R/aaGlobalVariables.R
In raubreywhite/dashboards_sykdomspuls: Depreciated - to be removed
#' Variables produced by the daily algorithm
#'
#' A variable containing the variables produced by the daily algorithm.
#' The variabels are as follows:
#'
#' @format A vector with one variable:
#' \describe{
#' \item{date}{Date of the observation}
#' }
#' Configuration of analyses
#'
#' This environment holds a number of important variables for
#' configuring the analyses that will be run.
#'
#' @format An environment containing 7 variables:
#' \describe{
#' \item{verbose}{Verbose?.}
#' \item{VERSION}{The version that we are currently running.}
#' \item{VERSIONS}{All available versions.}
#' \item{SYNDROMES}{A data.table of all the syndromes/analyses that will be run}
#' \item{tagsWithLong}{A convenience vector used to switch between tags and pretty names}
#' \item{AGES}{The age groups that we run analyses on.}
#' \item{smallMunicips}{Small municipalities that need to be censored.}
#' }
#' @export CONFIG
CONFIG <- new.env(parent = emptyenv())
CONFIG$verbose <- FALSE
CONFIG$VERSION <- 1
CONFIG$VERSIONS <- 1:2
CONFIG$MEM <- rbind(
data.table(
tag = "influensa",
syndrome = "influensa",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list("Legekontakt"),
syndromeOrConsult = "syndrome",
denominator = "consult_with_influenza",
age = jsonlite::toJSON(list("Totalt" = c("Totalt"))),
weeklyDenominatorFunction = "sum",
multiplicative_factor = 100,
namesLong = "Influensa",
include_as_syndromes = TRUE,
folder_name = "influensa",
namesShort = "Influensa",
excludeSeason = c("2009/2010"),
mem_outputs = list(c("charts", "county_sheet", "region_sheet", "norway_sheet")),
icpc2 = list("R80")
),
data.table(
tag = "influensa_all",
syndrome = "influensa_all",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_with_influenza",
age = jsonlite::toJSON(list(
"0-4" = c("0-4"), "5-14" = c("5-14"),
"15-64" = c("15-19", "20-29", "30-64"), "65+" = c("65+")
)),
weeklyDenominatorFunction = "sum",
multiplicative_factor = 100,
include_as_syndromes = TRUE,
folder_name = "influensa",
namesLong = "Influensa",
namesShort = "Influensa",
excludeSeason = c("2009/2010"),
mem_outputs = list(c("n_doctors_sheet")),
icpc2 = list("R80")
) ## ,
## data.table(
## tag = "gastro",
## syndrome = "gastro",
## alertInternal = TRUE,
## alertExternal = TRUE,
## websiteInternal = TRUE,
## age = jsonlite::toJSON(list("Totalt" = c("Totalt"), "0-4"=c("0-4"))),
## icpc2 = list("D13"),
## multiplicative_factor = 100,
## mem_outputs=list(c("charts")),
## contactType = list(c("Legekontakt", "Telefonkontakt")),
## syndromeOrConsult = "syndrome",
## denominator = "consult_without_influenza",
## weeklyDenominatorFunction = "sum",
## namesLong = "Mage-tarminfeksjoner",
## namesShort = "Mage-tarm",
## folder_name = "gastro",
## excludeSeason = c(""),
## include_as_syndromes = FALSE
## ),
## data.table(
## tag = "gastro-N",
## syndrome = "gastro",
## alertInternal = TRUE,
## alertExternal = TRUE,
## websiteInternal = TRUE,
## age = jsonlite::toJSON(list("Totalt" = c("Totalt"))),
## icpc2 = list("D13"),
## multiplicative_factor = 1,
## mem_outputs=list(c("charts")),
## contactType = list(c("Legekontakt", "Telefonkontakt")),
## syndromeOrConsult = "syndrome",
## denominator = "consult_without_influenza",
## weeklyDenominatorFunction = "return_one",
## namesLong = "Mage-tarminfeksjoner",
## namesShort = "Mage-tarm",
## excludeSeason = c(""),
## folder_name = "gastro-N",
## include_as_syndromes = FALSE
## )
)
CONFIG$BAYESIAN <- CONFIG$STANDARD <- rbind(
data.table(
tag = "gastro",
syndrome = "gastro",
alertInternal = TRUE,
alertExternal = TRUE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Mage-tarminfeksjoner",
namesShort = "Mage-tarm",
include_as_syndromes = TRUE
),
