fix: Ensure that all examples work; added example_pat_epa

DESCRIPTION

@@ -1,6 +1,6 @@
 Type: Package
 Package: AirSensor2
-Version: 0.5.3
+Version: 0.5.4
 Title: Process and Display Data from Air Quality Sensors
 Authors@R: c(
     person("Jonathan", "Callahan", email="[email protected]", role=c("aut","cre"))
@@ -38,7 +38,8 @@ Suggests:
     markdown,
     testthat (>= 2.1.0),
     rmarkdown,
-    roxygen2
+    roxygen2,
+    webshot
 Encoding: UTF-8
 Language: en-US
 LazyData: true

NEWS.md

@@ -1,3 +1,13 @@
+# AirSensor2 0.5.4
+
+- Updated various examples that referenced `example_pas` with the newer
+`example_pas_pm25`.
+- Added `example_pat_epa` with fields required to run `pat_applyCorrection()`.
+- Fixed the bug in `pat_create()` that generated:
+```
+Elements `last_modified`, `privacy`, `model`, `hardware`, `firmware_version`, etc. don't exist.
+```
+
 # AirSensor2 0.5.3
 
 Updated all Clarity functions to default to `format = "USFS2"` which returns

R/AirSensor2.R → R/AirSensor2-package.R

@@ -1,5 +1,6 @@
-#'
-#' @docType package
+#' @keywords internal
+"_PACKAGE"
+
 #' @name AirSensor2
 #' @title Air Quality Data Analysis for low-cost Sensors
 #' @description

R/data.R

@@ -1,7 +1,7 @@
 #' @encoding UTF-8
 #' @title Example raw PurpleAir Synoptic dataset
 #' @format A tibble with 39 rows and 18 columns of data.
-#' @description The \code{example_pas_raw} dataset provides a quickly loadable
+#' @description The \code{example_pas_pm25_raw} dataset provides a quickly loadable
 #' version of raw PurpleAir synoptic data for practicing and code examples
 #' This dataset contains data for sensors in a box around the Methow Valley
 #' in Washington state and was generated on 2024-03-12 by running:
@@ -48,8 +48,11 @@
 #' @encoding UTF-8
 #' @title Example enhanced PurpleAir Synoptic dataset
 #' @format A tibble with 2287 rows and 33 columns of data.
-#' @description The \code{example_pas} dataset provides a quickly loadable
-#' version of a \emph{pas} object for practicing and code examples.
+#' @description The \code{example_pas_pm25} dataset provides a quickly loadable
+#' version of a \emph{pas} object for practicing and code examples. This
+#' object contains metadata appropriate for generating \emph{pat} objects
+#' with \link{pat_create}.
+#'
 #' This dataset contains data for sensors in Washington and Oregon
 #' and was generated on 2024-03-12 by running:
 #'
@@ -84,8 +87,11 @@
 #' @encoding UTF-8
 #' @title Example enhanced PurpleAir Synoptic dataset
 #' @format A tibble with 122 rows and 22 columns of data.
-#' @description The \code{example_pas} dataset provides a quickly loadable
-#' version of a \emph{pas} object for practicing and code examples.
+#' @description The \code{example_pas_historical} dataset provides a quickly loadable
+#' version of a \emph{pas} object for practicing and code examples. This
+#' object contains fewer metadata fields than other \code{example_pas_~} objects
+#' and is intended for use with \link{pas_lifespanPlot}.
+#'
 #' This dataset contains data for sensors in Washington and Oregon
 #' and was generated on 2024-03-12 by running:
 #'
@@ -119,8 +125,10 @@
 #' @encoding UTF-8
 #' @title Example enhanced PurpleAir Synoptic dataset
 #' @format A tibble with 122 rows and 31 columns of data.
-#' @description The \code{example_pas} dataset provides a quickly loadable
-#' version of a \emph{pas} object for practicing and code examples.
+#' @description The \code{example_pas_metadata} dataset provides a quickly loadable
+#' version of a \emph{pas} object for practicing and code examples. This
+#' object contains more metadata than other \code{example_pas_~} objects.
+#'
 #' This dataset contains data for sensors in Washington and Oregon
 #' and was generated on 2024-03-12 by running:
 #'
@@ -179,8 +187,46 @@
 #' save(example_pat, file = "data/example_pat.rda")
 #' #' }
 #'
-#' @seealso example_pas
+#' @seealso example_pas_metadata
 #' @source https://www2.purpleair.com
 "example_pat"
 
