Set all date/time objects to UTC time zone

- closes #17 and fixed bug which was expressed for some years and certain time zones (e.g., ‘Europe/Berlin’ and year 1942, but not for ‘Europe/Zurich’ and year 1942) - bump version number Former-commit-id: c2503e611f0ef0fd0aba7f14c8942ed98054d796 [formerly c2f89c228a9d9112e459fbbeab7a72526c242211] Former-commit-id: a6fef13
DrylandEcology · Sep 28, 2016 · b980d70 · b980d70
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commit b980d70
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diff --git a/2_SWSF_p3of5_ExternalDataExtractions_v51.R b/2_SWSF_p3of5_ExternalDataExtractions_v51.R
@@ -847,7 +847,7 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 		dailyPPTceiling <- 1.5 * max(sapply(obs.hist.daily, FUN=function(obs) max(obs@data[,4]))) #Hamlet et al. 2010: "an arbitrary ceiling of 150% of the observed maximum precipitation value for each cell is also imposed by “spreading out” very large daily precipitation values into one or more adjacent days"
 
 		res <- try(lapply(obs.hist.daily, FUN=function(obs) {
-					month <- as.POSIXlt(paste(obs@year, obs@data[, "DOY"], sep="-"), format="%Y-%j")$mon + 1
+					month <- as.POSIXlt(paste(obs@year, obs@data[, "DOY"], sep="-"), format="%Y-%j", tz = "UTC")$mon + 1
 					ydelta <- delta_ts[delta_ts[, "Year"] == obs@year, -(1:2)]
 					tmax <- obs@data[, "Tmax_C"] + ydelta[month, "Tmax_C"]
 
@@ -871,7 +871,7 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 																if (any(i_rainyMYears <- obs.hist.monthly[obs.hist.monthly[, "Month"] == m, "PPT_cm"] > 0)) { #sample from the same historic month in an other with rainy days instead
 																	#Locate data of same month in other year
 																	i_newYear <- which(i_rainyMYears)[which.min(abs(obs.hist.monthly[obs.hist.monthly[, "Month"] == m, "PPT_cm"][i_rainyMYears] - m_ydelta))]
-																	newMonth <- as.POSIXlt(paste((newObs <- obs.hist.daily[i_newYear][[1]])@year, newObs@data[, "DOY"], sep="-"), format="%Y-%j")$mon + 1
+																	newMonth <- as.POSIXlt(paste((newObs <- obs.hist.daily[i_newYear][[1]])@year, newObs@data[, "DOY"], sep="-"), format="%Y-%j", tz = "UTC")$mon + 1
 																	newMonthData <- newObs@data[, "PPT_cm"][newMonth == m]
 																	#Adjust data
 																	newMonthData <- fix_PPTdata_length(data=newMonthData, targetLength=sum(im_month)) #adjust number of days in case we got a leap year February issue
@@ -880,7 +880,7 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 																	#Locate data of any month in any year
 																	i_newMYear <- which(i_rainyMonth)[which.min(abs(obs.hist.monthly[i_rainyMonth, "PPT_cm"] - m_ydelta))]
 																	i_newYear <- which(obs.hist.monthly[i_newMYear, "Year"] == sort(unique(obs.hist.monthly[, "Year"])))
-																	newMonth <- as.POSIXlt(paste((newObs <- obs.hist.daily[i_newYear][[1]])@year, newObs@data[, "DOY"], sep="-"), format="%Y-%j")$mon + 1
+																	newMonth <- as.POSIXlt(paste((newObs <- obs.hist.daily[i_newYear][[1]])@year, newObs@data[, "DOY"], sep="-"), format="%Y-%j", tz = "UTC")$mon + 1
 																	newMonthData <- newObs@data[, "PPT_cm"][newMonth == obs.hist.monthly[i_newMYear, "Month"]]
 																	#Adjust data
 																	newMonthData <- fix_PPTdata_length(data=newMonthData, targetLength=sum(im_month)) #adjust number of days in case we got a month with a different number of days
@@ -1037,7 +1037,8 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 	applyDelta_oneYear <- compiler::cmpfun(function(obs, delta_ts, ppt_fun, daily, monthly, ppt_type = c("simple", "detailed"), dailyPPTceiling, sigmaN, do_checks) {
 		ppt_type <- match.arg(ppt_type)
 
