From b1917e9b1458f8f0d139c07362ede8efe25c3d93 Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Tue, 12 Dec 2023 17:45:42 -0500 Subject: [PATCH 1/4] fix endpt refs missing pub_, pvt_ prefixes --- R/cache.R | 4 ++-- R/endpoints.R | 13 +++++++------ R/epidatacall.R | 7 ++++--- man/covidcast_epidata.Rd | 3 +++ man/epidata_call.Rd | 7 ++++--- man/pub_fluview_meta.Rd | 1 - man/pvt_norostat.Rd | 4 ++-- man/pvt_sensors.Rd | 2 +- man/pvt_twitter.Rd | 5 +++-- man/set_cache.Rd | 4 ++-- 10 files changed, 28 insertions(+), 22 deletions(-) diff --git a/R/cache.R b/R/cache.R index d544d760..cd94c92b 100644 --- a/R/cache.R +++ b/R/cache.R @@ -34,7 +34,7 @@ cache_environ$epidatr_cache <- NULL #' specify either `issues` before a certain date, or `as_of` before a certain #' date will actually cache. For example the call #' ``` -#' covidcast( +#' pub_covidcast( #' source = "jhu-csse", #' signals = "confirmed_7dav_incidence_prop", #' geo_type = "state", @@ -46,7 +46,7 @@ cache_environ$epidatr_cache <- NULL #' *won't* cache, since it is possible for the cache to be invalidated by new #' releases with no warning. On the other hand, the call #' ``` -#' covidcast( +#' pub_covidcast( #' source = "jhu-csse", #' signals = "confirmed_7dav_incidence_prop", #' geo_type = "state", diff --git a/R/endpoints.R b/R/endpoints.R index 25f3ed2e..9043243d 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -1320,7 +1320,7 @@ pub_fluview_clinical <- function(regions, epiweeks, ..., issues = NULL, lag = NU #' Metadata for the FluView endpoint #' @description #' API docs: -#' Returns information about the fluview endpoint. +#' #' @examples #' \dontrun{ #' pub_fluview_meta() @@ -1712,8 +1712,8 @@ pub_nidss_flu <- function(regions, epiweeks, ..., issues = NULL, lag = NULL, fet #' #' API docs: #' -#' This is the documentation of the API for accessing the NoroSTAT (norostat) -#' endpoint of the Delphi’s epidemiological data. +#' This is the documentation of the API for accessing the NoroSTAT endpoint of +#' the Delphi’s epidemiological data. #' #' @examples #' \dontrun{ @@ -1887,7 +1887,7 @@ pvt_quidel <- function(auth, locations, epiweeks, fetch_args = fetch_args_list() #' API docs: #' #' This is the documentation of the API for accessing the Digital Surveillance -#' Sensors (sensors) endpoint of the Delphi’s epidemiological Note: this +#' Sensors endpoint of the Delphi’s epidemiological Note: this #' repository was built to support modeling and forecasting efforts #' surrounding seasonal influenza (and dengue). In the current COVID-19 #' pandemic, syndromic surveillance data, like ILI data (influenza-like @@ -1942,8 +1942,9 @@ pvt_sensors <- function(auth, names, locations, epiweeks, fetch_args = fetch_arg #' @description #' API docs: #' -#' This is the API documentation for accessing the Twitter Stream (twitter) endpoint of Delphi’s epidemiological data. -#' Sourced from [Healthtweets](http://www.healthtweets.org/) +#' This is the API documentation for accessing the Twitter Stream endpoint of +#' Delphi’s epidemiological data. Sourced from +#' [Healthtweets](http://www.healthtweets.org/) #' #' @examples #' \dontrun{ diff --git a/R/epidatacall.R b/R/epidatacall.R index dbf3fc23..625a377e 100644 --- a/R/epidatacall.R +++ b/R/epidatacall.R @@ -201,9 +201,10 @@ fetch_args_list <- function( #' Fetches the data #' #' @details -#' `fetch` usually returns the data in tibble format, but a few of the endpoints -#' only support the JSON classic format (delphi, pvt_meta_norostat, and meta). -#' In that case a JSON-like nested list structure is returned instead. +#' `fetch` usually returns the data in tibble format, but a few of the +#' endpoints only support the JSON classic format (`pub_delphi`, +#' `pvt_meta_norostat`, and `pub_meta`). In that case a +#' JSON-like nested list structure is returned instead. #' #' @rdname epidata_call #' @param epidata_call an instance of `epidata_call` diff --git a/man/covidcast_epidata.Rd b/man/covidcast_epidata.Rd index 2ca1d0cf..630904b8 100644 --- a/man/covidcast_epidata.Rd +++ b/man/covidcast_epidata.Rd @@ -26,6 +26,9 @@ The \code{covidcast_epidata()} function fetches a list of all signals, and retur an object containing fields for every signal: \if{html}{\out{