data.table(
tag = "respiratoryinternal",
syndrome = "respiratoryinternal",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Luftveisinfeksjoner",
namesShort = "Luftvei",
include_as_syndromes = TRUE
),
data.table(
tag = "respiratoryexternal",
syndrome = "respiratoryexternal",
alertInternal = FALSE,
alertExternal = TRUE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Luftveisinfeksjoner",
namesShort = "Luftvei",
include_as_syndromes = TRUE
),
data.table(
tag = "influensa",
syndrome = "influensa",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list("Legekontakt"),
syndromeOrConsult = "syndrome",
denominator = "consult_with_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Influensa",
namesShort = "Influensa",
include_as_syndromes = TRUE
),
data.table(
tag = "lungebetennelse",
syndrome = "lungebetennelse",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Lungebetennelse diagnose",
namesShort = "Lungebet",
include_as_syndromes = TRUE
),
data.table(
tag = "bronkitt",
syndrome = "bronkitt",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Bronkitt diagnose",
namesShort = "Bronkitt",
include_as_syndromes = TRUE
),
data.table(
tag = "consult_with_influenza",
syndrome = "consult_with_influenza",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "consult",
denominator = "pop",
weeklyDenominatorFunction = "mean",
namesLong = "consult_with_influenza",
namesShort = "ConsWithInf",
include_as_syndromes = TRUE
),
data.table(
tag = "consult_without_influenza",
syndrome = "consult_without_influenza",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "consult",
denominator = "pop",
weeklyDenominatorFunction = "mean",
namesLong = "consult_without_influenza",
namesShort = "ConsWOInf",
include_as_syndromes = TRUE
),
data.table(
tag = "skabb",
syndrome = "skabb",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Skabb diagnose",
namesShort = "Skabb",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg1",
syndrome = "emerg1",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg1 diagnose",
namesShort = "emerg1",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg2",
syndrome = "emerg2",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg2 diagnose",
namesShort = "emerg2",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg3",
syndrome = "emerg3",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg3 diagnose",
namesShort = "emerg3",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg4",
syndrome = "emerg4",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg4 diagnose",
namesShort = "emerg4",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg5",
syndrome = "emerg5",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg5 diagnose",
namesShort = "emerg5",
include_as_syndromes = TRUE
),
data.table(
tag = "hoste",
syndrome = "hoste",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Hoste",
namesShort = "Hoste",
include_as_syndromes = TRUE
),
data.table(
tag = "akkut_ovre_luftveisinfeksjon",
syndrome = "akkut_ovre_luftveisinfeksjon",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "akkut_ovre_luftveisinfeksjon",
namesShort = "akkut_ovre_luftveisinfeksjon",
include_as_syndromes = TRUE
),
data.table(
tag = "luftveisinfeksjon_ika",
syndrome = "luftveisinfeksjon_ika",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "luftveisinfeksjon_ika",
namesShort = "luftveisinfeksjon_ika",
include_as_syndromes = TRUE
),
data.table(
tag = "luftveissykdom_ika",
syndrome = "luftveissykdom_ika",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "luftveissykdom_ika",
namesShort = "luftveissykdom_ika",
include_as_syndromes = TRUE
),
data.table(
tag = "virusinfeksjon_ika",
syndrome = "virusinfeksjon_ika",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "virusinfeksjon_ika",
namesShort = "virusinfeksjon_ika",
