From 8b5599e696f1ecff93d8c651f27a02e2da8dd873 Mon Sep 17 00:00:00 2001 From: "Logan C. Brooks" Date: Thu, 6 Apr 2023 15:41:59 -0700 Subject: [PATCH 1/4] Re-`document()` --- man/covid_hosp_facility.Rd | 28 ++++++++++--------- man/covid_hosp_facility_lookup.Rd | 28 ++++++++++--------- man/covid_hosp_state_timeseries.Rd | 22 +++++++-------- man/covidcast.Rd | 41 +++++++++++++++------------- man/covidcast_meta.Rd | 16 ++++++----- man/create_epidata_call.Rd | 28 +++++++++++++++++++ man/delphi.Rd | 10 ++++--- man/dengue_nowcast.Rd | 12 +++++---- man/ecdc_ili.Rd | 24 ++++++++++------- man/epirange.Rd | 4 +-- man/flusurv.Rd | 23 +++++++++------- man/fluview.Rd | 43 ++++++++++++------------------ man/fluview_clinical.Rd | 15 ++++++----- man/fluview_meta.Rd | 4 +-- man/gft.Rd | 18 +++++++------ man/kcdc_ili.Rd | 18 ++++++++----- man/meta.Rd | 4 +-- man/nidss_dengue.Rd | 17 +++++++----- man/nidss_flu.Rd | 20 ++++++++------ man/nowcast.Rd | 18 +++++++------ man/paho_dengue.Rd | 16 ++++++----- man/pvt_afhsb.Rd | 16 ++++++----- man/pvt_cdc.Rd | 14 +++++----- man/pvt_dengue_sensors.Rd | 16 ++++++----- man/pvt_ght.Rd | 16 ++++++----- man/pvt_meta_afhsb.Rd | 6 ++--- man/pvt_meta_norostat.Rd | 6 ++--- man/pvt_norostat.Rd | 14 +++++----- man/pvt_quidel.Rd | 14 +++++----- man/pvt_sensors.Rd | 16 ++++++----- man/pvt_twitter.Rd | 16 ++++++----- man/wiki.Rd | 18 +++++++------ 32 files changed, 323 insertions(+), 238 deletions(-) create mode 100644 man/create_epidata_call.Rd diff --git a/man/covid_hosp_facility.Rd b/man/covid_hosp_facility.Rd index daa9813a..5f02a196 100644 --- a/man/covid_hosp_facility.Rd +++ b/man/covid_hosp_facility.Rd @@ -2,34 +2,38 @@ % Please edit documentation in R/endpoints.R \name{covid_hosp_facility} \alias{covid_hosp_facility} -\title{fetch COVID hospitalization data for specific facilities} +\title{Fetch COVID hospitalization data for specific facilities} \usage{ covid_hosp_facility(hospital_pks, collection_weeks, publication_dates = NULL) } \arguments{ -\item{hospital_pks}{A character string of facility unique identifiers} +\item{hospital_pks}{string. A character string of facility unique identifiers.} -\item{collection_weeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{collection_weeks}{\code{\link{epirange}}. Epiweeks to fetch.} -\item{publication_dates}{An optional epirange publication dates to fetch, using epirange(startdate,enddate).} +\item{publication_dates}{\code{\link{epirange}}. Publication dates to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} + +See also the official description and data dictionary at for more information. } \description{ -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. +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. } \details{ -Starting October 1, 2022, some facilities are only required to report annually. The companion function \code{\link[=covid_hosp_facility_lookup]{covid_hosp_facility_lookup()}} can be used to look up facility identifiers in a variety of ways. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility.html} + +Starting October 1, 2022, some facilities are only required to report annually. +The companion function \code{\link[=covid_hosp_facility_lookup]{covid_hosp_facility_lookup()}} can be used to look up facility identifiers +in a variety of ways. } \examples{ +\donttest{ call <- covid_hosp_facility(hospital_pks = "100075", collection_weeks = epirange(20200101, 20200501)) -fetch_csv(call) +fetch_tbl(call) } -\references{ -API documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility.html} - -See also the official description and data dictionary at for more information. } \seealso{ \code{\link[=covid_hosp_facility_lookup]{covid_hosp_facility_lookup()}}, \code{\link[=epirange]{epirange()}} diff --git a/man/covid_hosp_facility_lookup.Rd b/man/covid_hosp_facility_lookup.Rd index 28c3ee82..1d68073e 100644 --- a/man/covid_hosp_facility_lookup.Rd +++ b/man/covid_hosp_facility_lookup.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/endpoints.R \name{covid_hosp_facility_lookup} \alias{covid_hosp_facility_lookup} -\title{fetch COVID hospitalization facility identifiers} +\title{Fetch COVID hospitalization facility identifiers} \usage{ covid_hosp_facility_lookup( state = NULL, @@ -13,33 +13,35 @@ covid_hosp_facility_lookup( ) } \arguments{ -\item{state}{A two-letter character string state abbreviation.} +\item{state}{string. A two-letter character string state abbreviation.} -\item{ccn}{A character string for facility CMS certification number.} +\item{ccn}{string. A character string for facility CMS certification number.} -\item{city}{A characater string for city name.} +\item{city}{string. A characater string for city name.} -\item{zip}{A numeric 5-digit zip code.} +\item{zip}{string. A 5-digit zip code.} -\item{fips_code}{A numeric 5-digit fips county code.} +\item{fips_code}{string. A 5-digit fips county code, zero-padded.