}}\preformatted{epidata <- covidcast_epidata() +#> Warning: No API key found. You will be limited to non-complex queries and encounter rate limits if you proceed. +#> i See `?save_api_key()` for details on obtaining and setting API keys. +#> This warning is displayed once every 8 hours. epidata$signals #> # A tibble: 443 x 3 #> source signal short_description diff --git a/man/epidata_call.Rd b/man/epidata_call.Rd index d0b62e73..c2ef4b6b 100644 --- a/man/epidata_call.Rd +++ b/man/epidata_call.Rd @@ -54,9 +54,10 @@ There are some other functions available for debugging and advanced usage: - \code{request_url} (for debugging): outputs the request URL from which data would be fetched (note additional parameters below) -\code{fetch} usually returns the data in tibble format, but a few of the endpoints -only support the JSON classic format (delphi, pvt_meta_norostat, and meta). -In that case a JSON-like nested list structure is returned instead. +\code{fetch} usually returns the data in tibble format, but a few of the +endpoints only support the JSON classic format (\code{pub_delphi}, +\code{pvt_meta_norostat}, and \code{pub_meta}). In that case a +JSON-like nested list structure is returned instead. } \examples{ \dontrun{ diff --git a/man/pub_fluview_meta.Rd b/man/pub_fluview_meta.Rd index 51e962b3..ab0c0b1a 100644 --- a/man/pub_fluview_meta.Rd +++ b/man/pub_fluview_meta.Rd @@ -14,7 +14,6 @@ pub_fluview_meta(fetch_args = fetch_args_list()) } \description{ API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/fluview_meta.html} -Returns information about the fluview endpoint. } \examples{ \dontrun{ diff --git a/man/pvt_norostat.Rd b/man/pvt_norostat.Rd index 8cf4ed10..837e16d8 100644 --- a/man/pvt_norostat.Rd +++ b/man/pvt_norostat.Rd @@ -23,8 +23,8 @@ This is point data only, and does not include minima or maxima. API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/norostat.html} -This is the documentation of the API for accessing the NoroSTAT (norostat) -endpoint of the Delphi’s epidemiological data. +This is the documentation of the API for accessing the NoroSTAT endpoint of +the Delphi’s epidemiological data. } \examples{ \dontrun{ diff --git a/man/pvt_sensors.Rd b/man/pvt_sensors.Rd index ec536fdf..f757b408 100644 --- a/man/pvt_sensors.Rd +++ b/man/pvt_sensors.Rd @@ -24,7 +24,7 @@ pvt_sensors(auth, names, locations, epiweeks, fetch_args = fetch_args_list()) API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/sensors.html} This is the documentation of the API for accessing the Digital Surveillance -Sensors (sensors) endpoint of the Delphi’s epidemiological Note: this +Sensors endpoint of the Delphi’s epidemiological Note: this repository was built to support modeling and forecasting efforts surrounding seasonal influenza (and dengue). In the current COVID-19 pandemic, syndromic surveillance data, like ILI data (influenza-like diff --git a/man/pvt_twitter.Rd b/man/pvt_twitter.Rd index 30763a74..ffee87b2 100644 --- a/man/pvt_twitter.Rd +++ b/man/pvt_twitter.Rd @@ -33,8 +33,9 @@ pvt_twitter( \description{ API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/twitter.html} -This is the API documentation for accessing the Twitter Stream (twitter) endpoint of Delphi’s epidemiological data. -Sourced from \href{http://www.healthtweets.org/}{Healthtweets} +This is the API documentation for accessing the Twitter Stream endpoint of +Delphi’s epidemiological data. Sourced from +\href{http://www.healthtweets.org/}{Healthtweets} } \examples{ \dontrun{ diff --git a/man/set_cache.Rd b/man/set_cache.Rd index 87c147f0..a3b42a1e 100644 --- a/man/set_cache.Rd +++ b/man/set_cache.Rd @@ -64,7 +64,7 @@ An important feature of the caching in this package is that only calls which specify either \code{issues} before a certain date, or \code{as_of} before a certain date will actually cache. For example the call -\if{html}{\out{
