diff --git a/DESCRIPTION b/DESCRIPTION index b4bb3020..222cb628 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -64,10 +64,10 @@ Description: Utilities for working with air quality monitoring data the United States 'EPA' and it's 'AirNow' air quality site . Additional sources of PM2.5 data made accessible by the package include: - 'AIRSIS' (password protected) + 'AIRSIS' (aka "Oceaneering", not public) and 'WRCC' . - Data compilations are provided by 'PWFSL' - . + Data compilations are hosted by the USFS 'AirFire' research team + . License: GPL-3 VignetteBuilder: knitr Repository: CRAN diff --git a/NEWS.md b/NEWS.md index 2840e477..b004f199 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ Documentation and other fixes to deal with CRAN check issues. +* Updated various URLs in function documentation. * Put all internet connected examples inside a `try({ ... })` block to fail gracefully when resources are not available. * Updated many examples to use the `Camp_Fire` dataset. diff --git a/R/PWFSLSmoke-deprecated.R b/R/PWFSLSmoke-deprecated.R index d36cee48..63d518d5 100644 --- a/R/PWFSLSmoke-deprecated.R +++ b/R/PWFSLSmoke-deprecated.R @@ -51,57 +51,57 @@ NULL #' @export #' @rdname PWFSLSmoke-deprecated -monitorGoogleMap <- function(ws_monitor, - slice = get("max"), - breaks = AQI$breaks_24, - colors = AQI$colors, - width = 640, - height = 640, - centerLon = NULL, - centerLat = NULL, - zoom = NULL, - maptype = "roadmap", - grayscale = FALSE, - map = NULL, - ...) { - +monitorGoogleMap <- function( + ws_monitor, + slice = get("max"), + breaks = AQI$breaks_24, + colors = AQI$colors, + width = 640, + height = 640, + centerLon = NULL, + centerLat = NULL, + zoom = NULL, + maptype = "roadmap", + grayscale = FALSE, + map = NULL, + ... +) { .Defunct("monitor_esriMap", package = "PWFSLSmoke") - } #' @export #' @rdname PWFSLSmoke-deprecated -monitorEsriMap <- function(ws_monitor, - slice = get("max"), - breaks = AQI$breaks_24, - colors = AQI$colors, - width = 640, - height = 640, - centerLon = NULL, - centerLat = NULL, - zoom = NULL, - maptype = "roadmap", - grayscale = FALSE, - map = NULL, - ...) { - +monitorEsriMap <- function( + ws_monitor, + slice = get("max"), + breaks = AQI$breaks_24, + colors = AQI$colors, + width = 640, + height = 640, + centerLon = NULL, + centerLat = NULL, + zoom = NULL, + maptype = "roadmap", + grayscale = FALSE, + map = NULL, + ... +) { .Defunct("monitor_staticmap", package = "PWFSLSmoke") - } #' @export #' @rdname PWFSLSmoke-deprecated -monitorPlot_timeOfDaySpaghetti <- function(ws_monitor, - monitorID=NULL, - tlim=NULL, - ylim=NULL, - aqiLines=TRUE, - shadedNight=TRUE, - title=NULL, - ...) { - +monitorPlot_timeOfDaySpaghetti <- function( + ws_monitor, + monitorID=NULL, + tlim=NULL, + ylim=NULL, + aqiLines=TRUE, + shadedNight=TRUE, + title=NULL, + ... +) { .Defunct(NULL, package = "PWFSLSmoke") - } @@ -114,34 +114,36 @@ monitorPlot_timeOfDaySpaghetti <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated -monitorDygraph <- function(ws_monitor, - title = "title", - ylab = "PM2.5 Concentration", - tlim = NULL, - rollPeriod = 1, - showLegend = TRUE) { - +monitorDygraph <- function( + ws_monitor, + title = "title", + ylab = "PM2.5 Concentration", + tlim = NULL, + rollPeriod = 1, + showLegend = TRUE +) { monitor_dygraph(ws_monitor, title, ylab, tlim, rollPeriod, showLegend) } #' @export #' @rdname PWFSLSmoke-deprecated -monitor_esriMap <- function(ws_monitor, - slice = get("max"), - breaks = AQI$breaks_24, - colors = AQI$colors, - width = 640, - height = 