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docs: resembling same format for link
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dsweber2 committed Sep 6, 2023
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74 changes: 41 additions & 33 deletions R/endpoints.R
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#' CDC page hits
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/cdc.html>
#'
#' @examples
Expand Down Expand Up @@ -51,13 +51,14 @@ pvt_cdc <- function(auth, locations, epiweeks, fetch_args = fetch_args_list()) {
}

#' COVID hospitalization facility identifiers
#' @description
#' API docs:
#' <https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility_lookup.html>
#'
#' Obtains unique identifiers and other metadata for COVID hospitalization
#' facilities of interest.
#' This is a companinon endpoint to the [covid_hosp_facility()] endpoint.
#'
#' API docs:
#' <https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility_lookup.html>
#'
#' @details Only one argument needs to be specified.
#' Combinations of the arguments are not currently supported.
Expand Down Expand Up @@ -133,14 +134,14 @@ covid_hosp_facility_lookup <- function(
}

#' COVID hospitalization data for specific facilities
#' @description
#' API docs:
#' <https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility.html>
#'
#' Obtains the COVID-19 reported patient impact and hospital capacity data by
#' facility. This dataset is provided by the US Department of Health & Human
#' Services via healthdata.gov.
#'
#' API docs:
#' <https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility.html>
#'
#' @details Starting October 1, 2022, some facilities are only required to
#' report annually. The companion function [covid_hosp_facility_lookup()] can be
#' used to look up facility identifiers in a variety of ways.
Expand Down Expand Up @@ -436,13 +437,13 @@ covid_hosp_facility <- function(
}

#' COVID Hospitalization Data by State
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp.html>.
#'
#' Obtains the COVID-19 reported patient impact and hospital capacity data by
#' state. This dataset is provided by the US Department of Health & Human
#' Services via healthdata.gov.
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp.html>.
#'
#' @details Starting October 1, 2022, some facilities are only required to
#' report annually.
#'
Expand Down Expand Up @@ -598,13 +599,14 @@ covid_hosp_state_timeseries <- function(states, dates, ..., issues = NULL, fetch
}

#' Metadata for covidcast endpoint
#' @description
#' API docs:
#' <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_meta.html>.
#'
#' Fetch a summary of metadata for all sources and signals that are available in
#' the API, along with basic summary statistics such as the dates they are
#' available, the geographic levels at which they are reported, and etc.
#'
#' API docs:
#' <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_meta.html>.
#'
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#'
Expand Down Expand Up @@ -646,7 +648,7 @@ covidcast_meta <- function(fetch_args = fetch_args_list()) {
}

#' COVID data via the covidcast endpoint
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html>
#'
#' COVIDcast public dashboard: <https://delphi.cmu.edu/covidcast/>
Expand Down Expand Up @@ -783,7 +785,7 @@ covidcast <- function(
}

#' Delphi's ILINet forecasts
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/delphi.html>
#'
#' @examples
Expand Down Expand Up @@ -814,7 +816,7 @@ delphi <- function(system, epiweek, fetch_args = fetch_args_list()) {
}

#' Delphi's PAHO Dengue nowcast
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/dengue_nowcast.html>
#'
#' @examples
Expand Down Expand Up @@ -848,7 +850,7 @@ dengue_nowcast <- function(locations, epiweeks, fetch_args = fetch_args_list())
}

#' Dengue digital surveillance sensors in PAHO member countries
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/dengue_sensors.html>
#'
#' @examples
Expand Down Expand Up @@ -893,11 +895,12 @@ pvt_dengue_sensors <- function(auth, names, locations, epiweeks, fetch_args = fe
}

#' ECDC ILI data
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/ecdc_ili.html>.
#'
#' Obtain information on influenza-like-illness from the European Centre for
#' Disease Prevention and Control.
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/ecdc_ili.html>.
#'
#' @details The list of location argument can be found in
#' <https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/ecdc_regions.txt>.
Expand Down Expand Up @@ -948,11 +951,12 @@ ecdc_ili <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_ar
}

#' FluSurv hospitalization data
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/flusurv.html>.
#'
#' Obtain information on flu hospitalization rates from the Center of Disease
#' Control.
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/flusurv.html>.
#' See also <https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html>.
#'
#' @details The list of location argument can be found in
Expand Down Expand Up @@ -1009,7 +1013,7 @@ flusurv <- function(locations, epiweeks, ..., issues = NULL, lag = NULL, fetch_a
}

