You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
457 lines
12 KiB
457 lines
12 KiB
#' Fetch FluView data
|
|
#'
|
|
#' @param regions a `list` of [delphi_regions]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param issues a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param lag a number of weeks
|
|
#' @param auth password for private imputed data
|
|
#' @export
|
|
fluview <- function(regions, epiweeks, issues, lag, auth) {
|
|
|
|
# Check parameters
|
|
if(missing(regions) || missing(epiweeks)) {
|
|
stop('`regions` and `epiweeks` are both required')
|
|
}
|
|
|
|
if(!missing(issues) && !missing(lag)) {
|
|
stop('`issues` and `lag` are mutually exclusive')
|
|
}
|
|
|
|
# Set up request
|
|
params <- list(
|
|
source = 'fluview',
|
|
regions = .list(regions),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
|
|
if (!missing(issues)) params$issues <- .list(issues)
|
|
|
|
if (!missing(lag)) params$lag <- lag
|
|
|
|
if (!missing(auth)) params$auth <- auth
|
|
|
|
# Make the API call
|
|
return(.request(params))
|
|
|
|
}
|
|
|
|
#' Fetch FluView virological data
|
|
#'
|
|
#' @param regions a `list` of [delphi_regions]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param issues a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param lag a number of weeks
|
|
#' @export
|
|
fluview_clinical <- function(regions, epiweeks, issues, lag) {
|
|
# Check parameters
|
|
if(missing(regions) || missing(epiweeks)) {
|
|
stop('`regions` and `epiweeks` are both required')
|
|
}
|
|
if(!missing(issues) && !missing(lag)) {
|
|
stop('`issues` and `lag` are mutually exclusive')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'fluview_clinical',
|
|
regions = .list(regions),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
if(!missing(issues)) {
|
|
params$issues <- .list(issues)
|
|
}
|
|
if(!missing(lag)) {
|
|
params$lag <- lag
|
|
}
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch FluSurv data
|
|
#'
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param issues a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param lag a number of weeks
|
|
#' @export
|
|
flusurv <- function(locations, epiweeks, issues, lag) {
|
|
# Check parameters
|
|
if(missing(locations) || missing(epiweeks)) {
|
|
stop('`locations` and `epiweeks` are both required')
|
|
}
|
|
if(!missing(issues) && !missing(lag)) {
|
|
stop('`issues` and `lag` are mutually exclusive')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'flusurv',
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
if(!missing(issues)) {
|
|
params$issues <- .list(issues)
|
|
}
|
|
if(!missing(lag)) {
|
|
params$lag <- lag
|
|
}
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Google Flu Trends data
|
|
#'
|
|
#' @param locations a `list` of [delphi_regions], [dephi_states], and/or [delphi_cities]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
gft <- function(locations, epiweeks) {
|
|
# Check parameters
|
|
if(missing(locations) || missing(epiweeks)) {
|
|
stop('`locations` and `epiweeks` are both required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'gft',
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Google Health Trends data
|
|
#'
|
|
#' @param auth authentication token
|
|
#' @param locations a `list` of [delphi_regions] and/or [delphi_cities]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param query google query
|
|
#' @export
|
|
ght <- function(auth, locations, epiweeks, query) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(locations) || missing(epiweeks) || missing(query)) {
|
|
stop('`auth`, `locations`, `epiweeks`, and `query` are all required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'ght',
|
|
auth = auth,
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks),
|
|
query = query
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch HealthTweets data
|
|
#'
|
|
#' @param auth twitter auth token
|
|
#' @param locations a `list` of [delphi_regions] and/or [delphi_cities]
|
|
#' @param dates a `list` of dates (`YYYYMMDD` format)
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
twitter <- function(auth, locations, dates, epiweeks) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(locations)) {
|
|
stop('`auth` and `locations` are both required')
|
|
}
|
|
if(!xor(missing(dates), missing(epiweeks))) {
|
|
stop('exactly one of `dates` and `epiweeks` is required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'twitter',
|
|
auth = auth,
|
|
locations = .list(locations)
|
|
)
|
|
if(!missing(dates)) {
|
|
params$dates <- .list(dates)
|
|
}
|
|
if(!missing(epiweeks)) {
|
|
params$epiweeks <- .list(epiweeks)
|
|
}
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Wikipedia access data
|
|
#'
|
|
#' @param articles a `list` of [delphi_articles]
|
|
#' @param dates a `list` of dates (`YYYYMMDD` format)
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param hours a `list` of hours
|
|
#' @export
|
|
wiki <- function(articles, dates, epiweeks, hours) {
|
|
# Check parameters
|
|
if(missing(articles)) {
|
|
stop('`articles` is required')
|
|
}
|
|
if(!xor(missing(dates), missing(epiweeks))) {
|
|
stop('exactly one of `dates` and `epiweeks` is required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'wiki',
|
|
articles = .list(articles)
|
|
)
|
|
if(!missing(dates)) {
|
|
params$dates <- .list(dates)
|
|
}
|
|
if(!missing(epiweeks)) {
|
|
params$epiweeks <- .list(epiweeks)
|
|
}
|
|
if(!missing(hours)) {
|
|
params$hours <- .list(hours)
|
|
}
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch CDC page hits
|
|
#'
|
|
#' @param auth auth token
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @export
