diff --git a/localExecutables/airsis_getYearlyData_exec.R b/localExecutables/airsis_getYearlyData_exec.R new file mode 100755 index 00000000..90c14c84 --- /dev/null +++ b/localExecutables/airsis_getYearlyData_exec.R @@ -0,0 +1,127 @@ +#!/usr/bin/env Rscript + +# Updated Jan 3, 2018 +# +# This script will download data for all airsis monitors for the specified time frame +# +# # Example +# airsis_getYearlyData_exec.R --startdate=20150101 --enddate=2016010223 --outputDir="~/Data/airsis" --fileName="airsis_2015" + +VERSION <- "0.0.1" + +suppressPackageStartupMessages( + { + library(methods) + library(optparse) + library(PWFSLSmoke) + library(MazamaSpatialUtils) + } +) + +########################################## + +saveAirsisData <- function(opt) { + + # Get all unitids + usfs_unitids <- airsis_availableUnits(opt$startdate, opt$enddate, provider = 'USFS') + apcd_unitids <- airsis_availableUnits(opt$startdate, opt$enddate, provider = 'APCD') + + # for usfs and apcd, make a list of ws_monitor objects for all units + monitors <- list() + + for ( provider in c("USFS", "APCD", "ARB2", "EPA")) { + + unitids <- airsis_availableUnits(opt$startdate, opt$enddate, provider = provider) + + for ( unitid in unitids ) { + result <- try (monitor <- airsis_createMonitorObject(startdate = opt$startdate, enddate = opt$enddate, provider = provider, unitID = unitid)) + if ("try-error" %in% class(result)) { + print(paste0("error loading ", provider, " ", unitid, ": ", geterrmessage())) + } else { + monitors[[paste0(unitid, "_", provider)]] <- monitor + } + } + + } + + all_monitors <- monitor_combine(monitors) + + # Set the name of all_monitors to fileName + if (is.null(opt$fileName)) { + fileName <- paste0('airsis_', opt$startdate, "_", opt$enddate) + } else { + fileName <- opt$fileName + } + + assign(fileName, all_monitors) + filePath <- paste0(opt$outputDir, '/', fileName, '.RData') + + # Save the RData file + save(list = fileName, file = filePath) + +} + +################################################################################ +# Main program + +# ----- Parse command line options --------------------------------------------- + +# Set up option parser +option_list <- list( + make_option(c("--startdate"),default=NULL, help="starting date of the data to be downloaded"), + make_option(c("--enddate"), default=NULL, help="ending date of the data to be downloaded"), + make_option(c("--outputDir"), default=getwd(), help="Output directory for generated RData files [default=\"%default\"]"), + make_option(c("--fileName"), default=NULL, help="name for the RData file"), + make_option(c("--logDir"), default=getwd(), help="Output directory for generated .log file [default=\"%default\"]"), + make_option(c("--spatialDataDir"), default='~/Data/Spatial', help="Directory containing spatial datasets used by MazamaSpatialUtils [default=\"%default\"]"), + make_option(c("-V","--version"), action="store_true", default=FALSE, help="Print out version number [default\"%default\"]") +) + +# Parse arguments +opt <- parse_args(OptionParser(option_list=option_list)) + +# Print out version and quit +if ( opt$version ) { + cat(paste0('createCSV_exec.R ',VERSION,'\n')) + quit() +} + +# Sanity checks +if ( is.null(opt$startdate) ) stop(paste0("startdate is required")) +if ( is.null(opt$enddate) ) stop(paste0("enddate is required")) +if ( !file.exists(opt$outputDir) ) stop(paste0("outputDir not found: ",opt$outputDir)) +if ( !file.exists(opt$logDir) ) stop(paste0("logDir not found: ",opt$logDir)) + +# Assign log file names +debugLog <- file.path(opt$logDir, paste0('airsis_getYearlyData_', '_DEBUG.log')) +infoLog <- file.path(opt$logDir, paste0('airsis_getYearlyData_', '_INFO.log')) +errorLog <- file.path(opt$logDir, paste0('airsis_getYearlyData_', '_ERROR.log')) + +# Set up logging +logger.setup(debugLog=debugLog, infoLog=infoLog, errorLog=errorLog) + +# Silence other warning messages +options(warn=-1) # -1=ignore, 0=save/print, 1=print, 2=error + +# Set up MazamaSpatialUtils +setSpatialDataDir(opt$spatialDataDir) ##FOR bash + +loadSpatialData("NaturalEarthAdm1") + + +# ----- Save airnow ws_monitor object as a RData file ------ + +result <- try( saveAirsisData(opt) ) + +if ( "try-error" %in% class(result) ) { + msg <- paste("Error saving airsis data: ", geterrmessage()) + logger.fatal(msg) +} else { + # Guarantee that the errorLog exists + if ( !file.exists(errorLog) ) dummy <- file.create(errorLog) + logger.info("Completed successfully!") +} + + + + diff --git a/localVignettes/AIRSIS_Data_Handling.Rmd b/localNotebooks/AIRSIS_Data_Handling.Rmd similarity index 100% rename from localVignettes/AIRSIS_Data_Handling.Rmd rename to localNotebooks/AIRSIS_Data_Handling.Rmd diff --git a/localVignettes/AIRSIS_Data_Handling.html b/localNotebooks/AIRSIS_Data_Handling.html similarity index 100% rename from localVignettes/AIRSIS_Data_Handling.html rename to localNotebooks/AIRSIS_Data_Handling.html diff --git a/localVignettes/AIRSIS_Raw_Data.Rmd b/localNotebooks/AIRSIS_Raw_Data.Rmd similarity index 100% rename from localVignettes/AIRSIS_Raw_Data.Rmd rename to localNotebooks/AIRSIS_Raw_Data.Rmd diff --git a/localVignettes/AIRSIS_Raw_Data.html b/localNotebooks/AIRSIS_Raw_Data.html similarity index 100% rename from localVignettes/AIRSIS_Raw_Data.html rename to localNotebooks/AIRSIS_Raw_Data.html diff --git a/localNotebooks/airsis_yearlyData.Rmd b/localNotebooks/airsis_yearlyData.Rmd new file mode 100644 index 00000000..cecc680b --- /dev/null +++ b/localNotebooks/airsis_yearlyData.Rmd @@ -0,0 +1,81 @@ +--- +title: "Yearly AIRSIS Data" +author: "Mazama Science" +date: "`r Sys.Date()`" +output: html_document +--- + +```{r, echo=FALSE} +knitr::opts_chunk$set(fig.width=7, fig.height=5) +``` + +# Setup + +Start by loading the PWFSLSmoke package and loading the data. + +```{r Setup, message=FALSE} +suppressPackageStartupMessages({ + library(PWFSLSmoke) + library(ggplot2) + library(gridExtra) +} + ) +logger.setLevel(ERROR) +load("~/Data/airsis/airsis_2015.RData") +load("~/Data/airsis/airsis_2016.Rdata") +``` + +# Orientation + +```{r mapping} +monitorLeaflet(airsis_2015) +monitorLeaflet(airsis_2016) +``` + +```{r} +days2015 <- sum(!is.na(airsis_2015$data[-1]))/24 +days2016 <- sum(!is.na(airsis_2016$data[-1]))/24 +deployments2015 <- ncol(airsis_2015$data) - 1 +deployments2016 <- ncol(airsis_2016$data) - 1 +``` + +Let's see how they were distributed through time: + +```{r} +counts2015 <- data.frame(time = airsis_2015$data$datetime, count = apply(airsis_2015$data[-1], 1, function(x) sum(!is.na(x)))) +counts2016 <- data.frame(time = airsis_2016$data$datetime, count = apply(airsis_2016$data[-1], 1, function(x) sum(!is.na(x)))) +plot1 <- ggplot(counts2015, aes(time, count))+ + geom_bar(stat="identity")+ + labs(title='2015', subtitle='number of deployments each hour') +plot2 <- ggplot(counts2016, aes(time, count))+ + geom_bar(stat="identity")+ + labs(title='2016', subtitle='number of deployments each hour') +grid.arrange(plot1, plot2, nrow = 2) +``` + +```{r monthly_maps} +basemap <- esriMap_getMap(bboxString = '-168.9,20.18,-58.68,70.51') +layout(matrix(c(3,3,1,2), 2, 2, byrow = TRUE), widths=c(1,1), heights=c(1,3)) +for ( month in 1:12) { + # First 2015 + tlim2015 <- if (month < 12) { + paste0('2015', stringr::str_pad(as.character(c(month, month+1)), 2, side = 'left', "0"), '01') + } else { + c('20151201', '20160101') + } + ws_monitor2015 <- monitor_subset(airsis_2015, tlim = tlim2015) + month_str <- strftime(ws_monitor2015$data$datetime[30], format = "%B") + tlim2016 <- if (month < 12) { + paste0('2016', stringr::str_pad(as.character(c(month, month+1)), 2, side = 'left', "0"), '01') + } else { + c('20161201', '20170101') + } + ws_monitor2016 <- monitor_subset(airsis_2016, tlim = tlim2016) + monitorEsriMap(ws_monitor2015, mapRaster = basemap, main = '2015') + monitorEsriMap(ws_monitor2016, mapRaster = basemap, main = '2016') + plot(0,0,axes = F, col = 'transparent') + text(0,0,month_str, cex = 3) + } +``` + + diff --git a/localNotebooks/airsis_yearlyData.html b/localNotebooks/airsis_yearlyData.html new file mode 100644 index 00000000..e33b6352 --- /dev/null +++ b/localNotebooks/airsis_yearlyData.html @@ -0,0 +1,230 @@ + + + + + + + + + + + + + + + +Yearly AIRSIS Data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + +
+