include_as_syndromes = TRUE
),
data.table(
tag = "rxx_for_corona",
syndrome = "rxx_for_corona",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "rxx_for_corona",
namesShort = "rxx_for_corona",
include_as_syndromes = TRUE
),
data.table(
tag = "corona",
syndrome = "corona",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt", "Ekonsultasjon")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Corona",
namesShort = "Corona",
include_as_syndromes = TRUE
)
)
CONFIG$MODELS <- list("mem" = CONFIG$MEM, "standard" = CONFIG$STANDARD)
CONFIG$SYNDROMES <- data.table(
tag = character(),
syndrome = character(),
syndromeOrConsult = character(),
namesLong = character(),
namesShort = character(),
alertInternal = logical(),
websiteInternal = logical(),
alertExternal = logical(),
contactType = list()
)
for (model in CONFIG$MODELS) {
for (i in 1:nrow(model)) {
config <- model[i]
if (config$include_as_syndromes) {
sub_config <- config[, names(CONFIG$SYNDROMES), with = FALSE]
if (config$tag %in% CONFIG$SYNDROMES[, tag]) {
if (!isTRUE(all.equal(CONFIG$SYNDROMES[tag == config$tag], sub_config))) {
stop(paste("tag, syndromeOrConsult, namesLong, namesShort, alertInternal, alertExternal, websiteInternal and contactType needs to be the same for the same syndrom across multiple models. It was not the same for", config$tag))
}
} else {
CONFIG$SYNDROMES <- rbind(CONFIG$SYNDROMES, sub_config)
}
}
}
}
CONFIG$tagsWithLong <- CONFIG$SYNDROMES$tag
names(CONFIG$tagsWithLong) <- CONFIG$SYNDROMES$namesLong
CONFIG$AGES <- list(
"Totalt" = c(0:105),
"0-4" = c(0:4),
"5-14" = c(5:14),
"15-19" = c(15:19),
"20-29" = c(20:29),
"30-64" = c(30:64),
"65+" = c(65:105)
)
CONFIG$smallMunicips <- c(
"municip1151",
"municip1835",
"municip1252",
"municip1739"
)
CONFIG$checkedOutOfDate <- FALSE
CONFIG$outOfDate <- list()
CONFIG$outOfDate[["norwayPopulation"]] <- TRUE
CONFIG$outOfDate[["norwayLocations"]] <- TRUE
CONFIG$outOfDate[["norwayMunicipMerging"]] <- TRUE
#' Global variables used for defining formats of data structures
#'
#' This environment holds a number of variables that are used for
#' defining the formats of data structures.
#'
#' @format An environment containing 5 variables:
#' \describe{
#' \item{REQ_DATA_RAW}{Required columns for raw data.}
#' \item{REQ_DATA_CLEAN}{Required columns for clean data.}
#' \item{REQ_DATA_ANALYSIS}{Required columns for data analysis.}
#' \item{REQ_RESULTS_BASIC}{Required columns for the results (basic, right after the analysis is run)}
#' \item{REQ_RESULTS_FULL}{Required columns for the full results (i.e. those that will be saved and used further)}
#' }
#' @export VARS
VARS <- new.env(parent = emptyenv())
VARS$REQ_DATA_RAW <- c(
"age",
"date",
"Kontaktype",
"Praksis",
"municip",
unique(CONFIG$SYNDROMES[syndromeOrConsult == "syndrome"]$syndrome),
"consult"
)
VARS$REQ_DATA_CLEAN <- c(
"granularity_geo",
"county_code",
"location_code",
"age",
"date",
"holiday",
"n",
"consult_without_influenza",
"consult_with_influenza",
"pop"
)
VARS$REQ_DATA_ANALYSIS <- c(
"age",
"date",
"municip",
"n",
"consult_with_influenza",
"consult_without_influenza",
"pop"
)
VARS$REQ_RESULTS_BASIC <- c(
"yrwk",
"year",
"week",
"x",
"date",
"holiday",
"n",
"denominator",
"threshold0",
"threshold2",
"threshold4",
"threshold6",
"zscore",
"cumE1",
"cumL1",
"cumU1",
"failed",
"uuid"
)
VARS$REQ_RESULTS_FULL <- c(
"v",
"granularity_time",
"granularity_geo",
"tag",
"type",
"county_code",
"location_code",
"location_name",
"age",
"status",
VARS$REQ_RESULTS_BASIC,
"file"
)
raubreywhite/dashboards_sykdomspuls documentation built on April 27, 2020, 6:11 p.m.
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#' Variables produced by the daily algorithm
#'
#' A variable containing the variables produced by the daily algorithm.