} } \value{ -an instance of epidata_call. +\code{\link{epidata_call}} } \description{ -Obtains unique identifiers and other metadata for COVID hospitalization facilities of interest. This is a companinon endpoint to the \code{\link[=covid_hosp_facility]{covid_hosp_facility()}} endpoint. +Obtains unique identifiers and other metadata for COVID hospitalization facilities of interest. +This is a companinon endpoint to the \code{\link[=covid_hosp_facility]{covid_hosp_facility()}} endpoint. } \details{ -Only one argument needs to be specified. Combinations of the arguments are not currently supported. For instance, specifying both city and state are not supported. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility_lookup.html} + +Only one argument needs to be specified. +Combinations of the arguments are not currently supported. +For instance, specifying both city and state are not supported. } \examples{ \donttest{ call <- covid_hosp_facility_lookup(state = "fl") -fetch_csv(call) -} +fetch_tbl(call) } -\references{ -API documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp_facility_lookup.html} } \seealso{ \code{\link[=covid_hosp_facility]{covid_hosp_facility()}} diff --git a/man/covid_hosp_state_timeseries.Rd b/man/covid_hosp_state_timeseries.Rd index 18a8c0f0..ca070816 100644 --- a/man/covid_hosp_state_timeseries.Rd +++ b/man/covid_hosp_state_timeseries.Rd @@ -7,29 +7,29 @@ covid_hosp_state_timeseries(states, dates, issues = NULL) } \arguments{ -\item{states}{A two letter character string state abbreviation.} +\item{states}{character vector. Two letter state abbreviations.} -\item{dates}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{dates}{\code{\link{epirange}}. Dates to fetch.} -\item{issues}{An optional parameter that takes the form YYYYMMDD. If issues is not specified, then the most recent issue is used by default.} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} + +See also the official description and data dictionary at for more information. } \description{ -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. +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. } \details{ +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp.html}. + Starting October 1, 2022, some facilities are only required to report annually. } \examples{ \donttest{ call <- covid_hosp_state_timeseries(states = "fl", dates = epirange(20200101, 20200501)) -fetch_csv(call) +fetch_tbl(call) } } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/covid_hosp.html}. - -See also the official description and data dictionary at for more information. -} diff --git a/man/covidcast.Rd b/man/covidcast.Rd index c4a58bb2..1781c19c 100644 --- a/man/covidcast.Rd +++ b/man/covidcast.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/endpoints.R \name{covidcast} \alias{covidcast} -\title{fetch covidcast data} +\title{Fetch covidcast data} \usage{ covidcast( data_source, @@ -17,31 +17,40 @@ covidcast( ) } \arguments{ -\item{data_source}{A character string representing a data source to query: (1) fb-survey; (2) jhu-csse; (3) google-symptoms; (4) doctor-visits; (5) quidel; (6) hhs. For more information about each data source, see \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_signals.html}.} +\item{data_source}{string. The data source to query (see: +\url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_signals.html}).} -\item{signals}{A character string representing signals from a specific source to query. A list of available signals for each data source can be found in \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals}. Each data source may have different signals.} +\item{signals}{string. The signals to query from a specific source (see: +\url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals}).} -\item{time_type}{Temporal resolution of the data. Most signals are available at time_type = "day" resolution. Some signals are only available at the time_type = "week" resolution.} +\item{time_type}{string. The temporal resolution of the data (either "day" or "week", depending on signal).} -\item{geo_type}{A character string that specifies geographic types: (1) county; (2) hrr, hospital referral region; (3) hhs; (4) msa, metropolitan statistical area; (5) dma, designated market areas; (6) state; (7) nation. See \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html} for details on which types are available for each data source.} +\item{geo_type}{string. The geographic resolution of the data (see: +\url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html}).} -\item{time_values}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{time_values}{\code{\link{epirange}}. The dates to fetch.} -\item{geo_values}{A character string that specified which geographies to return. "*" fetches all geographies. To fetch specific geographies, specify their IDs as a vector or a list of strings. More information can be found in \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html}.} +\item{geo_values}{character vector. The geographies to return. "*" fetches all. (See: +\url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html}.)} -\item{as_of}{data source to fetch} +\item{as_of}{\code{\link{epirange}}. Optionally, the as of date for the issues to fetech. If not specified, the most recent +data is returned. Mutually exclusive with \code{issues} or \code{lag}.} -\item{issues}{data source to fetch} +\item{issues}{\code{\link{epirange}}. Optionally, the issue of the data to fetch. If not specified, the most recent issue +is returned. Mutually exclusive with \code{as_of} or \code{lag}.