640, - centerLon = NULL, - centerLat = NULL, - zoom = NULL, - maptype = "worldStreetMap", - grayscale = FALSE, - mapRaster = NULL, - cex = par("cex") * 2.0, - pch = 16, - ...) { - +monitor_esriMap <- function( + ws_monitor, + slice = get("max"), + breaks = AQI$breaks_24, + colors = AQI$colors, + width = 640, + height = 640, + centerLon = NULL, + centerLat = NULL, + zoom = NULL, + maptype = "worldStreetMap", + grayscale = FALSE, + mapRaster = NULL, + cex = par("cex") * 2.0, + pch = 16, + ... +) { monitor_staticmap( ws_monitor, slice, breaks, colors, width, height, centerLon, centerLat, zoom, maptype = "world_topo", grayscale, mapRaster, @@ -151,17 +153,18 @@ monitor_esriMap <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated -monitorLeaflet <- function(ws_monitor, - slice = get("max"), - breaks = AQI$breaks_24, - colors = AQI$colors, - labels = AQI$names, - legendTitle = "Max AQI Level", - radius = 10, - opacity = 0.7, - maptype = "terrain", - popupInfo = c("siteName", "monitorID", "elevation")) { - +monitorLeaflet <- function( + ws_monitor, + slice = get("max"), + breaks = AQI$breaks_24, + colors = AQI$colors, + labels = AQI$names, + legendTitle = "Max AQI Level", + radius = 10, + opacity = 0.7, + maptype = "terrain", + popupInfo = c("siteName", "monitorID", "elevation") +) { monitor_leaflet( ws_monitor, slice, breaks, colors, labels, legendTitle, radius, opacity, maptype, popupInfo @@ -170,19 +173,20 @@ monitorLeaflet <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated -monitorMap <- function(ws_monitor, - slice = get("max"), - breaks = AQI$breaks_24, - colors = AQI$colors, - pch = par("pch"), - cex = par("cex"), - stateCol = "grey60", - stateLwd = 2, - countyCol = "grey70", - countyLwd = 1, - add = FALSE, - ...) { - +monitorMap <- function( + ws_monitor, + slice = get("max"), + breaks = AQI$breaks_24, + colors = AQI$colors, + pch = par("pch"), + cex = par("cex"), + stateCol = "grey60", + stateLwd = 2, + countyCol = "grey70", + countyLwd = 1, + add = FALSE, + ... +) { monitor_map( ws_monitor, slice, breaks, colors, pch, cex, stateCol, stateLwd, countyCol, countyLwd, add, @@ -192,27 +196,28 @@ monitorMap <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated -monitorMap_performance <- function(predicted, - observed, - threshold = AQI$breaks_24[3], - cex = par("cex"), - sizeBy = NULL, - colorBy = "heidikeSkill", - breaks = c(-Inf, .5, .6, .7, .8, Inf), - paletteFunc = grDevices::colorRampPalette( - RColorBrewer::brewer.pal( - length(breaks), "Purples" - )[-1] - ), - showLegend = TRUE, - legendPos = "topright", - stateCol = "grey60", - stateLwd = 2, - countyCol = "grey70", - countyLwd = 1, - add = FALSE, - ...) { - +monitorMap_performance <- function( + predicted, + observed, + threshold = AQI$breaks_24[3], + cex = par("cex"), + sizeBy = NULL, + colorBy = "heidikeSkill", + breaks = c(-Inf, .5, .6, .7, .8, Inf), + paletteFunc = grDevices::colorRampPalette( + RColorBrewer::brewer.pal( + length(breaks), "Purples" + )[-1] + ), + showLegend = TRUE, + legendPos = "topright", + stateCol = "grey60", + stateLwd = 2, + countyCol = "grey70", + countyLwd = 1, + add = FALSE, + ... +) { monitor_performanceMap( predicted, observed, threshold, cex, sizeBy, colorBy, breaks, paletteFunc, showLegend, legendPos, stateCol, stateLwd, @@ -223,18 +228,19 @@ monitorMap_performance <- function(predicted, #' @export #' @rdname PWFSLSmoke-deprecated -monitorPlot_dailyBarplot <- function(ws_monitor, - monitorID=NULL, - tlim=NULL, - minHours=18, - gridPos='', - gridCol='black', - gridLwd=0.5, - gridLty='solid', - labels_x_nudge=0, - labels_y_nudge=0, - ...) { - +monitorPlot_dailyBarplot <- function( + ws_monitor, + monitorID=NULL, + tlim=NULL, + minHours=18, + gridPos='', + gridCol='black', + gridLwd=0.5, + gridLty='solid', + labels_x_nudge=0, + labels_y_nudge=0, + ... +) { monitor_dailyBarplot( ws_monitor, monitorID, tlim, minHours, gridPos, gridCol, gridLwd, gridLty, @@ -245,27 +251,28 @@ monitorPlot_dailyBarplot <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated -monitorPlot_hourlyBarplot <- function(ws_monitor, - monitorID = NULL, - tlim = NULL, - localTime = TRUE, - style = 'AQI', - shadedNight = TRUE, - gridPos = '', - gridCol = 'black', - gridLwd = 0.5, - gridLty = 'solid', - labels_x_nudge = 0, - labels_y_nudge = 0, - dayCol = 'black', - dayLwd = 2, - dayLty = 'solid', - hourCol = 'black', - hourLwd = 1, - hourLty = 'solid', - hourInterval = 6, - ...) { - +monitorPlot_hourlyBarplot <- function( + ws_monitor, + monitorID = NULL, + tlim = NULL, + localTime = TRUE, + style = 'AQI', + shadedNight = TRUE, + gridPos = '', + gridCol = 'black', + gridLwd = 0.5, + gridLty = 'solid', + labels_x_nudge = 0, + labels_y_nudge = 0, + dayCol = 'black', + dayLwd = 2, + dayLty = 'solid', + hourCol = 'black', + hourLwd = 1, + hourLty = 'solid', + hourInterval = 6, + ... +) { monitor_hourlyBarplot( ws_monitor, monitorID, tlim, localTime, style, shadedNight, gridPos, gridCol, gridLwd, gridLty, labels_x_nudge, labels_y_nudge, @@ -277,27 +284,27 @@ monitorPlot_hourlyBarplot <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated monitorPlot_noData <- function(ws_monitor, monitorID=NULL, cex=2.5) { - monitor_noDataPlot(ws_monitor, monitorID, cex) } #' @export #' @rdname PWFSLSmoke-deprecated -monitorPlot_rollingMean <- 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) { - +monitorPlot_rollingMean <- 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( ws_monitor, monitorID, width, align, data.thresh, tlim, ylim, localTime, shadedNight, aqiLines, gridHorizontal, grid24hr, grid3hr, showLegend @@ -306,22 +313,23 @@ monitorPlot_rollingMean <- function(ws_monitor, #' @export #' @rdname PWFSLSmoke-deprecated -monitorPlot_timeseries <- function(ws_monitor, - monitorID=NULL, - tlim=NULL, - localTime=TRUE, - style=NULL, - shadedNight=FALSE, - add=FALSE, - gridPos='', - gridCol='black', - gridLwd=1, - gridLty='solid', - dayLwd=0, - hourLwd=0, - hourInterval=6, - ...) { - +monitorPlot_timeseries <- function( + ws_monitor, + monitorID=NULL, + tlim=NULL, + localTime=TRUE, + style=NULL, + shadedNight=FALSE, + add=FALSE, + gridPos='', + gridCol='black', + gridLwd=1, + gridLty='solid', + dayLwd=0, + hourLwd=0, + hourInterval=6, + ... +) { monitor_timeseriesPlot( ws_monitor, monitorID, tlim, localTime, style, shadedNight, add, gridPos, gridCol, gridLwd, gridLty, dayLwd, hourLwd, hourInterval, ... diff --git a/R/addGoogleAddress.R b/R/addGoogleAddress.R index 67baf7ef..b924302a 100644 --- a/R/addGoogleAddress.R +++ b/R/addGoogleAddress.R @@ -14,7 +14,7 @@ #' #' Address information is obtained by using the \pkg{ggmap} package. #' @return Input dataframe with additional columns: \code{siteName, countyName}. -#' @references \url{https://developers.google.com/maps/documentation/geocoding/intro} +#' @references \url{https://developers.google.com/maps/documentation/geocoding/overview} addGoogleAddress <- function( df, diff --git a/R/addGoogleElevation.R b/R/addGoogleElevation.R index ab8a2770..5b500b4b 100644 --- a/R/addGoogleElevation.R +++ b/R/addGoogleElevation.R @@ -12,7 +12,7 @@ #' #' Address