Setup

+

Start by loading the PWFSLSmoke package and loading the data.

+
suppressPackageStartupMessages({
+  library(PWFSLSmoke)
+  library(ggplot2)
+  library(gridExtra)
+}
+  )
+logger.setLevel(ERROR)
+load("~/Data/airsis/airsis_2015.RData")
+load("~/Data/airsis/airsis_2016.Rdata")
+
+
+

Orientation

+
monitorLeaflet(airsis_2015)
+
+ +
monitorLeaflet(airsis_2016)
+
+ +
days2015 <- sum(!is.na(airsis_2015$data[-1]))/24
+days2016 <- sum(!is.na(airsis_2016$data[-1]))/24
+deployments2015 <- ncol(airsis_2015$data) - 1
+deployments2016 <- ncol(airsis_2016$data) - 1
+

Let’s see how they were distributed through time:

+
counts2015 <-  data.frame(time = airsis_2015$data$datetime, count = apply(airsis_2015$data[-1], 1, function(x) sum(!is.na(x))))
+counts2016 <-  data.frame(time = airsis_2016$data$datetime, count = apply(airsis_2016$data[-1], 1, function(x) sum(!is.na(x))))
+plot1 <- ggplot(counts2015, aes(time, count))+
+  geom_bar(stat="identity")+
+  labs(title='2015', subtitle='number of deployments each hour')
+plot2 <- ggplot(counts2016, aes(time, count))+
+  geom_bar(stat="identity")+
+  labs(title='2016', subtitle='number of deployments each hour')
+grid.arrange(plot1, plot2, nrow = 2)
+
## Warning in plyr::split_indices(scale_id, n): '.Random.seed' is not an
+## integer vector but of type 'NULL', so ignored
+

+
basemap <- esriMap_getMap(bboxString = '-168.9,20.18,-58.68,70.51')
+layout(matrix(c(3,3,1,2), 2, 2, byrow = TRUE), widths=c(1,1), heights=c(1,3)) 
+for ( month in 1:12) {
+  # First 2015
+  tlim2015 <- if (month < 12) {
+    paste0('2015', stringr::str_pad(as.character(c(month, month+1)), 2, side = 'left', "0"), '01')
+  } else {
+    c('20151201', '20160101')
+  }
+  ws_monitor2015 <- monitor_subset(airsis_2015, tlim = tlim2015)
+  month_str <- strftime(ws_monitor2015$data$datetime[30], format = "%B")
+  tlim2016 <- if (month < 12) {
+    paste0('2016', stringr::str_pad(as.character(c(month, month+1)), 2, side = 'left', "0"), '01')
+  } else {
+    c('20161201', '20170101')
+  }
+  ws_monitor2016 <- monitor_subset(airsis_2016, tlim = tlim2016)
+  monitorEsriMap(ws_monitor2015, mapRaster = basemap, main = '2015')
+  monitorEsriMap(ws_monitor2016, mapRaster = basemap, main = '2016')
+  plot(0,0,axes = F, col = 'transparent')
+  text(0,0,month_str, cex = 3)
+  }
+

+
+ + + + +
+ + + + + + + +