} -\item{lag}{data source to fetch} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{as_of} or \code{issues}.} } \value{ -an instance of \code{epidata_call} +\code{\link{epidata_call}} } \description{ -fetch covidcast data +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html} +COVIDcast public dashboard: \url{https://delphi.cmu.edu/covidcast/} } \examples{ +\donttest{ call <- covidcast( data_source = "jhu-csse", signals = "confirmed_7dav_incidence_prop", @@ -50,14 +59,8 @@ call <- covidcast( time_values = epirange(20200601, 20200801), geo_values = "ca,fl" ) -fetch_csv(call) +fetch_tbl(call) } -\references{ -COVIDcast API documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html} - -Documentation for all COVIDcast sources and signals: \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals} - -COVIDcast public dashboard: \url{https://delphi.cmu.edu/covidcast/} } \seealso{ \code{\link[=covidcast_meta]{covidcast_meta()}}, \code{\link[=epirange]{epirange()}} diff --git a/man/covidcast_meta.Rd b/man/covidcast_meta.Rd index be9f1483..05c71751 100644 --- a/man/covidcast_meta.Rd +++ b/man/covidcast_meta.Rd @@ -2,23 +2,27 @@ % Please edit documentation in R/endpoints.R \name{covidcast_meta} \alias{covidcast_meta} -\title{fetch covidcast meta data} +\title{Fetch covidcast metadata} \usage{ covidcast_meta() } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ -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. +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. +} +\details{ +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_meta.html}. } \examples{ +\donttest{ call_meta <- covidcast_meta() fetch_classic(call_meta) - } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/covidcast_meta.html}. + } \seealso{ \code{\link[=covidcast]{covidcast()}} diff --git a/man/create_epidata_call.Rd b/man/create_epidata_call.Rd new file mode 100644 index 00000000..764f3aeb --- /dev/null +++ b/man/create_epidata_call.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/epidatacall.R +\name{create_epidata_call} +\alias{create_epidata_call} +\title{an abstraction that holds the information needed to make an epidata call} +\usage{ +create_epidata_call( + endpoint, + params, + meta = NULL, + only_supports_classic = FALSE +) +} +\arguments{ +\item{endpoint}{the epidata endpoint to call} + +\item{params}{the parameters to pass to the epidata endpoint} + +\item{meta}{meta data to attach to the epidata call} + +\item{only_supports_classic}{if true only classic format is supported} +} +\value{ +an epidata_call instance +} +\description{ +an abstraction that holds the information needed to make an epidata call +} diff --git a/man/delphi.Rd b/man/delphi.Rd index 18ac3691..7ca7e733 100644 --- a/man/delphi.Rd +++ b/man/delphi.Rd @@ -2,22 +2,24 @@ % Please edit documentation in R/endpoints.R \name{delphi} \alias{delphi} -\title{fetch Delphi's forecast} +\title{Fetch Delphi's ILINet forecasts} \usage{ delphi(system, epiweek) } \arguments{ -\item{system}{system to fetch} +\item{system}{string. The system name to fetch.} -\item{epiweek}{epiweek to fetch} +\item{epiweek}{\code{\link{epirange}}. The epiweeks to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/delphi.html } \examples{ +\donttest{ call <- delphi(system = "ec", epiweek = 202006) fetch_classic(call) } +} diff --git a/man/dengue_nowcast.Rd b/man/dengue_nowcast.Rd index f94dd32d..e2b20964 100644 --- a/man/dengue_nowcast.Rd +++ b/man/dengue_nowcast.Rd @@ -2,25 +2,27 @@ % Please edit documentation in R/endpoints.R \name{dengue_nowcast} \alias{dengue_nowcast} -\title{fetch Delphi's PAHO Dengue nowcast} +\title{Fetch Delphi's PAHO Dengue nowcast} \usage{ dengue_nowcast(locations, epiweeks) } \arguments{ -\item{locations}{locations to fetch} +\item{locations}{character vector. The locations to fetch.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/dengue_nowcast.html } \details{ -TODO: what are valid locations? +TODO: what are valid locations here? } \examples{ +\donttest{ call <- dengue_nowcast(locations = "?", epiweeks = epirange(201501, 202001)) fetch_classic(call) } +} diff --git a/man/ecdc_ili.Rd b/man/ecdc_ili.Rd index e66f0c07..cae05211 100644 --- a/man/ecdc_ili.Rd +++ b/man/ecdc_ili.Rd @@ -2,32 +2,36 @@ % Please edit documentation in R/endpoints.R \name{ecdc_ili} \alias{ecdc_ili} -\title{fetch ECDC data} +\title{Fetch ECDC data} \usage{ ecdc_ili(regions, epiweeks, issues = NULL, lag = NULL) } \arguments{ -\item{regions}{regions to fetch} +\item{regions}{character vector. The regions to fetch.} -\item{epiweeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} -\item{issues}{optionally specify the exact issues to fetch} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{optionally specify the issue lag} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ -Obtain information on influenza-like-illness from the European Center of Disease Control. +Obtain information on influenza-like-illness from the European Centre for Disease Prevention and Control. } \details{ -The list of location argument can be found in \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/ecdc_regions.txt}. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/ecdc_ili.html}. + +The list of location argument can be found in +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/ecdc_regions.txt}. } \examples{ +\donttest{ call <- ecdc_ili(regions = "austria", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/ecdc_ili.html}. } diff --git a/man/epirange.Rd b/man/epirange.Rd index 6dc9103b..5adf4f7e 100644 --- a/man/epirange.Rd +++ b/man/epirange.Rd @@ -7,9 +7,9 @@ epirange(from, to) } \arguments{ -\item{from}{A string or numeric that takes the form YYYYMMDD.} +\item{from}{A string or numeric that takes the form YYYYMMDD for dates or YYYYMM for epiweeks.} -\item{to}{A string or numeric that takes the form YYYYMMDD.} +\item{to}{A string or numeric that takes the form YYYYMMDD for dates or YYYYMM for epiweeks.} } \value{ EpiRange instance diff --git a/man/flusurv.Rd b/man/flusurv.Rd index 9d2a24e8..4767d2a3 100644 --- a/man/flusurv.Rd +++ b/man/flusurv.Rd @@ -2,32 +2,37 @@ % Please edit documentation in R/endpoints.R \name{flusurv} \alias{flusurv} -\title{fetch FluSurv virological data} +\title{Fetch FluSurv hospitalization data} \usage{ flusurv(locations, epiweeks, issues = NULL, lag = NULL) } \arguments{ -\item{locations}{A character string indicating location.} +\item{locations}{character vector. Character strings indicating location.} -\item{epiweeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} -\item{issues}{optionally specify the exact issues to fetch} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{optionally specify the issue lag} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ Obtain information on flu hospitalization rates from the Center of Disease Control. } \details{ -The list of location argument can be found in \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/flusurv_locations.txt}. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/flusurv.html}. +See also \url{https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html}. + +The list of location argument can be found in +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/flusurv_locations.txt}. } \examples{ +\donttest{ call <- flusurv(locations = "CA", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/flusurv.html}. See also \url{https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html}. } diff --git a/man/fluview.Rd b/man/fluview.Rd index 9b812476..9decdc8c 100644 --- a/man/fluview.Rd +++ b/man/fluview.Rd @@ -2,49 +2,40 @@ % Please edit documentation in R/endpoints.R \name{fluview} \alias{fluview} -\title{Obtains information on outpatient inluenza-like-illness (ILI) from Delphi's epidemiological data} +\title{Fetch FluView data} \usage{ fluview(regions, epiweeks, issues = NULL, lag = NULL, auth = NULL) } \arguments{ -\item{regions}{a character string that indicates a location such as national, HHS region, census division, most states and territories, and etc.} +\item{regions}{character vector. The locations to fetch. Can we any string IDs in national, HHS region, +census division, most states and territories, and so on. Full list link below.} -\item{epiweeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch in the form epirange(startweek,endweek), where startweek +and endweek are of the form YYYYWW (string or numeric).} -\item{issues}{an optional parameter that takes the form YYYYMMDD specifying the exact issues to fetch.} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{optionally specify the issue lag} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} -\item{auth}{optional authentication} - -\item{locations}{a character string that indicates a location such as national, HHS region, census division, most states and territories, and etc.} - -\item{Takes}{in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{auth}{string. Optionally, your authentication token.} } \value{ -an instance of epidata_call - -an instance of epidata_call +\code{\link{epidata_call}} } \description{ -Obtains information on outpatient inluenza-like-illness (ILI) from Delphi's epidemiological data +Obtains information on outpatient inluenza-like-illness (ILI) from U.S. Outpatient Influenza-like Illness Surveillance +Network (ILINet). } \details{ -The full list of location inputs can be accsssed at \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/src/acquisition/fluview/fluview_locations.py}. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/fluview.html}. +For more information on ILINet, see \url{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html}. -The full list of location inputs can be accsssed at \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/src/acquisition/fluview/fluview_locations.py}. +The full list of location inputs can be accsssed at +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/src/acquisition/fluview/fluview_locations.py}. } \examples{ -call <- nowcast(location = "ca", epiweeks = epirange(201201, 202001)) -fetch_classic(call) call <- fluview(regions = "nat", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/nowcast.html}. -fetch fluview data - -Obtains information on outpatient inluenza-like-illness (ILI) from U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). - -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/fluview.html}. For more information on ILINet, see \url{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html}. -} diff --git a/man/fluview_clinical.Rd b/man/fluview_clinical.Rd index e7fc38dd..fba10898 100644 --- a/man/fluview_clinical.Rd +++ b/man/fluview_clinical.Rd @@ -2,21 +2,24 @@ % Please edit documentation in R/endpoints.R \name{fluview_clinical} \alias{fluview_clinical} -\title{fetch FluView virological data} +\title{Fetch FluView virological data from clinical labs} \usage{ fluview_clinical(regions, epiweeks, issues = NULL, lag = NULL) } \arguments{ -\item{regions}{regions to fetch} +\item{regions}{character vector. The regions to fetch.