#' The variabels are as follows:
#'
#' @format A vector with one variable:
#' \describe{
#' \item{date}{Date of the observation}
#' }
#' Configuration of analyses
#'
#' This environment holds a number of important variables for
#' configuring the analyses that will be run.
#'
#' @format An environment containing 7 variables:
#' \describe{
#' \item{verbose}{Verbose?.}
#' \item{VERSION}{The version that we are currently running.}
#' \item{VERSIONS}{All available versions.}
#' \item{SYNDROMES}{A data.table of all the syndromes/analyses that will be run}
#' \item{tagsWithLong}{A convenience vector used to switch between tags and pretty names}
#' \item{AGES}{The age groups that we run analyses on.}
#' \item{smallMunicips}{Small municipalities that need to be censored.}
#' }
#' @export CONFIG
CONFIG <- new.env(parent = emptyenv())
CONFIG$verbose <- FALSE
CONFIG$VERSION <- 1
CONFIG$VERSIONS <- 1:2
CONFIG$MEM <- rbind(
data.table(
tag = "influensa",
syndrome = "influensa",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list("Legekontakt"),
syndromeOrConsult = "syndrome",
denominator = "consult_with_influenza",
age = jsonlite::toJSON(list("Totalt" = c("Totalt"))),
weeklyDenominatorFunction = "sum",
multiplicative_factor = 100,
namesLong = "Influensa",
include_as_syndromes = TRUE,
folder_name = "influensa",
namesShort = "Influensa",
excludeSeason = c("2009/2010"),
mem_outputs = list(c("charts", "county_sheet", "region_sheet", "norway_sheet")),
icpc2 = list("R80")
),
data.table(
tag = "influensa_all",
syndrome = "influensa_all",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_with_influenza",
age = jsonlite::toJSON(list(
"0-4" = c("0-4"), "5-14" = c("5-14"),
"15-64" = c("15-19", "20-29", "30-64"), "65+" = c("65+")
)),
weeklyDenominatorFunction = "sum",
multiplicative_factor = 100,
include_as_syndromes = TRUE,
folder_name = "influensa",
namesLong = "Influensa",
namesShort = "Influensa",
excludeSeason = c("2009/2010"),
mem_outputs = list(c("n_doctors_sheet")),
icpc2 = list("R80")
) ## ,
## data.table(
## tag = "gastro",
## syndrome = "gastro",
## alertInternal = TRUE,
## alertExternal = TRUE,
## websiteInternal = TRUE,
## age = jsonlite::toJSON(list("Totalt" = c("Totalt"), "0-4"=c("0-4"))),
## icpc2 = list("D13"),
## multiplicative_factor = 100,
## mem_outputs=list(c("charts")),
## contactType = list(c("Legekontakt", "Telefonkontakt")),
## syndromeOrConsult = "syndrome",
## denominator = "consult_without_influenza",
## weeklyDenominatorFunction = "sum",
## namesLong = "Mage-tarminfeksjoner",
## namesShort = "Mage-tarm",
## folder_name = "gastro",
## excludeSeason = c(""),
## include_as_syndromes = FALSE
## ),
## data.table(
## tag = "gastro-N",
## syndrome = "gastro",
## alertInternal = TRUE,
## alertExternal = TRUE,
## websiteInternal = TRUE,
## age = jsonlite::toJSON(list("Totalt" = c("Totalt"))),
## icpc2 = list("D13"),
## multiplicative_factor = 1,
## mem_outputs=list(c("charts")),
## contactType = list(c("Legekontakt", "Telefonkontakt")),
## syndromeOrConsult = "syndrome",
## denominator = "consult_without_influenza",
## weeklyDenominatorFunction = "return_one",
## namesLong = "Mage-tarminfeksjoner",
## namesShort = "Mage-tarm",
## excludeSeason = c(""),
## folder_name = "gastro-N",
## include_as_syndromes = FALSE
## )
)
CONFIG$BAYESIAN <- CONFIG$STANDARD <- rbind(
data.table(
tag = "gastro",
syndrome = "gastro",
alertInternal = TRUE,
alertExternal = TRUE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Mage-tarminfeksjoner",
namesShort = "Mage-tarm",
include_as_syndromes = TRUE
),
data.table(
tag = "respiratoryinternal",
syndrome = "respiratoryinternal",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Luftveisinfeksjoner",