information is obtained by using the \pkg{ggmap} package. #' @return Input dataframe with (possibly) additional column: \code{elevation}. -#' @references \url{https://developers.google.com/maps/documentation/elevation/intro} +#' @references \url{https://developers.google.com/maps/documentation/elevation/overview} addGoogleElevation <- function( df, diff --git a/R/airnow_loadAnnual.R b/R/airnow_loadAnnual.R index b4ef8101..43eddeeb 100644 --- a/R/airnow_loadAnnual.R +++ b/R/airnow_loadAnnual.R @@ -47,7 +47,7 @@ #' } #' #' Available AirNow RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/AirNow/RData}{https://haze.airfire.org/monitoring/AirNow/RData} +#' \href{https://haze.airfire.org/monitoring/AirNow/RData/}{https://haze.airfire.org/monitoring/AirNow/RData/} #' @seealso \code{\link{airnow_loadDaily}} #' @seealso \code{\link{airnow_loadLatest}} #' @examples diff --git a/R/airnow_loadDaily.R b/R/airnow_loadDaily.R index a9303e8e..19f48fab 100644 --- a/R/airnow_loadDaily.R +++ b/R/airnow_loadDaily.R @@ -45,7 +45,7 @@ #' } #' #' Available AirNow RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/AirNow/RData/latest}{https://haze.airfire.org/monitoring/AirNow/RData/latest} +#' \href{https://haze.airfire.org/monitoring/AirNow/RData/latest/}{https://haze.airfire.org/monitoring/AirNow/RData/latest/} #' @seealso \code{\link{airnow_loadAnnual}} #' @seealso \code{\link{airnow_loadLatest}} #' @examples diff --git a/R/airnow_loadLatest.R b/R/airnow_loadLatest.R index f4078a8d..28506b9e 100644 --- a/R/airnow_loadLatest.R +++ b/R/airnow_loadLatest.R @@ -45,7 +45,7 @@ #' } #' #' Avaialble RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/AirNow/RData/latest}{https://haze.airfire.org/monitoring/AirNow/RData/latest} +#' \href{https://haze.airfire.org/monitoring/AirNow/RData/latest/}{https://haze.airfire.org/monitoring/AirNow/RData/latest/} #' @seealso \code{\link{airnow_loadAnnual}} #' @seealso \code{\link{airnow_loadDaily}} #' @examples diff --git a/R/airsis_loadAnnual.R b/R/airsis_loadAnnual.R index a209dcb6..c91a4830 100644 --- a/R/airsis_loadAnnual.R +++ b/R/airsis_loadAnnual.R @@ -47,7 +47,7 @@ #' } #' #' Available AIRSIS RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/AIRSIS/RData}{https://haze.airfire.org/monitoring/AIRSIS/RData} +#' \href{https://haze.airfire.org/monitoring/AIRSIS/RData/}{https://haze.airfire.org/monitoring/AIRSIS/RData/} #' @seealso \code{\link{airsis_loadDaily}} #' @seealso \code{\link{airsis_loadLatest}} #' @examples diff --git a/R/airsis_loadDaily.R b/R/airsis_loadDaily.R index 789b0a71..f1008bc1 100644 --- a/R/airsis_loadDaily.R +++ b/R/airsis_loadDaily.R @@ -45,7 +45,7 @@ #' } #' #' Avaialble AIRSIS RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/AIRSIS/RData/latest}{https://haze.airfire.org/monitoring/AIRSIS/RData/latest} +#' \href{https://haze.airfire.org/monitoring/AIRSIS/RData/latest/}{https://haze.airfire.org/monitoring/AIRSIS/RData/latest/} #' @seealso \code{\link{airsis_loadAnnual}} #' @seealso \code{\link{airsis_loadLatest}} #' @examples diff --git a/R/airsis_loadLatest.R b/R/airsis_loadLatest.R index 5638365c..328e24ce 100644 --- a/R/airsis_loadLatest.R +++ b/R/airsis_loadLatest.R @@ -45,7 +45,7 @@ #' } #' #' Avaialble RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/AIRSIS/RData/latest}{https://haze.airfire.org/monitoring/AIRSIS/RData/latest} +#' \href{https://haze.airfire.org/monitoring/AIRSIS/RData/latest/}{https://haze.airfire.org/monitoring/AIRSIS/RData/latest/} #' @seealso \code{\link{airsis_loadAnnual}} #' @seealso \code{\link{airsis_loadDaily}} #' @examples diff --git a/R/monitor_nowcast.R b/R/monitor_nowcast.R index 986f821d..58900a62 100644 --- a/R/monitor_nowcast.R +++ b/R/monitor_nowcast.R @@ -32,9 +32,7 @@ #' .001 ppm for 'ozone' regardless of the precision of the data in the incoming \emph{ws_monitor} object. #' #' @references \url{https://en.wikipedia.org/wiki/Nowcast_(Air_Quality_Index)} -#' @references \url{https://www3.epa.gov/airnow/ani/pm25_aqi_reporting_nowcast_overview.pdf} #' @references \url{https://aqicn.org/faq/2015-03-15/air-quality-nowcast-a-beginners-guide/} -#' @references \url{https://airnow.zendesk.com/hc/en-us/articles/211625598-How-does-AirNow-make-the-Current-PM-Air-Quality-Index-AQI-maps-} #' @references https://forum.airnowtech.org/t/the-nowcast-for-ozone-and-pm/172 #' @references https://forum.airnowtech.org/t/the-aqi-equation/169 #' @references https://forum.airnowtech.org/t/how-does-airnow-handle-negative-hourly-concentrations/143 diff --git a/R/wrcc_loadAnnual.R b/R/wrcc_loadAnnual.R index 2ddbf3fa..722d8e9f 100644 --- a/R/wrcc_loadAnnual.R +++ b/R/wrcc_loadAnnual.R @@ -43,7 +43,7 @@ #' } #' #' Available WRCC RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/WRCC/RData}{https://haze.airfire.org/monitoring/WRCC/RData} +#' \href{https://haze.airfire.org/monitoring/WRCC/RData/}{https://haze.airfire.org/monitoring/WRCC/RData/} #' @seealso \code{\link{wrcc_loadDaily}} #' @seealso \code{\link{wrcc_loadLatest}} #' diff --git a/R/wrcc_loadDaily.R b/R/wrcc_loadDaily.R index a5855a0d..adfcd8bb 100644 --- a/R/wrcc_loadDaily.R +++ b/R/wrcc_loadDaily.R @@ -45,7 +45,7 @@ #' } #' #' Avaialble WRCC RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/WRCC/RData/latest}{https://haze.airfire.org/monitoring/WRCC/RData/latest} +#' \href{https://haze.airfire.org/monitoring/WRCC/RData/latest/}{https://haze.airfire.org/monitoring/WRCC/RData/latest/} #' @seealso \code{\link{wrcc_loadAnnual}} #' @seealso \code{\link{wrcc_loadLatest}} #' @examples diff --git a/R/wrcc_loadLatest.R b/R/wrcc_loadLatest.R index f3f75fa3..28ac71ac 100644 --- a/R/wrcc_loadLatest.R +++ b/R/wrcc_loadLatest.R @@ -45,7 +45,7 @@ #' } #' #' Avaialble RData and associated log files can be seen at: -#' \href{https://haze.airfire.org/monitoring/WRCC/RData/latest}{https://haze.airfire.org/monitoring/WRCC/RData/latest} +#' \href{https://haze.airfire.org/monitoring/WRCC/RData/latest/}{https://haze.airfire.org/monitoring/WRCC/RData/latest/} #' @seealso \code{\link{wrcc_loadAnnual}} #' @seealso \code{\link{wrcc_loadDaily}} #' @examples diff --git a/README.md b/README.md index 545efbcf..39d056aa 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,3 @@ ---- -title: "PWFSLSmoke" -pagetitle: PWFSLSmoke" ---- - [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/PWFSLSmoke)](https://cran.r-project.org/package=PWFSLSmoke) [![Downloads](http://cranlogs.r-pkg.org/badges/PWFSLSmoke)](https://cran.r-project.org/package=PWFSLSmoke) [![Build Status](https://travis-ci.org/MazamaScience/PWFSLSmoke.svg?branch=master)](https://travis-ci.org/MazamaScience/PWFSLSmoke) @@ -88,6 +83,6 @@ To run them you should: ---- This R package was created by [Mazama Science](http://mazamascience.com) and is -being funded by the USFS [AirFire Research Team](https://airfire.org). +being funded by the USFS [AirFire Research Team](https://www.airfire.org). diff --git a/docs/404.html b/docs/404.html index 1cbae232..e3a7b163 100644 --- a/docs/404.html +++ b/docs/404.html @@ -78,7 +78,7 @@ PWFSLSmoke - 1.2.116 + 1.2.117 @@ -166,7 +166,7 @@

Contents