- deaths[, cases_new := deaths_new]
return(deaths) }),
"vietnam" = Region$new(name = "vietnam",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Viet Nam Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Viet Nam. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "Viet Nam"),
covid_regional_data_identifier = "Vietnam"),
"test" = Region$new(name = "test",
covid_regional_data_identifier = "belgium",
cases_subregion_source = "region",
stable = FALSE,
case_modifier = function(cases) { return(generate_clean_cases(days_since_peak = 40)) },
publication_metadata = PublicationMetadata$new(
title = "Test",
description = "Null",
breakdown = "continent"))
)
full_file_suffix <- '-all-time'
for (original_location in DATASETS) {
location <- original_location$clone()
location$name <- paste0(location$name, '-full')
# explode the target folder path into parts to add the suffix
split_loc_path <- strsplit(location$target_folder, "/")
if (is(location, SuperRegion$classname)){
split_loc_path[[1]][2] <- paste0(split_loc_path[[1]][2], full_file_suffix)
}else{
split_loc_path[[1]][3] <- paste0(split_loc_path[[1]][3], full_file_suffix)
}
location$target_folder <- paste(split_loc_path[[1]], collapse = "/")
# repeat for summary dir
split_loc_path <- strsplit(location$summary_dir, "/")
if (is(location, SuperRegion$classname)){
split_loc_path[[1]][2] <- paste0(split_loc_path[[1]][2], full_file_suffix)
}else{
split_loc_path[[1]][3] <- paste0(split_loc_path[[1]][3], full_file_suffix)
}
location$summary_dir <- paste(split_loc_path[[1]], collapse = "/")
location$data_window <- Inf
DATASETS[[location$name]] <- location
}
epiforecasts/covid-rt-estimates documentation built on June 30, 2022, 8:30 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Requirements
if (!exists("Region", mode = "function")) source(here::here("R", "entities/region.R"))
if (!exists("SuperRegion", mode = "function")) source(here::here("R", "entities/super-region.R"))
if (!exists("add_uk", mode = "function")) source(here::here("R", "case-manipulation-utils.R"))
#' List of datasets (Regions / Super regions
#' Order is defined as follows:
#' 1. Priority
#' 2. ABC
#'
DATASETS <- list(
"united-kingdom" = Region$new(name = "united-kingdom", # leaving this as the default UK for historic purposes
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United Kingdom. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "United Kingdom"),
covid_regional_data_identifier = "UK",
reporting_delay = readRDS(here::here("data", "uk_onset_to_case.rds")),
case_modifier = function(cases) {
cases <- add_uk(cases)
return(cases) },
data_args = list(nhsregions = TRUE),
truncation = 4),
"united-kingdom-deaths" = Region$new(name = "united-kingdom-deaths",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United Kingdom.",
breakdown = "region",
country = "United Kingdom"),
covid_regional_data_identifier = "UK",
folder_name = "united-kingdom",
dataset_folder_name = "deaths",
reporting_delay = readRDS(here::here("data", "cocin_onset_to_death_delay.rds")),
case_modifier = function(deaths) {
deaths <- deaths[, cases_new := deaths_new]
deaths <- add_uk(deaths)
return(deaths) },
data_args = list(nhsregions = TRUE),
truncation = 4),
"united-kingdom-admissions" = Region$new(name = "united-kingdom-admissions",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Hospital Admissions",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United Kingdom.",
breakdown = "region",
country = "United Kingdom"),
covid_regional_data_identifier = "UK",
folder_name = "united-kingdom",
dataset_folder_name = "admissions",
case_modifier = function(admissions) {
admissions <- admissions[, cases_new := hosp_new]
admissions <- add_uk(admissions)
admissions <- admissions[!is.na(cases_new)]
return(admissions)
},
data_args = list(nhsregions = TRUE)),
"united-kingdom-local" = Region$new(name = "united-kingdom-local",
publication_metadata = PublicationMetadata$new(
title = "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting at the local authority level in the United Kingdom. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "authority",
country = "United Kingdom"),
cases_subregion_source = "level_2_region",
covid_regional_data_identifier = "UK",
reporting_delay = readRDS(here::here("data", "uk_onset_to_case.rds")),
data_args = list(level = "2"),
truncation = 4),
"united-kingdom-local-deaths" = Region$new(name = "united-kingdom-local-deaths",
publication_metadata = PublicationMetadata$new(
title = "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting at the local authority level in the United Kingdom.",
breakdown = "authority",
country = "United Kingdom"),
cases_subregion_source = "level_2_region",
covid_regional_data_identifier = "UK",
data_args = list(level = "2"),
folder_name = "united-kingdom-local",
dataset_folder_name = "deaths",
reporting_delay = readRDS(here::here("data", "cocin_onset_to_death_delay.rds")),
case_modifier = function(deaths) {
deaths <- deaths[, cases_new := deaths_new]
return(deaths) },
truncation = 4),
"united-kingdom-local-admissions" = Region$new(name = "united-kingdom-local-admissions",
publication_metadata = PublicationMetadata$new(
title = "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting at the local authority level in the United Kingdom.",
breakdown = "authority",
country = "United Kingdom"),
folder_name = "united-kingdom-local",
dataset_folder_name = "admissions",
cases_subregion_source = "level_2_region",
data = function() {
admissions <- covid19.nhs.data::get_admissions(level = "utla")
admissions <- data.table::setDT(admissions)
admissions <- admissions[, .(level_2_region = geo_name, date, cases_new = admissions)]
admissions <- admissions[!is.na(level_2_region)]
return(admissions)
}),
"united-states" = Region$new(name = "united-states",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United States of America. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "United States"),
covid_regional_data_identifier = "USA",
region_scale = "State"),
"regional-cases" = SuperRegion$new(name = "regional-cases",
publication_metadata = PublicationMetadata$new(
title = "Continent Summary Reproduction Number (R) Based on Reported Cases",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "continent"),
region_scale = "Region",
folder_name = "cases",
