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Merged
merged 4 commits into from
Sep 8, 2023
Merged

Cleanup cleanup #171

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b532cee
docs: minor fixes
dsweber2 Sep 8, 2023
35704f2
fix: single quotes for package names in title/desc
dsweber2 Sep 8, 2023
0812614
docs: correct return format
dsweber2 Sep 8, 2023
44c8730
docs: document (GHA)
dsweber2 Sep 8, 2023
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: epidatr
Type: Package
Title: Client for Delphi's Epidata API
Title: Client for Delphi's 'Epidata' API
Version: 1.0.0
Authors@R:
c(
Expand All @@ -17,7 +17,7 @@ Authors@R:
)
URL: https://cmu-delphi.github.io/epidatr/, https://github.com/cmu-delphi/epidatr
BugReports: https://github.com/cmu-delphi/epidatr/issues
Description: R Client for Delphi's Epidata API. Tools for fetching data in various forms.
Description: R Client for Delphi's 'Epidata' API. Tools for fetching data in various forms.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
Expand Down
2 changes: 1 addition & 1 deletion R/cache.R
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Expand Up @@ -187,7 +187,7 @@ set_cache <- function(cache_dir = NULL,
#' }
#' @param disable instead of setting a new cache, disable caching entirely;
#' defaults to `FALSE`
#' @param ... arguments passed to `set_cache`
#' @inheritDotParams set_cache
#' @seealso [`set_cache`] to start a new cache (and general caching info),
#' [`disable_cache`] to only disable without deleting, and [`cache_info`]
#' @export
Expand Down
56 changes: 28 additions & 28 deletions R/endpoints.R
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Expand Up @@ -16,7 +16,7 @@
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' See `fetch_args_list()` for details.
#' @return [`epidata_call`]
#' @return [`tibble`]
#'
#' @keywords endpoint
#' @export
Expand Down Expand Up @@ -76,7 +76,7 @@ pvt_cdc <- function(auth, locations, epiweeks, fetch_args = fetch_args_list()) {
#' @param zip string. A 5-digit zip code.
#' @param fips_code string. A 5-digit fips county code, zero-padded.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#'
#' @seealso [`pub_covid_hosp_facility()`]
#' @keywords endpoint
Expand Down Expand Up @@ -161,7 +161,7 @@ pub_covid_hosp_facility_lookup <- function(
#' @param ... not used for values, forces later arguments to bind by name
#' @param publication_dates [`timeset`]. Publication dates to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#'
#'
#' @seealso [`pub_covid_hosp_facility()`], [`epirange()`]
Expand Down Expand Up @@ -464,7 +464,7 @@ pub_covid_hosp_facility <- function(
#' most recent issue is returned.
#' @param ... not used for values, forces later arguments to bind by name
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#'
#' @keywords endpoint
#' @export
Expand Down Expand Up @@ -610,7 +610,7 @@ pub_covid_hosp_state_timeseries <- function(states, dates, ..., issues = NULL, f
#'
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#'
#' @return [`epidata_call`]
#' @return [`tibble`]
#'
#'
#' @examples
Expand Down Expand Up @@ -696,7 +696,7 @@ pub_covidcast_meta <- function(fetch_args = fetch_args_list()) {
#' the most recent issue is returned. Mutually exclusive with `as_of` or
#' `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#'
#'
#' @seealso [pub_covidcast_meta()], [covidcast_epidata()], [epirange()]
Expand Down Expand Up @@ -795,7 +795,7 @@ pub_covidcast <- function(
#' @param system character. System name to fetch.
#' @param epiweek [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`json`]
#' @keywords endpoint
#' @export
pub_delphi <- function(system, epiweek, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -829,7 +829,7 @@ pub_delphi <- function(system, epiweek, fetch_args = fetch_args_list()) {
#' @param locations character. Locations to fetch.
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_dengue_nowcast <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -867,7 +867,7 @@ pub_dengue_nowcast <- function(locations, epiweeks, fetch_args = fetch_args_list
#' @param locations character. Locations to fetch.
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pvt_dengue_sensors <- function(auth, names, locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -917,7 +917,7 @@ pvt_dengue_sensors <- function(auth, names, locations, epiweeks, fetch_args = fe
#' @param lag integer. Optionally, the lag of the issues to fetch. If not set,
#' the most recent issue is returned. Mutually exclusive with `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_ecdc_ili <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -974,7 +974,7 @@ pub_ecdc_ili <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetc
#' @param lag integer. Optionally, the lag of the issues to fetch. If not set,
#' the most recent issue is returned. Mutually exclusive with `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_flusurv <- function(locations, epiweeks, ..., issues = NULL, lag = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1030,7 +1030,7 @@ pub_flusurv <- function(locations, epiweeks, ..., issues = NULL, lag = NULL, fet
#' @param lag integer. Optionally, the lag of the issues to fetch. If not set,
#' the most recent issue is returned. Mutually exclusive with `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_fluview_clinical <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1078,7 +1078,7 @@ pub_fluview_clinical <- function(regions, epiweeks, ..., issues = NULL, lag = NU
#'
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#'
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_fluview_meta <- function(fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1123,7 +1123,7 @@ pub_fluview_meta <- function(fetch_args = fetch_args_list()) {