-		month <- 1 + as.POSIXlt(seq(ISOdate(obs@year, 1, 1), ISOdate(obs@year, 12, 31), by = "day"))$mon
+		month <- 1 + as.POSIXlt(seq(ISOdate(obs@year, 1, 1, tz = "UTC"),
+														ISOdate(obs@year, 12, 31, tz = "UTC"), by = "day"))$mon
 		ydeltas <- delta_ts[delta_ts[, "Year"] == obs@year, -(1:2)]
 		add_days <- ppt_fun[month] == "+"
 		mult_days <- !add_days
@@ -1083,7 +1084,6 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 
 	applyDeltas2 <- compiler::cmpfun(function(daily, monthly, years, delta_ts, ppt_fun, ppt_type = c("simple", "detailed"), dailyPPTceiling, sigmaN, do_checks = FALSE) {
 		ppt_type <- match.arg(ppt_type)
-		# daily_months <- 1 + as.POSIXlt(seq(ISOdate(years[1], 1, 1), ISOdate(years[length(years)], 12, 31), by = "day"))$mon
 
 		sw_list <- list()
 		totalPPT_to_remove <- 0
@@ -1606,7 +1606,7 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 							ftemp <- textConnection(success)
 						} else if (service == "opendap") {
 							ftemp <- textConnection((temp <- strsplit(success, split="\n\n", fixed=TRUE))[[1]][3])
-							ttemp <- as.POSIXlt("1950-01-01") + 86400 * as.numeric(scan(text=sub("\n", ",", temp[[1]][4], fixed=TRUE), what="character", sep=",", quiet=TRUE)[-1])
+							ttemp <- as.POSIXlt("1950-01-01", tz = "UTC") + 86400 * as.numeric(scan(text=sub("\n", ",", temp[[1]][4], fixed=TRUE), what="character", sep=",", quiet=TRUE)[-1])
 						}
 						success <- 0
 					}
@@ -1623,7 +1623,7 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 				if (service == "ncss") {
 					temp <- read.csv(ftemp, colClasses=c("POSIXct", "NULL", "NULL", "numeric")) #colnames = Time, Lat, Long, Variable
 					vtemp <- temp[, 2]
-					ttemp <- as.POSIXlt(temp[, 1])
+					ttemp <- as.POSIXlt(temp[, 1], tz = "UTC")
 				} else if (service == "opendap") {
 					vtemp <- read.csv(ftemp, colClasses=c("NULL", "numeric"), header=FALSE)[-1, ] #columns = Index, Variable
 				}
@@ -1738,8 +1738,8 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 			baseYear <- temp[sapply(temp, function(x) !is.na(x))][[1]]
 			stopifnot(length(baseYear) == 1)
 
-			firstDate <- as.POSIXlt(baseYear + tvals[1])
-			lastDate <- as.POSIXlt(baseYear + tvals[N])
+			firstDate <- as.POSIXlt(baseYear + tvals[1], tz = "UTC")
+			lastDate <- as.POSIXlt(baseYear + tvals[N], tz = "UTC")
 
 			startYear <- firstDate$year + 1900
 			startMonth <- firstDate$mon + 1
@@ -2459,11 +2459,11 @@ if (exinfo$GDODCPUCLLNL || exinfo$ExtractClimateChangeScenarios_CMIP5_BCSD_NEX_U
 		getYears <- list(n_first = nrow(temp1), first = temp1, n_second = nrow(temp2), second = temp2)
 
