0.3.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pesco
 Type: Package
 Title: Data fusion for air quality data
-Version: 0.2.4
-Date: 2015-06-22
+Version: 0.3.0
+Date: 2015-07-09
 Author: Lucia Paci, Giovanni Bonafe'
 Maintainer: G.Bonafe' <[email protected]>
 Imports: geoR, akima, fields, caTools, ncdf, timeDate, chron

NEWS

@@ -1,3 +1,21 @@
+Changes in pesco 0.3.0 [2015-07-09]
+=====================================
+ * now prepare.obs requires pollutant specification
+
+Changes in pesco 0.2.7 [2015-07-08]
+=====================================
+ * in read.qaria changed BST to Africa/Algiers
+ * bug fixed in prepare.obs
+
+Changes in pesco 0.2.6 [2015-07-01]
+=====================================
+ * modified read.ncdf.arpaer
+
+Changes in pesco 0.2.5 [2015-06-23]
+=====================================
+ * bug fixed in qaria2long
+ * modified read.ncdf.arpaer
+
 Changes in pesco 0.2.4 [2015-06-22]
 =====================================
  * bug fixed in read.sql

R/prepare.R

@@ -89,18 +89,18 @@ prepare.elev <- function(elev,
 }
 
 ## Observed data
-prepare.obs <- function(obs.daily, day,
+prepare.obs <- function(obs.daily, day, pollutant,
                         conc.min=10^-6) {
   time <- sort(unique(as.POSIXct(as.character(obs.daily$Time),tz="Africa/Algiers")))
   if(min(diff.POSIXt(time)) < as.difftime(1,units="days")) {
     stop("Cannot deal with sub-daily data.")
   }
   out <- subset(obs.daily, 
-                subset=(format(time,format="%Y-%m-%d")==
+                subset=(format(obs.daily$Time,format="%Y-%m-%d")==
                           format(as.POSIXct(day),format="%Y-%m-%d")))
-  out <- out[which(!is.na(out[,2])),]
-  out[,2] <- pmax(out[,2], conc.min)
-  rownames(out) <- 1:nrow(out)
+  out <- out[which(!is.na(out[,pollutant])),]
+  out[,pollutant] <- pmax(out[,pollutant], conc.min, na.rm=T)
+  if(nrow(out)>0) rownames(out) <- 1:nrow(out)
   return(out)
 }
 
@@ -113,7 +113,7 @@ prepare.day <- function(day,
                         verbose=FALSE) {
   ## select the required day from the observations
   obs.day <- prepare.obs(obs.daily=obs.daily, day=day)
-  if(verbose) print(paste("Prepared observations for day ",day,sep=""))
+  if(verbose) cat(paste("prepare.day: prepared observations for day ",day,"\n",sep=""))
 
   ## get the coordinates of the stations with valid data
   coords.pnt <- ll2utm(rlat=obs.day$Lat,
@@ -126,7 +126,7 @@ prepare.day <- function(day,
   emis.day <- prepare.emis(emis.winter=emis.winter,
                            emis.summer=emis.summer, 
                            day=day, x.pnt=x.pnt, y.pnt=y.pnt)
-  if(verbose) print(paste("Prepared emissions for day ",day,sep=""))
+  if(verbose) cat(paste("prepare.day: prepared emissions for day ",day,"\n",sep=""))
 
   ## get the coordinates of the reference grid
   x.grd <- emis.summer$coords$x
@@ -137,7 +137,7 @@ prepare.day <- function(day,
   ctm.day <- prepare.ctm(ctm.daily=ctm.daily, day=day, 
                          x.pnt=x.pnt, y.pnt=y.pnt, 
                          x.grd=x.grd, y.grd=y.grd)
-  if(verbose) print(paste("Prepared CTM concentrations for day ",day,sep=""))
+  if(verbose) cat(paste("prepare.day: prepared CTM concentrations for day ",day,"\n",sep=""))
 