#' FluView virological data from clinical labs
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/fluview_clinical.html>
#'
#' @examples
Expand Down Expand Up @@ -1065,7 +1069,7 @@ fluview_clinical <- function(regions, epiweeks, ..., issues = NULL, lag = NULL,
}

#' FluView metadata
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/fluview_meta.html>
#' @examples
#' \dontrun{
Expand All @@ -1091,11 +1095,12 @@ fluview_meta <- function(fetch_args = fetch_args_list()) {


#' FluView ILINet data
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/fluview.html>. For
#'
#' Obtains information on outpatient inluenza-like-illness (ILI) from U.S.
#' Outpatient Influenza-like Illness Surveillance Network (ILINet).
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/fluview.html>. For
#' more information on ILINet, see
#' <https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html>.
#'
Expand Down Expand Up @@ -1164,11 +1169,12 @@ fluview <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, auth = NU
}

#' Google Flu Trends data
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/gft.html>
#'
#' Obtains estimates of inluenza activity based on volume of certain search
#' queries from Google.
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/gft.html>
#'
#' @details Google has discontinued Flu Trends and this is now a static
#' endpoint. Possibile input for locations can be found in
Expand Down Expand Up @@ -1205,7 +1211,7 @@ gft <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
}

#' Google Health Trends data
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/ght.html>
#'
#' @examples
Expand Down Expand Up @@ -1249,7 +1255,7 @@ pvt_ght <- function(auth, locations, epiweeks, query, fetch_args = fetch_args_li
}

#' KCDC ILI data
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/kcdc_ili.html>
#'
#' @examples
Expand Down Expand Up @@ -1298,7 +1304,7 @@ kcdc_ili <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_ar
}

#' NoroSTAT metadata
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/meta_norostat.html>
#'
#' @examples
Expand All @@ -1321,7 +1327,7 @@ pvt_meta_norostat <- function(auth, fetch_args = fetch_args_list()) {
}

#' Api metadata
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/meta.html>
#'
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
Expand All @@ -1334,11 +1340,12 @@ meta <- function(fetch_args = fetch_args_list()) {
}

#' NIDSS dengue data
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/nidss_dengue.html>
#'
#' Obtains counts of confirmed dengue cases in Taiwan from Taiwan National
#' Infectious Disease Statistical System.
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/nidss_dengue.html>
#'
#' @details Possible location inputs can be found in
#' <https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt>
Expand Down Expand Up @@ -1373,11 +1380,12 @@ nidss_dengue <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
}

#' NIDSS flu data
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/nidss_flu.html>
#'
#' Obtains information on outpatient inluenza-like-illness from Taiwan National
#' Infectious Disease Statistical System.
#'
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/nidss_flu.html>
#'
#' @examples
#' \dontrun{
Expand Down Expand Up @@ -1428,7 +1436,7 @@ nidss_flu <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_a


#' NoroSTAT data (point data, no min/max)
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/norostat.html>
#'
#' @examples
Expand Down Expand Up @@ -1468,7 +1476,7 @@ pvt_norostat <- function(auth, locations, epiweeks, fetch_args = fetch_args_list
}

#' Delphi's ILI nowcast
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/nowcast.html>.
#'
#' Obtains information on outpatient inluenza-like-illness (ILI) from Delphi's
Expand Down Expand Up @@ -1505,7 +1513,7 @@ nowcast <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
}

#' PAHO Dengue data
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/paho_dengue.html>
#'
#' @examples
Expand Down Expand Up @@ -1556,7 +1564,7 @@ paho_dengue <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch
}

#' Quidel COVID-19 and influenza testing data
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/quidel.html>
#'
#' @examples
Expand Down Expand Up @@ -1596,7 +1604,7 @@ pvt_quidel <- function(auth, locations, epiweeks, fetch_args = fetch_args_list()
}

#' Digital surveillance sensors
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/sensors.html>
#'
#' @examples
Expand Down Expand Up @@ -1641,7 +1649,7 @@ pvt_sensors <- function(auth, names, locations, epiweeks, fetch_args = fetch_arg
}

#' HealthTweets data
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/twitter.html>
#'
#' @examples
Expand Down Expand Up @@ -1697,7 +1705,7 @@ pvt_twitter <- function(auth, locations, ..., dates = NULL, epiweeks = NULL, fet
}

#' Wikipedia access data
#'
#' @description
#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/wiki.html>
#'
#' ```{r results="asis", echo = FALSE}
Expand Down

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