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch in the form epirange(startweek,endweek), where startweek +and endweek are of the form YYYYWW (string or numeric).} -\item{issues}{optionally specify the exact issues to fetch} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{optionally specify the issue lag} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/fluview_clinical.html diff --git a/man/fluview_meta.Rd b/man/fluview_meta.Rd index 6d00edf5..0cd8eaba 100644 --- a/man/fluview_meta.Rd +++ b/man/fluview_meta.Rd @@ -2,12 +2,12 @@ % Please edit documentation in R/endpoints.R \name{fluview_meta} \alias{fluview_meta} -\title{fetch fluview meta data} +\title{Fetch FluView metadata} \usage{ fluview_meta() } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/fluview_meta.html diff --git a/man/gft.Rd b/man/gft.Rd index bb3c66fb..1da80988 100644 --- a/man/gft.Rd +++ b/man/gft.Rd @@ -2,28 +2,30 @@ % Please edit documentation in R/endpoints.R \name{gft} \alias{gft} -\title{fetch Google Flu Trends data} +\title{Fetch Google Flu Trends data} \usage{ gft(locations, epiweeks) } \arguments{ -\item{locations}{A character string that specifies a location to be fetched.} +\item{locations}{character vector. The locations to be fetched.} -\item{epiweeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}} The epiweeks to be fetched.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ Obtains estimates of inluenza activity based on volume of certain search queries from Google. } \details{ -Google has discontinues Flu Trends, and this is now a static endpoint. Possibile input for locations can be found in \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt}, \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt}, and \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/cities.txt}. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/gft.html} + +Google has discontinued Flu Trends and this is now a static endpoint. Possibile input for locations +can be found in \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/regions.txt}, +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/states.txt}, and +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/cities.txt}. } \examples{ call <- gft(locations = "hhs1", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/gft.html} -} diff --git a/man/kcdc_ili.Rd b/man/kcdc_ili.Rd index 2f745915..8eb74b24 100644 --- a/man/kcdc_ili.Rd +++ b/man/kcdc_ili.Rd @@ -2,21 +2,23 @@ % Please edit documentation in R/endpoints.R \name{kcdc_ili} \alias{kcdc_ili} -\title{fetch KCDC data} +\title{Fetch KCDC data} \usage{ kcdc_ili(regions, epiweeks, issues = NULL, lag = NULL) } \arguments{ -\item{regions}{regions to fetch} +\item{regions}{character vector. The regions to be fetched.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to be fetched.} -\item{issues}{optionally specify the exact issues to fetch} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{optionally specify the issue lag} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/kcdc_ili.html @@ -25,6 +27,8 @@ API docs: https://cmu-delphi.github.io/delphi-epidata/api/kcdc_ili.html TODO: find a non-trivial region } \examples{ +\donttest{ call <- kcdc_ili(regions = "?", epiweeks = epirange(201201, 202001)) -fetch_csv(call) +fetch_tbl(call) +} } diff --git a/man/meta.Rd b/man/meta.Rd index f1483002..ee64d90c 100644 --- a/man/meta.Rd +++ b/man/meta.Rd @@ -2,12 +2,12 @@ % Please edit documentation in R/endpoints.R \name{meta} \alias{meta} -\title{fetch api meta data} +\title{Fetch api metadata} \usage{ meta() } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/meta.html diff --git a/man/nidss_dengue.Rd b/man/nidss_dengue.Rd index fcd3feeb..5bdb0035 100644 --- a/man/nidss_dengue.Rd +++ b/man/nidss_dengue.Rd @@ -2,28 +2,31 @@ % Please edit documentation in R/endpoints.R \name{nidss_dengue} \alias{nidss_dengue} -\title{fetch NIDSS dengue data} +\title{Fetch NIDSS dengue data} \usage{ nidss_dengue(locations, epiweeks) } \arguments{ -\item{locations}{A character string that indicates region of interest or location of interest. Possible inputs include but are not limited to (1) nationwide, (2) central, (3) eastern, (4) kaoping, (5) northern, (6) southern, and (7) taipei.} +\item{locations}{character vector. The locations to fetch.} -\item{epiweeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetched.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ Obtains counts of confirmed dengue cases in Taiwan from Taiwan National Infectious Disease Statistical System. } \details{ -Possible location inputs can be found in \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt} and \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_locations.txt}. +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/nidss_dengue.html} + +Possible location inputs can be found in +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_regions.txt} and +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/labels/nidss_locations.txt}. } \examples{ +\donttest{ call <- nidss_dengue(locations = "taipei", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/nidss_dengue.html} } diff --git a/man/nidss_flu.Rd b/man/nidss_flu.Rd index 989957ac..aa9215a9 100644 --- a/man/nidss_flu.Rd +++ b/man/nidss_flu.Rd @@ -2,29 +2,33 @@ % Please edit documentation in R/endpoints.R \name{nidss_flu} \alias{nidss_flu} -\title{fetch NIDSS flu data} +\title{Fetch NIDSS flu data} \usage{ nidss_flu(regions, epiweeks, issues = NULL, lag = NULL) } \arguments{ -\item{regions}{regions to fetch} +\item{regions}{character vector. The regions to fetch.} -\item{epiweeks}{Takes in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} -\item{issues}{optional issues} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{optional lag} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ Obtains information on outpatient inluenza-like-illness from Taiwan National Infectious Disease Statistical System. } +\details{ +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/nidss_flu.html} +} \examples{ +\donttest{ call <- nidss_flu(regions = "taipei", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/nidss_flu.html} } diff --git a/man/nowcast.Rd b/man/nowcast.Rd index c6cfe22a..f951bae8 100644 --- a/man/nowcast.Rd +++ b/man/nowcast.Rd @@ -2,28 +2,30 @@ % Please edit documentation in R/endpoints.R \name{nowcast} \alias{nowcast} -\title{fetch Delphi's ILI nowcast} +\title{Fetch Delphi's ILI nowcast} \usage{ nowcast(locations, epiweeks) } \arguments{ -\item{locations}{a character string that indicates a location such as national, HHS region, census division, most states and territories, and etc.} +\item{locations}{character vector. The locations to fetch.} -\item{Takes}{in the form epirange(startdate,enddate), where startdate and enddate are of the form YYYYMMDD (can be passed as string or numeric).} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ -Obtains information on outpatient inluenza-like-illness (ILI) from Delphi's epidemiological data +API docs: \url{https://cmu-delphi.github.io/delphi-epidata/api/nowcast.html}. } \details{ -The full list of location inputs can be accsssed at \url{https://github.com/cmu-delphi/delphi-epidata/blob/main/src/acquisition/fluview/fluview_locations.py}. +Obtains information on outpatient inluenza-like-illness (ILI) from Delphi's epidemiological data + +The full list of location inputs can be accsssed at +\url{https://github.com/cmu-delphi/delphi-epidata/blob/main/src/acquisition/fluview/fluview_locations.py}. } \examples{ +\donttest{ call <- nowcast(location = "ca", epiweeks = epirange(201201, 202001)) fetch_classic(call) } -\references{ -API Documentation: \url{https://cmu-delphi.github.io/delphi-epidata/api/nowcast.html}. } diff --git a/man/paho_dengue.Rd b/man/paho_dengue.Rd index 1525eae2..7faee859 100644 --- a/man/paho_dengue.Rd +++ b/man/paho_dengue.Rd @@ -2,26 +2,30 @@ % Please edit documentation in R/endpoints.R \name{paho_dengue} \alias{paho_dengue} -\title{fetch Paho Dengue} +\title{Fetch PAHO Dengue} \usage{ paho_dengue(regions, epiweeks, issues = NULL, lag = NULL) } \arguments{ -\item{regions}{regions to fetch} +\item{regions}{character vector. The regions to fetch.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} -\item{issues}{issues to fetch} +\item{issues}{\code{\link{epirange}}. Optionally, the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{lag}.} -\item{lag}{lag to fetch} +\item{lag}{integer. Optionally, the lag of the issues to fetch. If not set, the most recent issue is returned. +Mutually exclusive with \code{issues}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/paho_dengue.html } \examples{ +\donttest{ call <- paho_dengue(regions = "ca", epiweeks = epirange(201201, 202001)) fetch_classic(call) } +} diff --git a/man/pvt_afhsb.Rd b/man/pvt_afhsb.Rd index 76c76067..4d2251ea 100644 --- a/man/pvt_afhsb.Rd +++ b/man/pvt_afhsb.Rd @@ -2,26 +2,28 @@ % Please edit documentation in R/endpoints.R \name{pvt_afhsb} \alias{pvt_afhsb} -\title{fetch AFHSB data (point data, no min/max)} +\title{Fetch AFHSB data (point data, no min/max)} \usage{ pvt_afhsb(auth, locations, epiweeks, flu_types) } \arguments{ -\item{auth}{character authentication token} +\item{auth}{string. Authentication token.} -\item{locations}{character locations to fetch} +\item{locations}{character vector. Locations to fetch (see docs).} -\item{epiweeks}{epirange epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. Epiweeks to fetch.} -\item{flu_types}{character flu_types to fetch} +\item{flu_types}{string. Flu types to fetch (see docs).} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/afhsb.html } \examples{ +\donttest{ call <- pvt_afhsb(auth = "yourkey", "fl,ca", epirange(202001, 202110), "flu1,flu2-flu1") -# fetch_csv(call) +fetch_tbl(call) +} } diff --git a/man/pvt_cdc.Rd b/man/pvt_cdc.Rd index 653edade..07482b6c 100644 --- a/man/pvt_cdc.Rd +++ b/man/pvt_cdc.Rd @@ -2,24 +2,26 @@ % Please edit documentation in R/endpoints.R \name{pvt_cdc} \alias{pvt_cdc} -\title{fetch CDC page hits} +\title{Fetch CDC page hits} \usage{ pvt_cdc(auth, epiweeks, locations) } \arguments{ -\item{auth}{character authentication token} +\item{auth}{string. Authentication token.} -\item{epiweeks}{epirange epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. Epiweeks to fetch.} -\item{locations}{character locations to fetch} +\item{locations}{character vector. Locations to fetch (see docs).} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/cdc.html } \examples{ +\donttest{ call <- pvt_cdc(auth = "yourkey", epirange(20210101, 20210201), "fl,ca") -# fetch_csv(call) +fetch_tbl(call) +} } diff --git a/man/pvt_dengue_sensors.Rd b/man/pvt_dengue_sensors.Rd index dac8a4c7..953890ad 100644 --- a/man/pvt_dengue_sensors.Rd +++ b/man/pvt_dengue_sensors.Rd @@ -2,21 +2,21 @@ % Please edit documentation in R/endpoints.R \name{pvt_dengue_sensors} \alias{pvt_dengue_sensors} -\title{fetch Delphi's digital surveillance sensors} +\title{Fetch Delphi's digital surveillance sensors for dengue in PAHO member countries} \usage{ pvt_dengue_sensors(auth, names, locations, epiweeks) } \arguments{ -\item{auth}{authenfication token} +\item{auth}{string. Your authentication token.} -\item{names}{names to fetch} +\item{names}{character vector. The list of names to fetch.} -\item{locations}{locations to fetch} +\item{locations}{character vector. The locations to fetch.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/dengue_sensors.html @@ -25,6 +25,8 @@ API docs: https://cmu-delphi.github.io/delphi-epidata/api/dengue_sensors.html TODO: what are valid locations and names? } \examples{ +\donttest{ call <- pvt_dengue_sensors(auth = "yourkey", names = "?", locations = "?", epiweeks = epirange(201501, 202001)) -# fetch_classic(call) +fetch_classic(call) +} } diff --git a/man/pvt_ght.Rd b/man/pvt_ght.Rd index dd06355d..d39b78bd 100644 --- a/man/pvt_ght.Rd +++ b/man/pvt_ght.Rd @@ -2,21 +2,21 @@ % Please edit documentation in R/endpoints.R \name{pvt_ght} \alias{pvt_ght} -\title{fetch Google Health Trends data} +\title{Fetch Google Health Trends data} \usage{ pvt_ght(auth, locations, epiweeks, query) } \arguments{ -\item{auth}{autentification} +\item{auth}{string. Your authentication token.} -\item{locations}{locations to fetch} +\item{locations}{character vector. The locations to be fetched.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to be fetched.} -\item{query}{query} +\item{query}{string. The query to be fetched.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/ght.html @@ -25,6 +25,8 @@ API docs: https://cmu-delphi.github.io/delphi-epidata/api/ght.html TODO: find a non-trivial query } \examples{ +\donttest{ call <- pvt_ght(auth = "yourkey", locations = "ca", epiweeks = epirange(201201, 202001), query = "?") -# fetch_classic(call) +fetch_classic(call) +} } diff --git a/man/pvt_meta_afhsb.Rd b/man/pvt_meta_afhsb.Rd index dc673346..274815de 100644 --- a/man/pvt_meta_afhsb.Rd +++ b/man/pvt_meta_afhsb.Rd @@ -2,15 +2,15 @@ % Please edit documentation in R/endpoints.R \name{pvt_meta_afhsb} \alias{pvt_meta_afhsb} -\title{fetch AFHSB meta data} +\title{Fetch AFHSB metadata} \usage{ pvt_meta_afhsb(auth) } \arguments{ -\item{auth}{authenfication token} +\item{auth}{string. Your authentication token.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/meta_afhsb.html diff --git a/man/pvt_meta_norostat.Rd b/man/pvt_meta_norostat.Rd index 9176ff3c..188e9a5f 100644 --- a/man/pvt_meta_norostat.Rd +++ b/man/pvt_meta_norostat.Rd @@ -2,15 +2,15 @@ % Please edit documentation in R/endpoints.R \name{pvt_meta_norostat} \alias{pvt_meta_norostat} -\title{fetch NoroSTAT meta data} +\title{Fetch NoroSTAT metadata} \usage{ pvt_meta_norostat(auth) } \arguments{ -\item{auth}{authenfication token} +\item{auth}{string. Your authentication token.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/meta_norostat.html diff --git a/man/pvt_norostat.Rd b/man/pvt_norostat.Rd index f6e03aa1..4d01a831 100644 --- a/man/pvt_norostat.Rd +++ b/man/pvt_norostat.Rd @@ -2,28 +2,30 @@ % Please edit documentation in R/endpoints.R \name{pvt_norostat} \alias{pvt_norostat} -\title{fetch NoroSTAT data (point data, no min/max)} +\title{Fetch NoroSTAT data (point data, no min/max)} \usage{ pvt_norostat(auth, location, epiweeks) } \arguments{ -\item{auth}{authenfication token} +\item{auth}{string. Your authentication key.} -\item{location}{location to fetch} +\item{location}{character vector. The locations to fetch.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/norostat.html } \examples{ +\donttest{ call <- pvt_norostat( auth = "yourkey", location = "Minnesota, Ohio, Oregon, Tennessee, and Wisconsin", epiweeks = epirange(201201, 202001) ) -# fetch_classic(call) +fetch_classic(call) +} } diff --git a/man/pvt_quidel.Rd b/man/pvt_quidel.Rd index 393f2b8d..f2fbe4f5 100644 --- a/man/pvt_quidel.Rd +++ b/man/pvt_quidel.Rd @@ -2,24 +2,26 @@ % Please edit documentation in R/endpoints.R \name{pvt_quidel} \alias{pvt_quidel} -\title{fetch Quidel data} +\title{Fetch Quidel COVID-19 and influenza testing data} \usage{ pvt_quidel(auth, epiweeks, locations) } \arguments{ -\item{auth}{authenfication token} +\item{auth}{string. Your authentication key.