v1.0.2 rename function names to avoid problems with S3 methods

Author: cas

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: plotFun
 Type: Package
 Title: Helper functions for plotting data
-Version: 1.0.1
+Version: 1.0.2
 Date: 2019-01-15
 Author: A. Casanueva
 Maintainer: A.Casanueva <ana.casanueva@meteoswiss.ch>

NAMESPACE

@@ -1,11 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-export(data.agg)
-export(plot.Grid)
-export(plot.Stn)
-export(plot.TimeSeries)
-export(plot.heat)
-export(plot.kde2d.hist)
+export(data_agg)
+export(plotFun.grid)
+export(plotFun.heat)
+export(plotFun.kde2d.hist)
+export(plotFun.stn)
+export(plotFun.ts)
 import(HeatStress)
 import(MASS)
 import(RColorBrewer)

NEWS

@@ -1,3 +1,7 @@
-* Changes in v.1.0.1
+* Changes in v1.0.2
+
+Change function names to avoid S3 methods.
+
+* Changes in v1.0.1
 
 Package ready to use

R/data.agg.R R/data_agg.RR/data.agg.R renamed to R/data_agg.R

@@ -19,17 +19,17 @@
 #' data.day <- array(runif(length(dates.day)*2, -5, 30), dim=c(length(dates.day),2)) 
 #' data.hour <- rnorm(length(dates.hour), mean=15, sd=2)
 #' # Aggregate from daily to annual
-#' data.agg(data.day, dates.day, agg="Y", aggFun="mean") 
+#' data_agg(data.day, dates.day, agg="Y", aggFun="mean") 
 #' # Aggregate from daily to monthly
-#' data.agg(data.day, dates.day, agg="M", aggFun="max") 
+#' data_agg(data.day, dates.day, agg="M", aggFun="max") 
 #' # Aggregate from daily to seasonal
-#' data.agg(data.day, dates.day, agg="S", aggFun="min") 
+#' data_agg(data.day, dates.day, agg="S", aggFun="min") 
 #' # Aggregate from hourly to daily
-#' data.agg(data.hour, dates.hour, agg="D", aggFun="mean") 
+#' data_agg(data.hour, dates.hour, agg="D", aggFun="mean") 
 #' }
 
 
-data.agg <- function(data, dates, agg=NULL, aggFun="mean", input.mch=FALSE){
+data_agg <- function(data, dates, agg=NULL, aggFun="mean", input.mch=FALSE){
 
 
   data <- as.matrix(data) # to avoid problems with 1 station (vector)
@@ -190,4 +190,4 @@ data.agg <- function(data, dates, agg=NULL, aggFun="mean", input.mch=FALSE){
   res <- list(data.agg=df, dates.agg=dates.agg, agg= agg, aggFun=aggFun)
   return(res)
 
-} # end data.agg
+} # end data_agg

R/plotFun.R

@@ -11,15 +11,15 @@
 #' The following plotting functions are implemented:
 #'  \itemize{
 #'  
-#'  \item \code{plot.Stn}: Plot a map of stations.
-#'  \item \code{plot.Grid}: Plot a map of a regular grid.
-#'  \item \code{plot.TimeSeries}: Plot time series with or without temporal aggregation.
-#'  \item \code{plot.kde2d.hist}: Plot a 2D Kernel density plot with the histograms of the marginal distributions.
-#'  \item \code{plot.heat}: Plot heat index as a function of the input variables.
+#'  \item \code{plotFun.stn}: Plot a map of stations.
+#'  \item \code{plotFun.grid}: Plot a map of a regular grid.
+#'  \item \code{plotFun.ts}: Plot time series with or without temporal aggregation.
+#'  \item \code{plotFun.kde2d.hist}: Plot a 2D Kernel density plot with the histograms of the marginal distributions.
+#'  \item \code{plotFun.heat}: Plot heat index as a function of the input variables.
 #'  
 #'  
 #'  Additional functions:  
-#'  \item \code{data.agg}: Function to obtain temporal aggregations (from hours to days and from days to months, seasons or years).
+#'  \item \code{data_agg}: Function to obtain temporal aggregations (from hours to days and from days to months, seasons or years).
 #'  \item \code{sort4plot}: Funtion to sort the data in ascending order before plot.
 