 		#Monthly time-series
-		getYears$first_dates <- lapply(1:getYears$n_first, FUN=function(it) as.POSIXlt(seq(from=as.POSIXlt(paste0(getYears$first[it, 1], "-01-01")), to=as.POSIXlt(paste0(getYears$first[it, 2], "-12-31")), by="1 month")))
-		getYears$second_dates <- lapply(1:getYears$n_second, FUN=function(it) as.POSIXlt(seq(from=as.POSIXlt(paste0(getYears$second[it, 1], "-01-01")), to=as.POSIXlt(paste0(getYears$second[it, 2], "-12-31")), by="1 month")))
+		getYears$first_dates <- lapply(1:getYears$n_first, FUN=function(it) as.POSIXlt(seq(from=ISOdate(getYears$first[it, 1], 1, 1, tz = "UTC"), to=ISOdate(getYears$first[it, 2], 12, 31, tz = "UTC"), by="1 month")))
+		getYears$second_dates <- lapply(1:getYears$n_second, FUN=function(it) as.POSIXlt(seq(from=ISOdate(getYears$second[it, 1], 1, 1, tz = "UTC"), to=ISOdate(getYears$second[it, 2], 12, 31, tz = "UTC")), by="1 month")))
 		#Days per month
-		getYears$first_dpm <- lapply(1:getYears$n_first, FUN=function(it) rle(as.POSIXlt(seq(from=as.POSIXlt(paste0(getYears$first[it, 1], "-01-01")), to=as.POSIXlt(paste0(getYears$first[it, 2], "-12-31")), by="1 day"))$mon)$lengths)
-		getYears$second_dpm <- lapply(1:getYears$n_second, FUN=function(it) rle(as.POSIXlt(seq(from=as.POSIXlt(paste0(getYears$second[it, 1], "-01-01")), to=as.POSIXlt(paste0(getYears$second[it, 2], "-12-31")), by="1 day"))$mon)$lengths)
+		getYears$first_dpm <- lapply(1:getYears$n_first, FUN=function(it) rle(as.POSIXlt(seq(from=ISOdate(getYears$first[it, 1], 1, 1, tz = "UTC"), to=ISOdate(getYears$first[it, 2], 12, 31, tz = "UTC")), by="1 day"))$mon)$lengths)
+		getYears$second_dpm <- lapply(1:getYears$n_second, FUN=function(it) rle(as.POSIXlt(seq(from=ISOdate(getYears$second[it, 1], 1, 1, tz = "UTC"), to=ISOdate(getYears$second[it, 2], 12, 31, tz = "UTC")), by="1 day"))$mon)$lengths)
 
 		#Logical on how to select from getYears
 		assocYears <- vector("list", length = 1 + length(reqRCPs) * nrow(future_yrs))

diff --git a/2_SWSF_p4of5_Code_v51.R b/2_SWSF_p4of5_Code_v51.R
@@ -666,7 +666,7 @@ if(do_weather_source){
 			#	- Grids: Geographic Coordinate Reference: WGS_1984; Projection: Lambert Conformal Conic
 			#	- Cells size: 1000 x 1000 m
 			#	- All Daymet years, including leap years, have 1 - 365 days. For leap years, the Daymet database includes leap day. Values for December 31 are discarded from leap years to maintain a 365-day year.
-			there <- simstartyr >= 1980 && endyr <= as.POSIXlt(Sys.time())$year+1900 - 1
+			there <- simstartyr >= 1980 && endyr <= as.POSIXlt(Sys.time(), tz = "UTC")$year+1900 - 1
 			if (any(there)) {
         there <- (SWRunInformation[runIDs_sites, "X_WGS84"] >= -179 &
                   SWRunInformation[runIDs_sites, "X_WGS84"] <= -5) &
@@ -4907,7 +4907,7 @@ do_OneSite <- function(i_sim, i_labels, i_SWRunInformation, i_sw_input_soillayer
 