#' @param auth string. Optionally, restricted access key (not the same as API
#' key).
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_fluview <- function(
Expand Down Expand Up @@ -1198,7 +1198,7 @@ pub_fluview <- function(
#' @param epiweeks [`timeset`] Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#'
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_gft <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1235,7 +1235,7 @@ pub_gft <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param query string. The query to be fetched.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pvt_ght <- function(auth, locations, epiweeks, query, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1277,7 +1277,7 @@ pvt_ght <- function(auth, locations, epiweeks, query, fetch_args = fetch_args_li
#' @param lag integer. Optionally, the lag of the issues to fetch. If not set,
#' the most recent issue is returned. Mutually exclusive with `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_kcdc_ili <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1320,7 +1320,7 @@ pub_kcdc_ili <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetc
#' }
#' @param auth string. Restricted access key (not the same as API key).
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`json`]
#' @keywords endpoint
#' @export
pvt_meta_norostat <- function(auth, fetch_args = fetch_args_list()) {
Expand All @@ -1339,7 +1339,7 @@ pvt_meta_norostat <- function(auth, fetch_args = fetch_args_list()) {
#'
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#'
#' @return [`epidata_call`]
#' @return [`json`]
#' @keywords endpoint
#' @export
pub_meta <- function(fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1367,7 +1367,7 @@ pub_meta <- function(fetch_args = fetch_args_list()) {
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#'
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_nidss_dengue <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1406,7 +1406,7 @@ pub_nidss_dengue <- function(locations, epiweeks, fetch_args = fetch_args_list()
#' @param lag integer. Optionally, the lag of the issues to fetch. If not set,
#' the most recent issue is returned. Mutually exclusive with `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_nidss_flu <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1458,7 +1458,7 @@ pub_nidss_flu <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fet
#' @param locations character. Locations to fetch.
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pvt_norostat <- function(auth, locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1499,7 +1499,7 @@ pvt_norostat <- function(auth, locations, epiweeks, fetch_args = fetch_args_list
#' @param locations character. Locations to fetch.
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_nowcast <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1535,7 +1535,7 @@ pub_nowcast <- function(locations, epiweeks, fetch_args = fetch_args_list()) {
#' @param lag integer. Optionally, the lag of the issues to fetch. If not set,
#' the most recent issue is returned. Mutually exclusive with `issues`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_paho_dengue <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1586,7 +1586,7 @@ pub_paho_dengue <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, f
#' @param locations character. Locations to fetch.
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pvt_quidel <- function(auth, locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1628,7 +1628,7 @@ pvt_quidel <- function(auth, locations, epiweeks, fetch_args = fetch_args_list()
#' @param locations character. Locations to fetch.
#' @param epiweeks [`timeset`]. Epiweeks to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pvt_sensors <- function(auth, names, locations, epiweeks, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1674,7 +1674,7 @@ pvt_sensors <- function(auth, names, locations, epiweeks, fetch_args = fetch_arg
#' @param epiweeks [`timeset`]. Epiweeks to fetch. Mutually exclusive with
#' `dates`.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pvt_twitter <- function(auth, locations, ..., dates = NULL, epiweeks = NULL, fetch_args = fetch_args_list()) {
Expand Down Expand Up @@ -1727,7 +1727,7 @@ pvt_twitter <- function(auth, locations, ..., dates = NULL, epiweeks = NULL, fet
#' @param language string. Language to fetch.
#' @param hours integer. Optionally, the hours to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`epidata_call`]
#' @return [`tibble`]
#' @keywords endpoint
#' @export
pub_wiki <- function(
Expand Down
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -82,7 +82,7 @@ Note that for the time being, the private endpoints (i.e. those prefixed with
`pvt`) will require a separate key that needs to be passed as an argument.

[mit-image]: https://img.shields.io/badge/License-MIT-yellow.svg
[mit-url]: https://opensource.org/license/mit
[mit-url]: https://opensource.org/license/mit/
[github-actions-image]: https://github.com/cmu-delphi/epidatr/workflows/ci/badge.svg
[github-actions-url]: https://github.com/cmu-delphi/epidatr/actions

Expand Down
20 changes: 19 additions & 1 deletion man/clear_cache.Rd
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4 changes: 2 additions & 2 deletions man/epidatr-package.Rd
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2 changes: 1 addition & 1 deletion man/pub_covid_hosp_facility.Rd
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2 changes: 1 addition & 1 deletion man/pub_covid_hosp_facility_lookup.Rd
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2 changes: 1 addition & 1 deletion man/pub_covid_hosp_state_timeseries.Rd
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2 changes: 1 addition & 1 deletion man/pub_covidcast.Rd
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