 
+#' @encoding UTF-8
+#' @title Example PurpleAir Timeseries dataset with EPA fields
+#' @format A list containing two tibbles named 'meta' and 'data'.
+#' @description The \code{example_pat} dataset provides a quickly loadable
+#' version of a \emph{pat} object for practicing and code examples. This
+#' \emph{pat} object contains the `pm2.5_cf` fields required for the EPA
+#' correction algorithm used in \link{pat_applyCorrection}.
+#'
+#' This dataset contains 24 hours worth of data for a single PurpleAir sensor
+#' and was generated on 2024-10-30 by running:
+#'
+#' \preformatted{
+#' library(AirSensor2)
+#'
+#' source("global_vars.R") # contains PurpleAir_API_READ_KEY
+#'
+#' example_pat_epa <-
+#'   pat_create(
+#'     api_key = PurpleAir_API_READ_KEY,
+#'     pas = example_pas_metadata,
+#'     sensor_index = "95189",
+#'     startdate = "2024-03-01",
+#'     enddate = "2024-03-03",
+#'     timezone = "America/Los_Angeles",
+#'     average = 0,
+#'     fields = PurpleAir_PAT_EPA_HOURLY_FIELDS
+#'   )
+#'
+#' save(example_pat_epa, file = "data/example_pat_epa.rda")
+#' #' }
+#'
+#' @seealso example_pas_metadata
+#' @source https://www2.purpleair.com
+"example_pat_epa"
+
+
+
+

R/pas_createNew.R

@@ -98,7 +98,9 @@
 #'     location_type = 0
 #'   )
 #'
-#' pas %>% pas_leaflet()
+#' if ( interactive() ) {
+#'   pas %>% pas_leaflet()
+#' }
 #'
 #' }, silent = FALSE)
 #' }

R/pas_filterNearMonitor.R

@@ -141,11 +141,5 @@ pas_filterNearMonitor <- function(
 
 if ( FALSE ) {
 
-  library(AirMonitor)
-
-  pas <- example_pas %>% pas_filter(countyName == "Okanogan")
-  monitor <- NW_Megafires %>% monitor_filter(countyName == "Okanogan")
-  radius <- "1 km"
-
 
 }

R/pas_leaflet.R

@@ -59,11 +59,11 @@
 #' library(AirSensor2)
 #'
 #' if ( interactive() ) {
-#'   pas_leaflet(example_pas, parameter = "pm2.5_60minute")
+#'   pas_leaflet(example_pas_pm25, parameter = "pm2.5_60minute")
 #'
-#'   pas_leaflet(example_pas, parameter = "temperature")
+#'   pas_leaflet(example_pas_pm25, parameter = "temperature")
 #'
-#'   pas_leaflet(example_pas, parameter = "humidity")
+#'   pas_leaflet(example_pas_pm25, parameter = "humidity")
 #' }
 
 pas_leaflet <- function(

R/pat_applyCorrection.R

@@ -93,7 +93,7 @@ pat_applyCorrection <- function(
 if ( FALSE ) {
 
   api_key = PurpleAir_API_READ_KEY
-  pas = example_pas
+  pas = example_pas_pm25
   sensor_index = "76545"
   startdate = "2023-01-01"
   enddate = "2023-01-08"

