docs: WIP: graceful failure in examples

MazamaScience · Nov 19, 2021 · b1b7dbc · b1b7dbc
1 parent 8e43abe
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Showing 47 changed files with 222 additions and 135 deletions.
diff --git a/R/airnow_loadAnnual.R b/R/airnow_loadAnnual.R
@@ -71,7 +71,7 @@ airnow_loadAnnual <- function(year = NULL,
                               baseUrl = 'https://haze.airfire.org/monitoring',
                               dataDir = NULL) {
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(year) ) {
     stop("Required parameter 'year' is missing.")

diff --git a/R/airsis_createDataDataframe.R b/R/airsis_createDataDataframe.R
@@ -24,7 +24,7 @@ airsis_createDataDataframe <- function(
 
   logger.debug(" ----- airsis_createDataDataframe() ----- ")
 
-  # ----- Validate Parameters --------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   # Sanity check -- tbl must have deploymentID
   if ( !'deploymentID' %in% names(tbl) ) {

diff --git a/R/airsis_createRawDataframe.R b/R/airsis_createRawDataframe.R
@@ -67,7 +67,7 @@ airsis_createRawDataframe <- function(
 
   logger.debug(" ----- airsis_createRawDataframe() ----- ")
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(provider) ) {
     logger.error("Required parameter 'provider' is missing")

diff --git a/R/airsis_loadAnnual.R b/R/airsis_loadAnnual.R
@@ -71,7 +71,7 @@ airsis_loadAnnual <- function(year = NULL,
                               baseUrl = 'https://haze.airfire.org/monitoring',
                               dataDir = NULL) {
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(year) ) {
     stop("Required parameter 'year' is missing.")

diff --git a/R/downloadDataFile.R b/R/downloadDataFile.R
@@ -23,7 +23,7 @@ downloadDataFile <- function(
   ...
 ) {
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(filename) ) {
     stop("Required parameter 'filename' is missing.")

diff --git a/R/epa_loadAnnual.R b/R/epa_loadAnnual.R
@@ -50,7 +50,7 @@ epa_loadAnnual <- function(
   dataDir = NULL
 ) {
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   # Sanity Check -- validate parameter code
   # validParameterCodes <- c("44201", "42401", "42101", "42602", "88101", "88502",

diff --git a/R/generic_parseData.R b/R/generic_parseData.R
@@ -52,7 +52,7 @@ generic_parseData <- function(
   configList = NULL
 ) {
 
-  # Validate input ----------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   # Make sure fileString is a string (one element character vector)
   if (

diff --git a/R/monitor_collapse.R b/R/monitor_collapse.R
@@ -83,7 +83,7 @@ monitor_collapse <- function(
 
   }
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( monitor_isEmpty(ws_monitor) ) {
     stop("ws_monitor object contains zero monitors")

diff --git a/R/monitor_dailyStatistic.R b/R/monitor_dailyStatistic.R
@@ -55,7 +55,7 @@ monitor_dailyStatistic <- function(
   minHours = 18
 ) {
 
-  # Validate arguments ---------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( monitor_isEmpty(ws_monitor) )
     stop("ws_monitor object contains zero monitors")

diff --git a/R/monitor_downloadAnnual.R b/R/monitor_downloadAnnual.R
@@ -71,7 +71,7 @@ monitor_downloadAnnual <- function(
   ...
 ) {
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(year) ) {
     stop("Required parameter 'year' is missing.")

diff --git a/R/monitor_getCurrentStatus.R b/R/monitor_getCurrentStatus.R
@@ -107,7 +107,8 @@ monitor_getCurrentStatus <- function(
 
   logger.debug("----- monitor_getCurrentStatus() -----")
 
-  # Sanity checks --------------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
+
   logger.trace("Performing sanity checks on `ws_monitor` parameter.")
 
   if ( !monitor_isMonitor(ws_monitor) ) {

diff --git a/R/monitor_getDailyMean.R b/R/monitor_getDailyMean.R
@@ -32,7 +32,7 @@ monitor_getDailyMean <- function(
   enddate = NULL
 ) {
 
-  # Validate arguments ---------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( !monitor_isMonitor(ws_monitor) )
     stop("Required parameter 'ws_monitor' is not a valid ws_monitor object.")