|
|
cdc <- function(auth, epiweeks, locations) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(epiweeks) || missing(locations)) {
|
|
stop('`auth`, `epiweeks`, and `locations` are all required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'cdc',
|
|
auth = auth,
|
|
epiweeks = .list(epiweeks),
|
|
locations = .list(locations)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Quidel data
|
|
#'
|
|
#' @param auth auth token
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @export
|
|
quidel <- function(auth, epiweeks, locations) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(epiweeks) || missing(locations)) {
|
|
stop('`auth`, `epiweeks`, and `locations` are all required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'quidel',
|
|
auth = auth,
|
|
epiweeks = .list(epiweeks),
|
|
locations = .list(locations)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch NoroSTAT data (point data, no min/max)
|
|
#'
|
|
#' @param auth auth token
|
|
#' @param location a single [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
norostat <- function(auth, location, epiweeks) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(location) || missing(epiweeks)) {
|
|
stop('`auth`, `location`, and `epiweeks` are all required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'norostat',
|
|
auth = auth,
|
|
location = location,
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch NoroSTAT metadata
|
|
#'
|
|
#' @param auth auth token
|
|
#' @export
|
|
meta_norostat <- function(auth) {
|
|
# Check parameters
|
|
if(missing(auth)) {
|
|
stop('`auth` is required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'meta_norostat',
|
|
auth = auth
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch NIDSS flu data
|
|
#'
|
|
#' @param regions a `list` of [delphi_regions]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @param issues a `list` of issues
|
|
#' @param lag a number of weeks
|
|
#' @export
|
|
nidss_flu <- function(regions, epiweeks, issues, lag) {
|
|
# Check parameters
|
|
if(missing(regions) || missing(epiweeks)) {
|
|
stop('`regions` and `epiweeks` are both required')
|
|
}
|
|
if(!missing(issues) && !missing(lag)) {
|
|
stop('`issues` and `lag` are mutually exclusive')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'nidss_flu',
|
|
regions = .list(regions),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
if(!missing(issues)) {
|
|
params$issues <- .list(issues)
|
|
}
|
|
if(!missing(lag)) {
|
|
params$lag <- lag
|
|
}
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch NIDSS dengue data
|
|
#'
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
nidss_dengue <- function(locations, epiweeks) {
|
|
# Check parameters
|
|
if(missing(locations) || missing(epiweeks)) {
|
|
stop('`locations` and `epiweeks` are both required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'nidss_dengue',
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Delphi's forecast
|
|
#'
|
|
#' @param system (not sure)
|
|
#' @param epiweek an epiweek (fomat `YYYYWW`)
|
|
#' @export
|
|
delphi <- function(system, epiweek) {
|
|
# Check parameters
|
|
if(missing(system) || missing(epiweek)) {
|
|
stop('`system` and `epiweek` are both required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'delphi',
|
|
system = system,
|
|
epiweek = epiweek
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Delphi's digital surveillance sensors
|
|
#'
|
|
#' @param auth auth token
|
|
#' @param names sensor name?
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
sensors <- function(auth, names, locations, epiweeks) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(names) || missing(locations) || missing(epiweeks)) {
|
|
stop('`auth`, `names`, `locations`, and `epiweeks` are all required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'sensors',
|
|
auth = auth,
|
|
names = .list(names),
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Delphi's digital surveillance sensors
|
|
#'
|
|
#' @param auth auth token
|
|
#' @param names sensor names?
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
dengue_sensors <- function(auth, names, locations, epiweeks) {
|
|
# Check parameters
|
|
if(missing(auth) || missing(names) || missing(locations) || missing(epiweeks)) {
|
|
stop('`auth`, `names`, `locations`, and `epiweeks` are all required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'dengue_sensors',
|
|
auth = auth,
|
|
names = .list(names),
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Delphi's wILI nowcast
|
|
#'
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
nowcast <- function(locations, epiweeks) {
|
|
# Check parameters
|
|
if(missing(locations) || missing(epiweeks)) {
|
|
stop('`locations` and `epiweeks` are both required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'nowcast',
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch Delphi's PAHO Dengue nowcast
|
|
#'
|
|
#' @param locations a `list` of [delphi_regions] and/or [dephi_states]
|
|
#' @param epiweeks a `list` of epiweeks (format for an epiweek is `YYYYWW`)
|
|
#' @export
|
|
dengue_nowcast <- function(locations, epiweeks) {
|
|
# Check parameters
|
|
if(missing(locations) || missing(epiweeks)) {
|
|
stop('`locations` and `epiweeks` are both required')
|
|
}
|
|
# Set up request
|
|
params <- list(
|
|
source = 'dengue_nowcast',
|
|
locations = .list(locations),
|
|
epiweeks = .list(epiweeks)
|
|
)
|
|
# Make the API call
|
|
return(.request(params))
|
|
}
|
|
|
|
#' Fetch API metadata
|
|
#'
|
|
#' @export
|
|
meta <- function() {
|
|
return(.request(list(source='meta')))
|
|
}
|
|
|
|
|