R/pat_create.R

@@ -64,7 +64,7 @@
 #' # Create a pat object
 #' pat <-
 #'   pat_create(
-#'     pas = example_pas,
+#'     pas = example_pas_pm25,
 #'     sensor_index = "76545",
 #'     startdate = "2023-01-01",
 #'     enddate = "2023-01-03",
@@ -76,7 +76,7 @@
 #' # Run data download in parallel (faster)
 #' pat <-
 #'   pat_create(
-#'     pas = example_pas,
+#'     pas = example_pas_pm25,
 #'     sensor_index = "76545",
 #'     startdate = "2023-01-01",
 #'     enddate = "2023-01-03",
@@ -338,9 +338,14 @@ pat_create <- function(
       "sensorManufacturer"
     )
 
+  # NOTE:  Typically, the following names will not be found in pas_single:
+  # NOTE:    last_modified, model, hardware, firmware_version, firmware_upgrade
+  available_metaNames <-
+    intersect(names(pas_single), pat_metaNames)
+
   meta <-
     pas_single %>%
-    dplyr::select(dplyr::all_of(pat_metaNames))
+    dplyr::select(dplyr::all_of(available_metaNames))
 
   # TODO:  This step can be removed when AirMonitor gets upgraded to replace
   # TODO:  'zip' with 'postalCode'.
@@ -382,6 +387,15 @@ if ( FALSE ) {
   verbose = TRUE
 
 
+
+  pas = example_pas_pm25
+  sensor_index = "76545"
+  startdate = "2023-01-01"
+  enddate = "2023-01-03"
+  timezone = "UTC"
+
+
+
   pat <-
     pat_create(
       api_key = api_key,

R/pat_createHourly.R

@@ -64,15 +64,15 @@
 #'
 #' pat <-
 #'   pat_createHourly(
-#'     pas = example_pas,
+#'     pas = example_pas_pm25,
 #'     sensor_index = "76545",
 #'     startdate = "2023-01-01",
 #'     enddate = "2023-01-08",
 #'     timezone = "UTC",
 #'     verbose = TRUE
 #'   )
 #'
-#' View(pat$meta[1:100,])
+#' View(pat$data[1:100,])
 #'
 #' }, silent = FALSE)
 #' }
@@ -135,7 +135,7 @@ pat_createHourly <- function(
 if ( FALSE ) {
 
   api_key = PurpleAir_API_READ_KEY
-  pas = example_pas
+  pas = example_pas_pm25
   sensor_index = "76545"
   startdate = "2023-01-01"
   enddate = "2023-01-09"

R/pat_createRaw.R

@@ -58,15 +58,15 @@
 #'
 #' pat <-
 #'   pat_createRaw(
-#'     pas = example_pas,
+#'     pas = example_pas_pm25,
 #'     sensor_index = "76545",
 #'     startdate = "2023-01-01",
 #'     enddate = "2023-01-03",
 #'     timezone = "UTC",
 #'     verbose = TRUE
 #'   )
 #'
-#' View(pat$meta[1:100,])
+#' View(pat$data[1:100,])
 #'
 #' }, silent = FALSE)
 #' }
@@ -129,7 +129,7 @@ pat_createRaw <- function(
 if ( FALSE ) {
 
   api_key = PurpleAir_API_READ_KEY
-  pas = example_pas
+  pas = example_pas_pm25
   sensor_index = "76545"
   startdate = "2023-01-01"
   enddate = "2023-01-03"

R/pat_filter.R

@@ -30,7 +30,7 @@
 #'
 #' # Unhealthy values
 #' example_pat %>%
-#'   pat_filter(pm2.5_atm_a > 55.5, pm2.5_atm_b > 55.5) %>%
+#'   pat_filter(pm2.5_atm_a > 25, pm2.5_atm_b > 25) %>%
 #'   pat_getData() %>%
 #'   head()
 #'

R/pat_toMonitor.R

@@ -28,13 +28,12 @@
 #'
 #' # AirSensor2 package
 #' library(AirSensor2)
-#'
 #' monitor <-
-#'   example_pat %>%
-#'   pat_toMonitor(
-#'   )
+#'   example_pat_epa %>%
+#'   pat_toMonitor()
 #'
 #' AirMonitor::monitor_timeseriesPlot(monitor, shadedNight = TRUE)
+#'
 #' }, silent = FALSE)
 #' }