diff --git a/R/monitor_leaflet.R b/R/monitor_leaflet.R
@@ -43,6 +43,9 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' # Napa Fires -- October, 2017
 #' ca <- airnow_load(2017) %>%
 #'   monitor_subset(tlim = c(20171001,20171101), stateCodes = 'CA')
@@ -51,6 +54,8 @@
 #' monitor_leaflet(CA_very_unhealthy_monitors,
 #'                legendTitle = "October, 2017",
 #'                maptype = "toner")
+#'
+#' }, silent = FALSE)
 #' }
 
 monitor_leaflet <- function(

diff --git a/R/monitor_load.R b/R/monitor_load.R
@@ -26,18 +26,25 @@
 #' @return A \emph{ws_monitor} object with PM2.5 monitoring data.
 #' @examples
 #' \dontrun{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' ca <- monitor_load(20170601,20171001) %>% monitor_subset(stateCodes='CA')
+#'
+#' }, silent = FALSE)
 #' }
 
-monitor_load <- function(startdate = NULL,
-                         enddate = NULL,
-                         monitorIDs = NULL,
-                         parameter="PM2.5",
-                         baseUrl="https://haze.airfire.org/monitoring",
-                         dataDir = NULL,
-                         aqsPreference = "airnow") {
-
-  # Validate parameters --------------------------------------------------------
+monitor_load <- function(
+  startdate = NULL,
+  enddate = NULL,
+  monitorIDs = NULL,
+  parameter = "PM2.5",
+  baseUrl = "https://haze.airfire.org/monitoring",
+  dataDir = NULL,
+  aqsPreference = "airnow"
+) {
+
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(startdate) ) {
     stop(paste0("Required parameter 'startdate' is missing"))

diff --git a/R/monitor_loadAnnual.R b/R/monitor_loadAnnual.R
@@ -56,18 +56,25 @@
 #' @seealso \code{\link{monitor_loadLatest}}
 #' @examples
 #' \dontrun{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' monitor_loadAnnual(2014) %>%
 #'   monitor_subset(stateCodes='MT', tlim=c(20140801,20140901)) %>%
 #'   monitor_map()
+#'
+#' }, silent = FALSE)
 #' }
 
-monitor_loadAnnual <- function(year = NULL,
-                               parameter='PM2.5',
-                               baseUrl='https://haze.airfire.org/monitoring',
-                               dataDir = NULL,
-                               aqsPreference = "airnow") {
+monitor_loadAnnual <- function(
+  year = NULL,
+  parameter = 'PM2.5',
+  baseUrl = 'https://haze.airfire.org/monitoring',
+  dataDir = NULL,
+  aqsPreference = "airnow"
+) {
 
-  # Validate parameters --------------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( is.null(year) ) {
     stop("Required parameter 'year' is missing.")

diff --git a/R/monitor_loadDaily.R b/R/monitor_loadDaily.R
@@ -60,14 +60,21 @@
 #' @seealso \code{\link{monitor_loadAnnual}}
 #' @examples
 #' \dontrun{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' monitor_loadDaily() %>%
 #'   monitor_subset(stateCodes=CONUS) %>%
 #'   monitor_map()
+#'
+#' }, silent = FALSE)
 #' }
 
-monitor_loadDaily <- function(parameter='PM2.5',
-                              baseUrl='https://haze.airfire.org/monitoring/latest/RData',
-                              dataDir = NULL) {
+monitor_loadDaily <- function(
+  parameter = 'PM2.5',
+  baseUrl = 'https://haze.airfire.org/monitoring/latest/RData',
+  dataDir = NULL
+) {
 
   airnow <- airnow_loadDaily(parameter, baseUrl, dataDir)
   airsis <- airsis_loadDaily(parameter, baseUrl, dataDir)

diff --git a/R/monitor_loadLatest.R b/R/monitor_loadLatest.R
@@ -60,14 +60,21 @@
 #' @seealso \code{\link{monitor_loadDaily}}
 #' @examples
 #' \dontrun{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' monitor_loadLatest() %>%
 #'   monitor_subset(stateCodes=CONUS) %>%
 #'   monitor_map()
+#'
+#' }, silent = FALSE)
 #' }
 
-monitor_loadLatest <- function(parameter='PM2.5',
-                               baseUrl='https://haze.airfire.org/monitoring/latest/RData/',
-                               dataDir = NULL) {
+monitor_loadLatest <- function(
+  parameter = 'PM2.5',
+  baseUrl = 'https://haze.airfire.org/monitoring/latest/RData/',
+  dataDir = NULL
+) {
 
   airnow <- airnow_loadLatest(parameter, baseUrl, dataDir)
   airsis <- airsis_loadLatest(parameter, baseUrl, dataDir)

diff --git a/R/monitor_performance.R b/R/monitor_performance.R
@@ -21,6 +21,9 @@
 #' @seealso \link{skill_confusionMatrix}
 #' @examples
 #' \donttest{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' library(PWFSLSmoke)
 #'
 #' # If daily avg data were the prediciton and Spokane were
@@ -43,9 +46,19 @@
 #' skillful <- monitor_subset(wa_dailyAvg, monitorIDs=skillfulIDs)
 #'
 #' monitor_leaflet(skillful)
+#'
+#' }, silent = FALSE)
 #' }
 