 						#Regeneration year=RY: RYdoy=1 == start of seed dispersal = start of 'regeneration year'
 						Doy_SeedDispersalStart <- max(round(param$Doy_SeedDispersalStart0 + param$SeedDispersalStart_DependencyOnMeanTempJanuary * TmeanJan, 0) %% 365, 1)
-						moveByDays <- ifelse(Doy_SeedDispersalStart ==  1, 1, max(as.numeric(as.POSIXlt(paste(simTime$useyrs[1] - 1, "-12-31", sep="")) - as.POSIXlt(paste(simTime$useyrs[1] - 1, "-01-01", sep=""))) + 1 - (Doy_SeedDispersalStart - 1) %% 365, 1))
+						moveByDays <- ifelse(Doy_SeedDispersalStart ==  1, 1, max(as.numeric(ISOdate(simTime$useyrs[1] - 1, 12, 31, tz = "UTC") - ISOdate(simTime$useyrs[1] - 1, 1, 1, tz = "UTC")) + 1 - (Doy_SeedDispersalStart - 1) %% 365, 1))
 						#Calculate regeneration year dates
 						if (startyr > simstartyr) {
 						  #start earlier to complete RY

diff --git a/2_SWSF_p5of5_Functions_v51.R b/2_SWSF_p5of5_Functions_v51.R
@@ -474,17 +474,17 @@ simTiming <- compiler::cmpfun(function(startyr, simstartyr, endyr) {
   res <- list()
   #simyrs <- simstartyr:endyr
   #no.simyr <- endyr - simstartyr + 1
-  temp <- as.POSIXlt(paste0(startyr, "-01-01"))
+  temp <- ISOdate(startyr, 1, 1, tz = "UTC")
 
   res[["useyrs"]] <- startyr:endyr
 
   res[["no.useyr"]] <- endyr - startyr + 1
   res[["no.usemo"]] <- res[["no.useyr"]] * 12
-  res[["no.usedy"]] <- as.numeric(as.POSIXlt(paste0(endyr, "-12-31")) - temp) + 1
+  res[["no.usedy"]] <- as.numeric(ISOdate(endyr, 12, 31, tz = "UTC") - temp) + 1
 
   res[["discardyr"]] <- startyr - simstartyr
   res[["discardmo"]] <- res[["discardyr"]] * 12
-  res[["discarddy"]] <- as.numeric(temp - as.POSIXlt(paste0(simstartyr, "-01-01")))
+  res[["discarddy"]] <- as.numeric(temp - ISOdate(simstartyr, 1, 1, tz = "UTC"))
 
   res[["index.useyr"]] <- res[["discardyr"]] + seq_len(res[["no.useyr"]])
   res[["index.usemo"]] <- res[["discardmo"]] + seq_len(res[["no.usemo"]])
@@ -497,16 +497,16 @@ simTiming_ForEachUsedTimeUnit <- compiler::cmpfun(function(st, sim_tscales, lati
   res <- list()
 
   if (any(sim_tscales == "daily")) {
-    temp <- as.POSIXlt(seq(from = as.POSIXlt(paste0(min(st$useyrs), "-01-01")),
-                           to = as.POSIXlt(paste0(max(st$useyrs), "-12-31")),
+    temp <- as.POSIXlt(seq(from = ISOdate(min(st$useyrs), 1, 1, tz = "UTC"),
+                           to = ISOdate(max(st$useyrs), 12, 31, tz = "UTC"),
                            by = "1 day"))
 
     res$doy_ForEachUsedDay <- res$doy_ForEachUsedDay_NSadj <- temp$yday + 1
     res$month_ForEachUsedDay <- res$month_ForEachUsedDay_NSadj <- temp$mon + 1
     res$year_ForEachUsedDay <- res$year_ForEachUsedDay_NSadj <- temp$year + 1900
 
