ex direct from database, title, * notes, Renviron

the delphi endpoint's fetch_classic output has been modified to just
names, since the full output is too long
Secrets moved to the .Reviron file.
Duplicate copy of Google Health Trends removed
various references fixed

Author: dsweber2

vignettes/endpoints.Rmd

@@ -1,10 +1,10 @@
 ---
-title: "COVIDcast API Client"
+title: "Endpoint Examples"
 author: "Delphi Group"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{COVIDcast API Client}
+  %\VignetteIndexEntry{Endpoint Examples}
   %\VignetteEngine{knitr::rmarkdown}
   \usepackage[utf8]{inputenc}
 ---
@@ -23,6 +23,7 @@ library("dplyr")
 ```
 
 The API endpoints, organized by data sources.
+Some endpoints allow for the use of `*` to access data at all locations. Check the help for a given endpoint to see if it supports `*`.
 
 ## COVIDcast Main Endpoint
 
@@ -59,6 +60,17 @@ covidcast(
 ) %>% fetch_tbl()
 ```
 County geo_values are [FIPS codes](https://en.wikipedia.org/wiki/List_of_United_States_FIPS_codes_by_county) and are discussed more here: <https://cmu-delphi.github.io/delphi-epidata/api/covidcast_geography.html>. The example above is for Orange County, California.
+Since `covidcast` is an endpoint which supports `*`, here is an example of its use:
+```{r}
+covidcast(
+  data_source = "fb-survey",
+  signals = "smoothed_accept_covid_vaccine",
+  geo_type = "county",
+  time_type = "day",
+  time_values = epirange(20201221, 20201225),
+  geo_values = "*"
+) %>% fetch_tbl()
+```
 
 ## Other Covid Endpoints
 
@@ -121,10 +133,10 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/delphi.html>
 Example call:
 
 ```{r}
-delphi(system = "ec", epiweek = 201501) %>% fetch_classic()
+del <- delphi(system = "ec", epiweek = 201501) %>% fetch_classic()
+names(del$epidata$forecast)
 ```
 
-
 ### FluSurv hospitalization data
 
 API docs: <https://cmu-delphi.github.io/delphi-epidata/api/flusurv.html>
@@ -170,8 +182,6 @@ Example call:
 fluview_meta() %>% fetch_tbl()
 ```
 
-TODO broken?
-
 ### Google Flu Trends data
 API docs: <https://cmu-delphi.github.io/delphi-epidata/api/gft.html>
 
@@ -186,9 +196,9 @@ API docs: <https://cmu-delphi.github.io/delphi-epidata/api/kcdc_ili.html>
 
 Function reference: <https://cmu-delphi.github.io/epidatr/reference/kcdc_ili.html>
 
-kcdc_ili(regions = "01", epiweeks = epirange(199001, 202301)) %>% fetch_tbl()
-TODO example is broken
-
+```{r}
+kcdc_ili(regions = "ROK", epiweeks = 200436) %>% fetch_tbl()
+```
 ### NIDSS Flu
 API docs: <https://cmu-delphi.github.io/delphi-epidata/api/nidss_flu.html>
 
@@ -237,9 +247,8 @@ API docs: <https://cmu-delphi.github.io/delphi-epidata/api/paho_dengue.html>
 Function reference: <https://cmu-delphi.github.io/epidatr/reference/paho_dengue.html>
 
 ```{r, eval=FALSE}
-paho_dengue(regions = "1", epiweeks = epirange(200201, 202319)) %>% fetch_tbl()
+paho_dengue(regions = "ca", epiweeks = epirange(200201, 202319)) %>% fetch_tbl()
 ```
-TODO this is disallowed (http 401)
 
 ## Other Endpoints
 ### Wikipedia Access
@@ -252,23 +261,20 @@ wiki(language = "en", articles = "influenza", epiweeks = epirange(202001, 202319
 ```
 # Private methods
 
-These require private access keys to use. To actually run these locally, if you have stored these secrets in `secrets.R` in the root directory of this project, first run
-```{r, eval=FALSE}
-source("../secrets.R")
-```
-Each source has it's own auth that it needs, which is the first argument.
+These require private access keys to use. To actually run these locally, you will need to store these secrets in your `.Reviron` file, or set them as environmental variables.
 
 ### AFHSB metadata
 
-API docs: <https://cmu-delphi.github.io/delphi-epidata/api/ght.html>
+API docs: <https://cmu-delphi.github.io/delphi-epidata/api/meta_afhsb.html>
 
-Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_ght.html>
+Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_meta_afhsb.html>
 
 Example call:
 ```{r, eval=FALSE}
-pvt_afhsb_meta(auth = SECRET_API_AUTH_AFHSB) %>% fetch_classic()
+pvt_meta_afhsb(auth = Sys.getenv("SECRET_API_AUTH_AFHSB")) %>% fetch_classic()
 ```
 TODO internal server error
+not on the server I was given access to
 
 ### AFHSB data
 
@@ -279,10 +285,11 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_afhsb.ht
 Example call:
 
 ```{r, eval=FALSE}
-pvt_afhsb(auth = SECRET_API_AUTH_AFHSB, locations = "mn", epiweeks = epirange(202002, 202110), flu_types = "flu1") %>% fetch_tbl()
+pvt_afhsb(auth = Sys.getenv("SECRET_API_AUTH_AFHSB"), locations = "mn", epiweeks = epirange(202002, 202110), flu_types = "flu1") %>% fetch_tbl()
 ```
 