case_modifier = function(regional_cases) {
regional_cases <- regional_cases[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date", "un_region")][, region := un_region]
global_cases <- data.table::copy(regional_cases)[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date")][, region := "Global"]
regional_cases <- data.table::rbindlist(list(regional_cases, global_cases),
fill = TRUE, use.names = TRUE)
}),
"regional-deaths" = SuperRegion$new(name = "regional-deaths",
publication_metadata = PublicationMetadata$new(
title = "Continent Summary Reproduction Number (R) Based on Reported Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "continent"),
region_scale = "Region",
folder_name = "deaths",
case_modifier = function(regional_deaths) {
regional_deaths <- regional_deaths[country != "Cases_on_an_international_conveyance_Japan"]
regional_deaths <- regional_deaths[, cases_new := deaths_new]
regional_deaths <- regional_deaths[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date", "un_region")][, region := un_region]
global_deaths <- data.table::copy(regional_deaths)[, .(cases_new = sum(cases_new, na.rm = TRUE)),
by = c("date")][, region := "Global"]
regional_deaths <- data.table::rbindlist(list(regional_deaths, global_deaths),
fill = TRUE, use.names = TRUE)
}),
"cases" = SuperRegion$new(name = "cases",
publication_metadata = PublicationMetadata$new(
title = "National Reproduction Number (R) Based on Reported Cases",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "country"),
case_modifier = function(cases) {
cases <- cases[, region := country]
}),
"deaths" = SuperRegion$new(name = "deaths",
publication_metadata = PublicationMetadata$new(
title = "National Reproduction Number (R) Estimates Based on Reported Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "country"),
case_modifier = function(deaths) {
deaths <- deaths[country != "Cases_on_an_international_conveyance_Japan"]
deaths <- deaths[, cases_new := deaths_new]
deaths <- deaths[, region := country]
}),
"belgium" = Region$new(name = "belgium",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Belgium Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Belgium. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "Belgium")),
"brazil" = Region$new(name = "brazil",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Brazil Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Brazil. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Brazil")),
"canada" = Region$new(name = "canada",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Canada Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Canada. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Canada")),
"colombia" = Region$new(name = "colombia",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Colombia Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Colombia. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "Colombia")),
"germany" = Region$new(name = "germany",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Germany Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Germany. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Germany")),
"india" = Region$new(name = "india",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for India Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in India. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "India"),
case_modifier = function(cases) {
cases <- cases[!(level_1_region %in% "Unknown")]
return(cases)
}),
"italy" = Region$new(name = "italy",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Italy Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Italy. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "Italy")),
"south-africa" = Region$new(name = "south-africa",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in South Africa. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "state",
country = "South Africa"),
covid_regional_data_identifier = "South Africa",
case_modifier = function(cases) {
cases <- cases[!is.na(level_1_region)]
return(cases) }),
"south-africa-deaths" = Region$new(name = "south-africa-deaths",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Deaths",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in South Africa.",
breakdown = "state",
country = "South Africa"),
covid_regional_data_identifier = "South Africa",
folder_name = "south-africa",
dataset_folder_name = "deaths",
reporting_delay = readRDS(here::here("data", "cocin_onset_to_death_delay.rds")),
case_modifier = function(deaths) {
deaths <- deaths[, cases_new := deaths_new]
return(deaths) }),
"vietnam" = Region$new(name = "vietnam",
publication_metadata = PublicationMetadata$new(
title = "National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Viet Nam Based on Test Results",
description = "Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Viet Nam. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.",
breakdown = "region",
country = "Viet Nam"),
covid_regional_data_identifier = "Vietnam"),
"test" = Region$new(name = "test",
covid_regional_data_identifier = "belgium",
cases_subregion_source = "region",
stable = FALSE,
case_modifier = function(cases) { return(generate_clean_cases(days_since_peak = 40)) },
publication_metadata = PublicationMetadata$new(
title = "Test",
description = "Null",
breakdown = "continent"))
)
full_file_suffix <- '-all-time'
for (original_location in DATASETS) {
location <- original_location$clone()
location$name <- paste0(location$name, '-full')
# explode the target folder path into parts to add the suffix
split_loc_path <- strsplit(location$target_folder, "/")
if (is(location, SuperRegion$classname)){
split_loc_path[[1]][2] <- paste0(split_loc_path[[1]][2], full_file_suffix)
}else{
split_loc_path[[1]][3] <- paste0(split_loc_path[[1]][3], full_file_suffix)
}
location$target_folder <- paste(split_loc_path[[1]], collapse = "/")
# repeat for summary dir
split_loc_path <- strsplit(location$summary_dir, "/")
if (is(location, SuperRegion$classname)){
split_loc_path[[1]][2] <- paste0(split_loc_path[[1]][2], full_file_suffix)
}else{
split_loc_path[[1]][3] <- paste0(split_loc_path[[1]][3], full_file_suffix)
}
location$summary_dir <- paste(split_loc_path[[1]], collapse = "/")
location$data_window <- Inf
DATASETS[[location$name]] <- location
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.