 #'  } 

R/plot.colorbar.R R/plotFun.colorbar.RR/plot.colorbar.R renamed to R/plotFun.colorbar.R

@@ -11,7 +11,7 @@
 #' @author Ana Casanueva (16.02.2017)
 #' 
 
-plot.colorbar <- function(breaks, palette=palette, unit.text, cex.unit, cex.textcbar) {
+plotFun.colorbar <- function(breaks, palette=palette, unit.text, cex.unit, cex.textcbar) {
 
 
   # noo only write some labels, but all colours!!

R/plot.Grid.R R/plotFun.grid.RR/plot.Grid.R renamed to R/plotFun.grid.R

@@ -26,7 +26,7 @@
 #' @param export.format "png" or "pdf" format.
 #' @param lon.points vector of longitudes for grid points to be marked in the map.
 #' @param lat.points vector of latitudes for grid points to be marked in the map.
-#' @export plot.Grid
+#' @export plotFun.grid
 #' @details Packages classInt and maps needed.
 #' @import classInt maps
 #' @author Ana Casanueva (24.05.2017)
@@ -36,10 +36,10 @@
 #' y <- seq(35,55); n=length(y)
 #' tas <- array(runif(n*m*6, -5, 30), dim=c(6,m,n)) # time, lon lat.
 #' # Single plot
-#' plot.Grid(tas[1,,], lon=x, lat = y, lonLims = c(-10,30), latLims = c(35,65), width.cbar = 0.2, 
+#' plotFun.grid(tas[1,,], lon=x, lat = y, lonLims = c(-10,30), latLims = c(35,65), width.cbar = 0.2, 
 #' breaks = seq(10,20), title.main = "Mean Temp.", unit.text = "degC", cex.main=1.5)
 #' # Multi-plots
-#' plot.Grid(list(tas[1,,], tas[2,,], tas[3,,], tas[4,,], tas[5,,], tas[6,,]), 
+#' plotFun.grid(list(tas[1,,], tas[2,,], tas[3,,], tas[4,,], tas[5,,], tas[6,,]), 
 #' lon=x, lat = y, lonLims = c(-10,30), latLims = c(35,65), lattice=c(2,3), width.cbar = 0.1, 
 #' breaks = seq(10,20), window.height = 8, window.width = 12, 
 #' title.single = c("Temp1","Temp2","Temp3","Temp4","Temp5","Temp6"), cex.single = 1.3, 
@@ -48,7 +48,7 @@
 
 
 
-plot.Grid <- function(data, lon, lat, lonLims=c(min(lon),max(lon)), latLims=c(min(lat),max(lat)), lattice=NULL, breaks= NULL, palette=rainbow(10), window.width=8, window.height=6, title.main=NULL, title.single=NULL,  unit.text=NULL, cex.main=1,  cex.single=1, cex.unit=1, cex.textcbar=1, width.cbar=0.1, disp.warnings=FALSE, export=FALSE, export.format=NULL, export.path=NULL, lon.points=NA, lat.points=NA){
+plotFun.grid <- function(data, lon, lat, lonLims=c(min(lon),max(lon)), latLims=c(min(lat),max(lat)), lattice=NULL, breaks= NULL, palette=rainbow(10), window.width=8, window.height=6, title.main=NULL, title.single=NULL,  unit.text=NULL, cex.main=1,  cex.single=1, cex.unit=1, cex.textcbar=1, width.cbar=0.1, disp.warnings=FALSE, export=FALSE, export.format=NULL, export.path=NULL, lon.points=NA, lat.points=NA){
 
 	# Verification checks 
 	try(if(export & is.null(export.format)) stop("Cannot save plot: missing export.format"))
@@ -72,11 +72,11 @@ plot.Grid <- function(data, lon, lat, lonLims=c(min(lon),max(lon)), latLims=c(mi
 		if(is.null(breaks)) breaks <- set.Breaks(data)
 
 		# Plot
-		plot.Grid1(data, lon, lat, lonLims, latLims, breaks, palette, cex.main, title.main, lon.points=lon.points, lat.points=lat.points)
+		plotFun.grid1(data, lon, lat, lonLims, latLims, breaks, palette, cex.main, title.main, lon.points=lon.points, lat.points=lat.points)
 
 		# Include colorbar
 		par(mar=c(3,0.6,3,5))
-		plot.colorbar(breaks, palette, unit.text, cex.unit, cex.textcbar)
+		plotFun.colorbar(breaks, palette, unit.text, cex.unit, cex.textcbar)
 
 	} else{
 		# Number of real plots to make
@@ -110,7 +110,7 @@ plot.Grid <- function(data, lon, lat, lonLims=c(min(lon),max(lon)), latLims=c(mi
 
 		# Plot subplots
 		for (i in 1:n){
-			plot.Grid1(data[[i]], lon, lat, lonLims, latLims, breaks, palette, cex.single, title.single[i], lon.points=lon.points, lat.points=lat.points)
+			plotFun.grid1(data[[i]], lon, lat, lonLims, latLims, breaks, palette, cex.single, title.single[i], lon.points=lon.points, lat.points=lat.points)
 		}
 