     if (latitude < 0 && account_NorthSouth) {
-      dshift <- as.POSIXlt(paste(st$useyrs, 6, 30, sep = "-"))$yday + 1	#new month either at end of year or in the middle because the two halfs (6+6 months) of a year are of unequal length (182 (183 if leap year) and 183 days): I chose to have a new month at end of year (i.e., 1 July -> 1 Jan & 30 June -> 31 Dec; but, 1 Jan -> July 3/4): and instead of a day with doy=366, there are two with doy=182
+      dshift <- as.POSIXlt(ISOdate(st$useyrs, 6, 30, tz = "UTC"))$yday + 1	#new month either at end of year or in the middle because the two halfs (6+6 months) of a year are of unequal length (182 (183 if leap year) and 183 days): I chose to have a new month at end of year (i.e., 1 July -> 1 Jan & 30 June -> 31 Dec; but, 1 Jan -> July 3/4): and instead of a day with doy=366, there are two with doy=182
       res$doy_ForEachUsedDay_NSadj <- unlist(lapply(seq_along(st$useyrs), function(x) {
         temp <- res$doy_ForEachUsedDay[st$useyrs[x] == res$year_ForEachUsedDay]
         c(temp[-(1:dshift[x])], temp[1:dshift[x]])
@@ -596,8 +596,8 @@ sw_SiteClimate_Ambient <- compiler::cmpfun(function(weatherList, year.start, yea
         dailyTempMean <- c(dailyTempMean, temp.dailyTempMean)
       }
 
-      month_forEachDoy <- as.POSIXlt(seq(from = as.POSIXlt(paste0(years[y], "-01-01")),
-                                         to = as.POSIXlt(paste0(years[y], "-12-31")),
+      month_forEachDoy <- as.POSIXlt(seq(from = ISOdate(years[y], 1, 1, tz = "UTC"),
+                                         to = ISOdate(years[y], 12, 31, tz = "UTC"),
                                          by = "1 day"))$mon + 1
 
       tempMean <- tempMean + tapply(temp.dailyTempMean, month_forEachDoy, mean)
@@ -2031,13 +2031,13 @@ ExtractGriddedDailyWeatherFromMaurer2002_NorthAmerica <- compiler::cmpfun(functi
     colnames(weath.data) <- c("year", "month", "day", "prcp_mm", "Tmax_C", "Tmin_C", "Wind_mPERs")
 
     #times
-    date <- seq(from=as.Date(with(weath.data[1, ], paste(year, month, day, sep="-")), format="%Y-%m-%d"),
-        to=as.Date(with(weath.data[nrow(weath.data), ], paste(year, month, day, sep="-")), format="%Y-%m-%d"),
-        by="1 day")
+    doy <- 1 + as.POSIXlt(seq(from = with(weath.data[1, ], ISOdate(year, month, day, tz = "UTC")),
+        to = with(weath.data[nrow(weath.data), ], ISOdate(year, month, day, tz = "UTC")),
+        by = "1 day"))$yday
 
     # conversion precipitation: mm/day -> cm/day
-    data_all <- with(weath.data, data.frame(doy=1 + as.POSIXlt(date)$yday, Tmax_C, Tmin_C, prcp_mm/10))
-    colnames(data_all) <- c("DOY", "Tmax_C", "Tmin_C", "PPT_cm")
+    data_all <- with(weath.data, data.frame(
+      DOY = doy, Tmax_C = Tmax_C, Tmin_C = Tmin_C, PPT_cm = prcp_mm / 10))
 
     years <- startYear:endYear
     n_years <- length(years)
@@ -2046,7 +2046,7 @@ ExtractGriddedDailyWeatherFromMaurer2002_NorthAmerica <- compiler::cmpfun(functi
     for(y in seq_along(years)) {
       data_sw <- data_all[weath.data$year == years[y], ]
       data_sw[, -1] <- round(data_sw[, -1], 2) #weather.digits
-      weathDataList[[y]]<-new("swWeatherData",
+      weathDataList[[y]] <- new("swWeatherData",
                               year = years[y],
                               data = data.matrix(data_sw, rownames.force = FALSE)) #strip row.names, otherwise they consume about 60% of file size
     }

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SWSF
 Title: SOILWAT Simulation Framework
-Version: 1.6.2
-Date: 2016-09-24
+Version: 1.6.3
+Date: 2016-09-28
 Authors@R: c(person("Daniel", "Schlaepfer", email = "daniel.schlaepfer@unibas.ch", role = c("aut", "cre")),
 			person("Caitlin", "Andrews", role = "ctb", email = "not@available.com"))
 			person("Ryan", "Murphy", role = "ctb", email = "not@available.com"))