namesShort = "Luftvei",
include_as_syndromes = TRUE
),
data.table(
tag = "respiratoryexternal",
syndrome = "respiratoryexternal",
alertInternal = FALSE,
alertExternal = TRUE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Luftveisinfeksjoner",
namesShort = "Luftvei",
include_as_syndromes = TRUE
),
data.table(
tag = "influensa",
syndrome = "influensa",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list("Legekontakt"),
syndromeOrConsult = "syndrome",
denominator = "consult_with_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Influensa",
namesShort = "Influensa",
include_as_syndromes = TRUE
),
data.table(
tag = "lungebetennelse",
syndrome = "lungebetennelse",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Lungebetennelse diagnose",
namesShort = "Lungebet",
include_as_syndromes = TRUE
),
data.table(
tag = "bronkitt",
syndrome = "bronkitt",
alertInternal = TRUE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Bronkitt diagnose",
namesShort = "Bronkitt",
include_as_syndromes = TRUE
),
data.table(
tag = "consult_with_influenza",
syndrome = "consult_with_influenza",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "consult",
denominator = "pop",
weeklyDenominatorFunction = "mean",
namesLong = "consult_with_influenza",
namesShort = "ConsWithInf",
include_as_syndromes = TRUE
),
data.table(
tag = "consult_without_influenza",
syndrome = "consult_without_influenza",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "consult",
denominator = "pop",
weeklyDenominatorFunction = "mean",
namesLong = "consult_without_influenza",
namesShort = "ConsWOInf",
include_as_syndromes = TRUE
),
data.table(
tag = "skabb",
syndrome = "skabb",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Skabb diagnose",
namesShort = "Skabb",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg1",
syndrome = "emerg1",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg1 diagnose",
namesShort = "emerg1",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg2",
syndrome = "emerg2",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg2 diagnose",
namesShort = "emerg2",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg3",
syndrome = "emerg3",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg3 diagnose",
namesShort = "emerg3",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg4",
syndrome = "emerg4",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg4 diagnose",
namesShort = "emerg4",
include_as_syndromes = TRUE
),
data.table(
tag = "emerg5",
syndrome = "emerg5",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = FALSE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "emerg5 diagnose",
namesShort = "emerg5",
include_as_syndromes = TRUE
),
data.table(
tag = "hoste",
syndrome = "hoste",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Hoste",
namesShort = "Hoste",
include_as_syndromes = TRUE
),
data.table(
tag = "akkut_ovre_luftveisinfeksjon",
syndrome = "akkut_ovre_luftveisinfeksjon",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "akkut_ovre_luftveisinfeksjon",
namesShort = "akkut_ovre_luftveisinfeksjon",
include_as_syndromes = TRUE
),
data.table(
tag = "luftveisinfeksjon_ika",
syndrome = "luftveisinfeksjon_ika",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "luftveisinfeksjon_ika",
namesShort = "luftveisinfeksjon_ika",
include_as_syndromes = TRUE
),
data.table(
tag = "luftveissykdom_ika",
syndrome = "luftveissykdom_ika",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "luftveissykdom_ika",
namesShort = "luftveissykdom_ika",
include_as_syndromes = TRUE
),
data.table(
tag = "virusinfeksjon_ika",
syndrome = "virusinfeksjon_ika",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "virusinfeksjon_ika",
namesShort = "virusinfeksjon_ika",