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} -\item{locations}{locations to fetch} +\item{locations}{character vector. The locations to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/quidel.html } \examples{ +\donttest{ call <- pvt_quidel(auth = "yourkey", epiweeks = epirange(201201, 202001), locations = "hhs1") -# fetch_classic(call) +fetch_classic(call) +} } diff --git a/man/pvt_sensors.Rd b/man/pvt_sensors.Rd index fcc28c2c..961a6109 100644 --- a/man/pvt_sensors.Rd +++ b/man/pvt_sensors.Rd @@ -2,26 +2,28 @@ % Please edit documentation in R/endpoints.R \name{pvt_sensors} \alias{pvt_sensors} -\title{fetch Delphi's digital surveillance sensors} +\title{Fetch Delphi's digital surveillance sensors} \usage{ pvt_sensors(auth, names, locations, epiweeks) } \arguments{ -\item{auth}{authenfication token} +\item{auth}{string. Your authentication key.} -\item{names}{names to fetch} +\item{names}{character vector. The names of the sensors to fetch.} -\item{locations}{locations to fetch} +\item{locations}{character vector. The locations to fetch.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/sensors.html } \examples{ +\donttest{ call <- pvt_sensors(auth = "yourkey", names = "sar3", locations = "nat", epiweeks = epirange(201501, 202001)) -# fetch_classic(call) +fetch_classic(call) +} } diff --git a/man/pvt_twitter.Rd b/man/pvt_twitter.Rd index e437fd32..842c665b 100644 --- a/man/pvt_twitter.Rd +++ b/man/pvt_twitter.Rd @@ -2,26 +2,28 @@ % Please edit documentation in R/endpoints.R \name{pvt_twitter} \alias{pvt_twitter} -\title{fetch HealthTweets data} +\title{Fetch HealthTweets data} \usage{ pvt_twitter(auth, locations, dates = NULL, epiweeks = NULL) } \arguments{ -\item{auth}{autentification} +\item{auth}{string. Your authentication key.} -\item{locations}{locations to fetch} +\item{locations}{character vector. The locations to fetch.} -\item{dates}{epiweeks to fetch} +\item{dates}{\code{\link{epirange}}. The dates to fetch. Mutually exclusive with \code{epiweeks}.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch. Mutually exclusive with \code{dates}.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/twitter.html } \examples{ +\donttest{ call <- pvt_twitter(auth = "yourkey", locations = "CA", epiweeks = epirange(201501, 202001)) -# fetch_csv(call) +fetch_tbl(call) +} } diff --git a/man/wiki.Rd b/man/wiki.Rd index 2b73ffc5..c1d4a441 100644 --- a/man/wiki.Rd +++ b/man/wiki.Rd @@ -2,28 +2,30 @@ % Please edit documentation in R/endpoints.R \name{wiki} \alias{wiki} -\title{fetch Wikipedia access data} +\title{Fetch Wikipedia access data} \usage{ wiki(articles, dates = NULL, epiweeks = NULL, hours = NULL, language = "en") } \arguments{ -\item{articles}{articles to fetch} +\item{articles}{character vector. The articles to fetch.} -\item{dates}{dates to fetch} +\item{dates}{\code{\link{epirange}}. The dates to fetch. Mutually exclusive with \code{epiweeks}.} -\item{epiweeks}{epiweeks to fetch} +\item{epiweeks}{\code{\link{epirange}}. The epiweeks to fetch. Mutually exclusive with \code{dates}.} -\item{hours}{hours to fetch} +\item{hours}{integer. Optionally, the hours to fetch.} -\item{language}{language} +\item{language}{string. The language to fetch.} } \value{ -an instance of epidata_call +\code{\link{epidata_call}} } \description{ API docs: https://cmu-delphi.github.io/delphi-epidata/api/wiki.html } \examples{ +\donttest{ call <- wiki(articles = "avian_influenza", epiweeks = epirange(201501, 202001)) -fetch_csv(call) +fetch_tbl(call) +} } From 736d58aada943dddb5219fe7971923ae48f77030 Mon Sep 17 00:00:00 2001 From: "Logan C. Brooks" Date: Thu, 6 Apr 2023 15:43:15 -0700 Subject: [PATCH 2/4] Check for pkgdown failures on PRs to dev branch --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 087f0b05..847176d3 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -4,7 +4,7 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] + branches: [main, master, dev] release: types: [published] workflow_dispatch: From be1a03cad04f9e68df02c8888a8a14a28913aab3 Mon Sep 17 00:00:00 2001 From: "Logan C. Brooks" Date: Thu, 6 Apr 2023 15:43:39 -0700 Subject: [PATCH 3/4] Deploy pkgdown web site off of `dev` updates, not just `main` --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 847176d3..102631df 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -2,7 +2,7 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master] + branches: [main, master, dev] pull_request: branches: [main, master, dev] release: From f2e89bb3cc31eac62c0c5c0222dace8575fcde23 Mon Sep 17 00:00:00 2001 From: "Logan C. Brooks" Date: Thu, 6 Apr 2023 15:48:23 -0700 Subject: [PATCH 4/4] Add comments in CI files regarding changes from templates/samples --- .github/workflows/pkgdown.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 102631df..513d4b58 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -1,5 +1,8 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +# +# Edits from above workflow: also check pkgdown for PRs to `dev` branch, and +# update the documentation web site on pushes to `dev` branch. on: push: branches: [main, master, dev]