 		# Fill with empty plots when necessary (i.e. to fill the matrix)
@@ -124,60 +124,11 @@ plot.Grid <- function(data, lon, lat, lonLims=c(min(lon),max(lon)), latLims=c(mi
 
 		# Include colorbar
 		par(mar=c(3,0.6,3,4))
-		plot.colorbar(breaks, palette, unit.text, cex.unit, cex.textcbar)
+		plotFun.colorbar(breaks, palette, unit.text, cex.unit, cex.textcbar)
 		# Plot title
 		mtext(title.main, outer = TRUE, cex = cex.main)
 	}
 
 	if (export & !is.null(export.format) & !is.null(export.path)) dev.off()
 }
 
-#' Plot grid (single plot).
-#' 
-#' Plot a figure based on a regular grid, for a single plot.
-#' 
-#' @param x matrix to be plotted. 
-#' @param lon array of longitudes
-#' @param lat array of latitudes
-#' @param lonLims 2-elemtent vector with the range of longitudes to be plotted. By default all the data is plotted.
-#' @param latLims 2-elemtent vector with the range of latitudes to be plotted. By default all the data is plotted.
-#' @param breaks vector of values defining the intervals to be used in the colorbar. 
-#' @param palette character vector with the colors for the plot. They will be interpolated to match the number of intervals defined by breaks.
-#' @param title.main character string with the title.
-#' @param cex.main numeric value giving the title expansion factor. Default: 1.
-#' @param lon.points vector of longitudes for grid points to be marked in the map.
-#' @param lat.points vector of latitudes for grid points to be marked in the map.
-#'
-#' @author Ana Casanueva (16.02.2017)
-#' 
-
-plot.Grid1 <- function(x, lon, lat, lonLims,latLims,  breaks= breaks, palette=palette, cex.main, title.main, lon.points=lon.points, lat.points=lat.points) {
-
-	# Plot subregion or not
-	ind.x <- which(lon >= lonLims[1] & lon <= lonLims[2])
-	ind.y <- which(lat >= latLims[1] & lat <= latLims[2])
-	lon <- lon[ind.x]
-	lat <- lat[ind.y]
-	x <- x[ind.x, ind.y]
-
-	# Number of intervals to plot
-	lev <- length(breaks)-1; 
-
-	# Interpolate palette to the number of levels
-	cols <- colorRampPalette(palette)(lev)
-
-	# set values above and below the break to the maximum and minimum for plotting.
-	x[which(x<min(breaks))] <- min(breaks)
-	x[which(x>max(breaks))] <- max(breaks)
-	if(!is.null(which(x < min(breaks))) | !is.null(which(x > max(breaks))))	print("Warning: values out of the range have been set to maximum or minimum of the colorbar")
-
-	# plot map
-	par(mar=c(0.3,0.3,2,0)) # reduce space around plot
-	image(lon, lat, x, breaks= breaks, col=cols, main=title.main, cex.main=cex.main, xaxt="n", yaxt="n", xlab=NA, ylab=NA)
-	points(lon.points, lat.points, lwd=2, cex=1.5)
-	map(add=T)
-}
-
-
-
-

R/plotFun.grid1.R

@@ -0,0 +1,46 @@
+#' Plot grid (single plot).
+#' 
+#' Plot a figure based on a regular grid, for a single plot.
+#' 
+#' @param x matrix to be plotted. 
+#' @param lon array of longitudes
+#' @param lat array of latitudes
+#' @param lonLims 2-elemtent vector with the range of longitudes to be plotted. By default all the data is plotted.
+#' @param latLims 2-elemtent vector with the range of latitudes to be plotted. By default all the data is plotted.
+#' @param breaks vector of values defining the intervals to be used in the colorbar. 
+#' @param palette character vector with the colors for the plot. They will be interpolated to match the number of intervals defined by breaks.
+#' @param title.main character string with the title.
+#' @param cex.main numeric value giving the title expansion factor. Default: 1.
+#' @param lon.points vector of longitudes for grid points to be marked in the map.
+#' @param lat.points vector of latitudes for grid points to be marked in the map.
+#'
+#' @author Ana Casanueva (16.02.2017)
+#' 
+
+plotFun.grid1 <- function(x, lon, lat, lonLims,latLims,  breaks= breaks, palette=palette, cex.main, title.main, lon.points=lon.points, lat.points=lat.points) {
+  
+  # Plot subregion or not
+  ind.x <- which(lon >= lonLims[1] & lon <= lonLims[2])
+  ind.y <- which(lat >= latLims[1] & lat <= latLims[2])
+  lon <- lon[ind.x]
+  lat <- lat[ind.y]
+  x <- x[ind.x, ind.y]
+  
+  # Number of intervals to plot
+  lev <- length(breaks)-1; 
+  
+  # Interpolate palette to the number of levels
+  cols <- colorRampPalette(palette)(lev)
+  
+  # set values above and below the break to the maximum and minimum for plotting.
+  if(length(which(x < min(breaks)))!=0 | length(which(x > max(breaks)))!=0)	print("Warning: values out of the range have been set to maximum or minimum of the colorbar")
+  x[which(x<min(breaks))] <- min(breaks)
+  x[which(x>max(breaks))] <- max(breaks)
+  
+  # plot map
+  par(mar=c(0.3,0.3,2,0)) # reduce space around plot
+  image(lon, lat, x, breaks= breaks, col=cols, main=title.main, cex.main=cex.main, xaxt="n", yaxt="n", xlab=NA, ylab=NA)
+  points(lon.points, lat.points, lwd=2, cex=1.5)
+  map(add=T)
+}
+