include_as_syndromes = TRUE
),
data.table(
tag = "rxx_for_corona",
syndrome = "rxx_for_corona",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "rxx_for_corona",
namesShort = "rxx_for_corona",
include_as_syndromes = TRUE
),
data.table(
tag = "corona",
syndrome = "corona",
alertInternal = FALSE,
alertExternal = FALSE,
websiteInternal = TRUE,
contactType = list(c("Legekontakt", "Telefonkontakt", "Ekonsultasjon")),
syndromeOrConsult = "syndrome",
denominator = "consult_without_influenza",
weeklyDenominatorFunction = "sum",
namesLong = "Corona",
namesShort = "Corona",
include_as_syndromes = TRUE
)
)
CONFIG$MODELS <- list("mem" = CONFIG$MEM, "standard" = CONFIG$STANDARD)
CONFIG$SYNDROMES <- data.table(
tag = character(),
syndrome = character(),
syndromeOrConsult = character(),
namesLong = character(),
namesShort = character(),
alertInternal = logical(),
websiteInternal = logical(),
alertExternal = logical(),
contactType = list()
)
for (model in CONFIG$MODELS) {
for (i in 1:nrow(model)) {
config <- model[i]
if (config$include_as_syndromes) {
sub_config <- config[, names(CONFIG$SYNDROMES), with = FALSE]
if (config$tag %in% CONFIG$SYNDROMES[, tag]) {
if (!isTRUE(all.equal(CONFIG$SYNDROMES[tag == config$tag], sub_config))) {
stop(paste("tag, syndromeOrConsult, namesLong, namesShort, alertInternal, alertExternal, websiteInternal and contactType needs to be the same for the same syndrom across multiple models. It was not the same for", config$tag))
}
} else {
CONFIG$SYNDROMES <- rbind(CONFIG$SYNDROMES, sub_config)
}
}
}
}
CONFIG$tagsWithLong <- CONFIG$SYNDROMES$tag
names(CONFIG$tagsWithLong) <- CONFIG$SYNDROMES$namesLong
CONFIG$AGES <- list(
"Totalt" = c(0:105),
"0-4" = c(0:4),
"5-14" = c(5:14),
"15-19" = c(15:19),
"20-29" = c(20:29),
"30-64" = c(30:64),
"65+" = c(65:105)
)
CONFIG$smallMunicips <- c(
"municip1151",
"municip1835",
"municip1252",
"municip1739"
)
CONFIG$checkedOutOfDate <- FALSE
CONFIG$outOfDate <- list()
CONFIG$outOfDate[["norwayPopulation"]] <- TRUE
CONFIG$outOfDate[["norwayLocations"]] <- TRUE
CONFIG$outOfDate[["norwayMunicipMerging"]] <- TRUE
#' Global variables used for defining formats of data structures
#'
#' This environment holds a number of variables that are used for
#' defining the formats of data structures.
#'
#' @format An environment containing 5 variables:
#' \describe{
#' \item{REQ_DATA_RAW}{Required columns for raw data.}
#' \item{REQ_DATA_CLEAN}{Required columns for clean data.}
#' \item{REQ_DATA_ANALYSIS}{Required columns for data analysis.}
#' \item{REQ_RESULTS_BASIC}{Required columns for the results (basic, right after the analysis is run)}
#' \item{REQ_RESULTS_FULL}{Required columns for the full results (i.e. those that will be saved and used further)}
#' }
#' @export VARS
VARS <- new.env(parent = emptyenv())
VARS$REQ_DATA_RAW <- c(
"age",
"date",
"Kontaktype",
"Praksis",
"municip",
unique(CONFIG$SYNDROMES[syndromeOrConsult == "syndrome"]$syndrome),
"consult"
)
VARS$REQ_DATA_CLEAN <- c(
"granularity_geo",
"county_code",
"location_code",
"age",
"date",
"holiday",
"n",
"consult_without_influenza",
"consult_with_influenza",
"pop"
)
VARS$REQ_DATA_ANALYSIS <- c(
"age",
"date",
"municip",
"n",
"consult_with_influenza",
"consult_without_influenza",
"pop"
)
VARS$REQ_RESULTS_BASIC <- c(
"yrwk",
"year",
"week",
"x",
"date",
"holiday",
"n",
"denominator",
"threshold0",
"threshold2",
"threshold4",
"threshold6",
"zscore",
"cumE1",
"cumL1",
"cumU1",
"failed",
"uuid"
)
VARS$REQ_RESULTS_FULL <- c(
"v",
"granularity_time",
"granularity_geo",
"tag",
"type",
"county_code",
"location_code",
"location_name",
"age",
"status",
VARS$REQ_RESULTS_BASIC,
"file"
)
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