Merge branch 'master' of https://git2.projectlocker.com/MazamaScience…

…/PWFSLSmoke

localExecutables/airsis_getYearlyData_exec.R

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+#!/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!")
+}
+
+
+
+

localNotebooks/airsis_yearlyData.Rmd

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+---
+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)
+  }
+```
+
+