-monitor_performance <- function(predicted, observed, t1, t2, metric=NULL, FPCost=1, FNCost=1) {
+monitor_performance <- function(
+  predicted,
+  observed,
+  t1,
+  t2,
+  metric=NULL,
+  FPCost = 1,
+  FNCost = 1
+) {
 
   # Run skill_confusionMatrix on fake data to get a list of all metrics
   metricNames <- names(skill_confusionMatrix(sample(c(TRUE,FALSE),10,replace=TRUE), sample(c(TRUE,FALSE),10,replace=TRUE)))

diff --git a/R/monitor_performanceMap.R b/R/monitor_performanceMap.R
@@ -42,6 +42,9 @@
 #' @seealso \link{monitor_performance}
 #' @examples
 #' \dontrun{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' library(PWFSLSmoke)
 #'
 #' # Napa Fires -- October, 2017
@@ -54,6 +57,8 @@
 #'                                        radius = 50)
 #' monitor_performanceMap(ca, Vallejo, cex = 2)
 #' title('Heidke Skill of monitors predicting another monitor.')
+#'
+#' }, silent = FALSE)
 #' }
 
 monitor_performanceMap <- function(

diff --git a/R/monitor_rollingMean.R b/R/monitor_rollingMean.R
@@ -33,7 +33,12 @@
 #'        col=c('black','red','blue'), lwd=c(1,1,2))
 #' title('Smoky Monitors in Washington -- August, 2015')
 
-monitor_rollingMean <- function(ws_monitor, width=8, data.thresh=75, align="center") {
+monitor_rollingMean <- function(
+  ws_monitor,
+  width = 8,
+  data.thresh = 75,
+  align = "center"
+) {
 
   data <- ws_monitor$data
   meta <- ws_monitor$meta

diff --git a/R/monitor_rollingMeanPlot.R b/R/monitor_rollingMeanPlot.R
@@ -62,20 +62,22 @@
 #'                            monitorIDs = c("410190002_01"))
 #' monitor_rollingMeanPlot(Roseburg, shadedNight = TRUE)
 
-monitor_rollingMeanPlot <- function(ws_monitor,
-                                    monitorID = NULL,
-                                    width = 3,
-                                    align = "center",
-                                    data.thresh = 75,
-                                    tlim = NULL,
-                                    ylim = NULL,
-                                    localTime = TRUE,
-                                    shadedNight = FALSE,
-                                    aqiLines = TRUE,
-                                    gridHorizontal = FALSE,
-                                    grid24hr = FALSE,
-                                    grid3hr = FALSE,
-                                    showLegend = TRUE) {
+monitor_rollingMeanPlot <- function(
+  ws_monitor,
+  monitorID = NULL,
+  width = 3,
+  align = "center",
+  data.thresh = 75,
+  tlim = NULL,
+  ylim = NULL,
+  localTime = TRUE,
+  shadedNight = FALSE,
+  aqiLines = TRUE,
+  gridHorizontal = FALSE,
+  grid24hr = FALSE,
+  grid3hr = FALSE,
+  showLegend = TRUE
+) {
 
   # Sanity check
   if ( monitor_isEmpty(ws_monitor) ) {

diff --git a/R/monitor_stamenmap.R b/R/monitor_stamenmap.R
@@ -43,13 +43,18 @@
 #'
 #' @examples
 #' \donttest{
+#' # Fail gracefully if any resources are not available
+#' try({
+#'
 #' library(PWFSLSmoke)
 #'
 #' N_M <- Northwest_Megafires
 #' # monitor_leaflet(N_M) # to identify Spokane monitorIDs
 #' Spokane <- monitor_subsetBy(N_M, stringr::str_detect(N_M$meta$monitorID,'^53063'))
 #' Spokane <- monitor_subset(Spokane, tlim=c(20150815, 20150831))
 #' monitor_stamenmap(Spokane)
+#'
+#' }, silent = FALSE)
 #' }
 #'
 #' @seealso \code{\link{staticmap_getStamenmapBrick}}
@@ -116,7 +121,7 @@ monitor_stamenmap <- function(
 
   }
 
-  # ----- Validate Parameters --------------------------------------------------
+  # ----- Validate parameters --------------------------------------------------
 
   if ( monitor_isEmpty(ws_monitor) )
     stop("ws_monitor object contains zero monitors")