 TODO 500 internal server error
+not on the server I was given access to
 
 ### CDC
 
@@ -292,7 +299,7 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_cdc.html
 
 Example call:
 ```{r, eval=FALSE}
-pvt_cdc(auth = SECRET_API_AUTH_CDC, epiweeks = epirange(202003, 20234), locations = "ma") %>% fetch_tbl()
+pvt_cdc(auth = Sys.getenv("SECRET_API_AUTH_CDC"), epiweeks = epirange(202003, 202304), locations = "ma") %>% fetch_tbl()
 ```
 
 ### Dengue Digital Surveillance Sensors
@@ -304,9 +311,8 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/dengue_senso
 Example call:
 
 ```{r, eval=FALSE}
-pvt_dengue_sensors(auth = SECRET_API_SENSORS, names = ) %>% fetch_tbl()
+pvt_dengue_sensors(auth = Sys.getenv("SECRET_API_AUTH_SENSORS"), names = "ght", locations = "ag", epiweeks = epirange(201404, 202004)) %>% fetch_tbl()
 ```
-TODO not in the reference docs either...
 
 ### Google Health Trends
 
@@ -316,18 +322,7 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_ght.html
 
 Example call:
 ```{r, eval=FALSE}
-pvt_ght(auth = SECRET_API_AUTH_CDC, epiweeks = epirange(202003, 20234), locations = "ma") %>% fetch_tbl()
-```
-
-### Google Health Trends
-
-API docs: <https://cmu-delphi.github.io/delphi-epidata/api/ght.html>
-
-Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_ght.html>
-
-Example call:
-```{r, eval=FALSE}
-pvt_ght(auth = SECRET_API_AUTH_CDC, epiweeks = epirange(202003, 20234), locations = "ma") %>% fetch_tbl()
+pvt_ght(auth = Sys.getenv("SECRET_API_AUTH_GHT"), epiweeks = epirange(199301, 202304), locations = "ma", query = "how to get over the flu") %>% fetch_tbl()
 ```
 
 ### NoroSTAT metadata
@@ -338,18 +333,18 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_meta_nor
 
 Example call:
 ```{r, eval=FALSE}
-pvt_meta_norostat(auth = SECRET_API_AUTH_NOROSTAT) %>% fetch_classic()
+pvt_meta_norostat(auth = Sys.getenv("SECRET_API_AUTH_NOROSTAT")) %>% fetch_classic()
 ```
 
-### NoroSTAT NoroSTAT data
+### NoroSTAT data
 
 API docs: <https://cmu-delphi.github.io/delphi-epidata/api/norostat.html>
 
 Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_norostat.html>
 
 Example call:
 ```{r, eval=FALSE}
-pvt_norostat(auth = SECRET_API_AUTH_NOROSTAT, locations = "mn", epiweeks = epirange(201301, 202105)) %>% fetch_tbl()
+pvt_norostat(auth = Sys.getenv("SECRET_API_AUTH_NOROSTAT"), locations = "ma", epiweeks = epirange(199001, 202105)) %>% fetch_classic()
 ```
 TODO can't seem to get a relevant sample, the example in the reference section is borked.
 
@@ -361,7 +356,7 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_quidel.h
 
 Example call:
 ```{r, eval=FALSE}
-pvt_quidel(auth = SECRET_API_AUTH_QUIDEL, locations = "hhs1", epiweeks = epirange(200301, 202105)) %>% fetch_tbl()
+pvt_quidel(auth = Sys.getenv("SECRET_API_AUTH_QUIDEL"), locations = "hhs1", epiweeks = epirange(200301, 202105)) %>% fetch_tbl()
 ```
 
 ### Sensors
@@ -372,16 +367,16 @@ Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_sensors.
 
 Example call:
 ```{r, eval=FALSE}
-pvt_sensors(auth = SECRET_API_AUTH_SENSORS, names = "sar3", locations = "nat", epiweeks = epirange(200301, 202105)) %>% fetch_tbl()
+pvt_sensors(auth = Sys.getenv("SECRET_API_AUTH_SENSORS"), names = "sar3", locations = "nat", epiweeks = epirange(200301, 202105)) %>% fetch_tbl()
 ```
 
 ### Twitter
 
-API docs: <https://cmu-delphi.github.io/delphi-epidata/api/sensors.html>
+API docs: <https://cmu-delphi.github.io/delphi-epidata/api/twitter.html>
 
-Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_sensors.html>
+Function reference: <https://cmu-delphi.github.io/epidatr/reference/pvt_twitter.html>
 
 Example call:
 ```{r, eval=FALSE}
-pvt_twitter(auth = SECRET_API_AUTH_TWITTER, locations = "nat", epiweeks = epirange(200301, 202105)) %>% fetch_tbl()
+pvt_twitter(auth = Sys.getenv("SECRET_API_AUTH_TWITTER"), locations = "nat", epiweeks = epirange(200301, 202105)) %>% fetch_tbl()
 ```