   ## prepare elevation for the required day
   if(is.null(elev)) {
@@ -146,7 +146,7 @@ prepare.day <- function(day,
     elev.day <- prepare.elev(elev=elev,
                              x.pnt=x.pnt, y.pnt=y.pnt, 
                              z.pnt=obs.day$Elev)  
-    if(verbose) print(paste("Prepared elevation for day ",day,sep=""))
+    if(verbose) cat(paste("prepare.day: prepared elevation for day ",day,"\n",sep=""))
   }
 
   Out <- list(obs.day=obs.day, 

R/read.R

@@ -17,7 +17,11 @@ read.ncdf.arpaer <- function(con=NULL, pollutant="pm10", lev=1,
   Time <- as.POSIXct(get.var.ncdf(nc,varid="Times"), 
                      format="%Y-%m-%d_%H:%M:%S", tz=tz.in)
   Time <- tz.change(x=Time,tz.in=tz.in,tz.out=tz.out)
-  value  <- get.var.ncdf(nc,varid=pollutant)
+  opts <- c(pollutant, toupper(pollutant), tolower(pollutant))
+  vars <- names(nc$var)
+  pp <- intersect(opts, vars)
+  if(length(pp)==0) stop(paste(pollutant,"not found in",con))
+  value  <- get.var.ncdf(nc,varid=pp)
   if(length(dim(value))==4) {
     value <- value[,,lev,]
   } else if (length(dim(value))!=3) {
@@ -175,7 +179,7 @@ read.qaria <- function(file) {
   } else {
     strTime <- paste(strTime," 00:00",sep="")    
   }
-  Time <- as.POSIXct(strTime,tz="BST")
+  Time <- as.POSIXct(strTime,tz="Africa/Algiers")
   out <- data.frame(Time=Time, Value=dat[,ncol(dat)])
   names(out)[2] <- names(dat)[ncol(dat)]
   return(out)
@@ -206,7 +210,7 @@ qaria2long <- function(datafiles,
     if(is.null(codes)) {
       code <- substr(datafiles[i],
                       rev(gregexpr("_",datafiles[i])[[1]])[1]+1,
-                      rev(gregexpr("\\.",datafiles[i])[[1]][1]-1))
+                      rev(gregexpr("\\.",datafiles[i])[[1]])[1]-1)
     } else {
       code <- codes[i]
     }

demo/daily.synthesis.R

@@ -6,7 +6,7 @@
 
 #' ## Demo: How to prepare daily data for PESCO
 #' You can reproduce the following R code with 
-#' ```demo(daily.sinthesis)``` after loading package ```pesco```.
+#' ```demo(daily.synthesis)``` after loading package ```pesco```.
 
 ## load package
 require(pesco)
@@ -50,5 +50,6 @@ data(PM10.ctm)
 ## calculate daily averages
 PM10.ctm.ave <- dailyCtm(PM10.ctm, statistic="mean")
 rm(PM10.ctm)
+library(fields)
 filled.contour(PM10.ctm.ave$data[,,1],color.palette=tim.colors)
 

man/prepare.functions.Rd

@@ -25,7 +25,8 @@ prepare.emis(emis.winter, emis.summer, day,
 prepare.elev(elev, x.pnt, y.pnt, 
              z.pnt = rep(NA,length(x.pnt)),
              x.grd = NULL, y.grd = NULL)   
-prepare.obs(obs.daily, day, conc.min = 10^-6)
+prepare.obs(obs.daily, day, pollutant,
+             conc.min = 10^-6)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
@@ -44,6 +45,7 @@ prepare.obs(obs.daily, day, conc.min = 10^-6)
  \describe{
  \item{coords}{coordinates, a list of 2 numeric vectors x and y}
  \item{data}{numeric vector}}}
+\item{pollutant}{name of the column with pollutant concentations}
 \item{verbose}{logical; if \code{TRUE} some messages are given}
 \item{x.pnt}{numeric vector of x coordinates of the stations}
 \item{y.pnt}{numeric vector of y coordinates of the stations}