}}\preformatted{covidcast( +\if{html}{\out{
}}\preformatted{pub_covidcast( source = "jhu-csse", signals = "confirmed_7dav_incidence_prop", geo_type = "state", @@ -77,7 +77,7 @@ date will actually cache. For example the call \emph{won't} cache, since it is possible for the cache to be invalidated by new releases with no warning. On the other hand, the call -\if{html}{\out{
}}\preformatted{covidcast( +\if{html}{\out{
}}\preformatted{pub_covidcast( source = "jhu-csse", signals = "confirmed_7dav_incidence_prop", geo_type = "state", From 117bb84647883c1bf07d6ac6734c7c1a07fa5077 Mon Sep 17 00:00:00 2001 From: nmdefries Date: Tue, 12 Dec 2023 22:48:20 +0000 Subject: [PATCH 2/4] docs: document (GHA) --- man/covidcast_epidata.Rd | 3 --- 1 file changed, 3 deletions(-) diff --git a/man/covidcast_epidata.Rd b/man/covidcast_epidata.Rd index 630904b8..2ca1d0cf 100644 --- a/man/covidcast_epidata.Rd +++ b/man/covidcast_epidata.Rd @@ -26,9 +26,6 @@ The \code{covidcast_epidata()} function fetches a list of all signals, and retur an object containing fields for every signal: \if{html}{\out{
}}\preformatted{epidata <- covidcast_epidata() -#> Warning: No API key found. You will be limited to non-complex queries and encounter rate limits if you proceed. -#> i See `?save_api_key()` for details on obtaining and setting API keys. -#> This warning is displayed once every 8 hours. epidata$signals #> # A tibble: 443 x 3 #> source signal short_description From 439d18f398bc4106e562b49f2b090e99df648bfd Mon Sep 17 00:00:00 2001 From: nmdefries <42820733+nmdefries@users.noreply.github.com> Date: Tue, 12 Dec 2023 18:46:45 -0500 Subject: [PATCH 3/4] missing period Co-authored-by: Dmitry Shemetov --- R/endpoints.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/endpoints.R b/R/endpoints.R index 9043243d..ebc74fce 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -1887,7 +1887,7 @@ pvt_quidel <- function(auth, locations, epiweeks, fetch_args = fetch_args_list() #' API docs: #' #' This is the documentation of the API for accessing the Digital Surveillance -#' Sensors endpoint of the Delphi’s epidemiological Note: this +#' Sensors endpoint of the Delphi’s epidemiological. Note: this #' repository was built to support modeling and forecasting efforts #' surrounding seasonal influenza (and dengue). In the current COVID-19 #' pandemic, syndromic surveillance data, like ILI data (influenza-like From c7e95f67d0050301a03b31f9db2c8f225f5d4257 Mon Sep 17 00:00:00 2001 From: nmdefries Date: Tue, 12 Dec 2023 23:48:26 +0000 Subject: [PATCH 4/4] docs: document (GHA) --- man/pvt_sensors.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/pvt_sensors.Rd b/man/pvt_sensors.Rd index f757b408..24073803 100644 --- a/man/pvt_sensors.Rd +++ b/man/pvt_sensors.Rd @@ -24,7 +24,7 @@ pvt_sensors(auth, names, locations, epiweeks, fetch_args = fetch_args_list()) API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/sensors.html} This is the documentation of the API for accessing the Digital Surveillance -Sensors endpoint of the Delphi’s epidemiological Note: this +Sensors endpoint of the Delphi’s epidemiological. Note: this repository was built to support modeling and forecasting efforts surrounding seasonal influenza (and dengue). In the current COVID-19 pandemic, syndromic surveillance data, like ILI data (influenza-like