R/plot.heat.R R/plotFun.heat.RR/plot.heat.R renamed to R/plotFun.heat.R

@@ -23,27 +23,27 @@
 #' @details The two input variables of the desired index need to be provided, tas and either td or hu. Needed packages: HeatStress, RColorBrewer.
 #' @import HeatStress RColorBrewer
 #' @author Ana Casanueva, 13.12.2018
-#' @export plot.heat
+#' @export plotFun.heat
 #' @examples \dontrun{
 #' # Generate data
 #' tas <- rnorm(150, mean=15, sd=2)
 #' dew <- rnorm(150, mean=8, sd=1)
 #' hurs <- sample(1:100,150, replace=T)
 #' # Plot the heat plot
-#' plot.heat(hu=hurs, ta=tas, heat.index="wbt", title="Heat stress plot", cex.main=1.5, 
+#' plotFun.heat(hu=hurs, ta=tas, heat.index="wbt", title="Heat stress plot", cex.main=1.5, 
 #' xlab="Relative Humidity", ylab="Air temp.", n.bins=500)
 #' # Add points, change index
-#' plot.heat(hu=hurs, ta=tas, heat.index="swbgt", title="Heat stress plot", cex.main=1.5, 
+#' plotFun.heat(hu=hurs, ta=tas, heat.index="swbgt", title="Heat stress plot", cex.main=1.5, 
 #' xlab="Relative Humidity", ylab="Air temp.", n.bins=500, add.points=F)
 #' # Add contours, change index
-#' plot.heat(td=dew, ta=tas, heat.index="wbgt.shade", title="Heat stress plot", cex.main=1.5, 
+#' plotFun.heat(td=dew, ta=tas, heat.index="wbgt.shade", title="Heat stress plot", cex.main=1.5, 
 #' xlab="Dew point temp.", ylab="Air temp.", n.bins=500, add.contours=F)
 #' }
 
 
 
 
-plot.heat <- function(hu=NULL, td=NULL, ta, xlim=NULL, ylim=range(ta, na.rm=T), heat.index=NULL,  breaks.index=NULL, title=NULL, cex.main=1.5, xlab=NULL, ylab=NULL, n.bins=500, add.points=TRUE, add.contours=TRUE, unit.text=NULL, cex.unit=1, cex.textcbar=1.3){
+plotFun.heat <- function(hu=NULL, td=NULL, ta, xlim=NULL, ylim=range(ta, na.rm=T), heat.index=NULL,  breaks.index=NULL, title=NULL, cex.main=1.5, xlab=NULL, ylab=NULL, n.bins=500, add.points=TRUE, add.contours=TRUE, unit.text=NULL, cex.unit=1, cex.textcbar=1.3){
 
 
 	if(n.bins>100) message("Patience: number of bins is ", n.bins)
@@ -112,7 +112,7 @@ plot.heat <- function(hu=NULL, td=NULL, ta, xlim=NULL, ylim=range(ta, na.rm=T),
 
 	# add color bar
 	par(mar=c(3,0.6,3,4.5))
-	plot.colorbar(round(breaks.index,4), palette=cols, unit.text, cex.unit, cex.textcbar)
+	plotFun.colorbar(round(breaks.index,4), palette=cols, unit.text, cex.unit, cex.textcbar)
 
 }
 

R/plot.kde2d.hist.R R/plotFun.kde2d.hist.RR/plot.kde2d.hist.R renamed to R/plotFun.kde2d.hist.R

@@ -1,6 +1,6 @@
-#' Plot 2-dimensional kernel density plots and the histograms of the two input variables.
+#' Plot a 2-dimensional kernel density plot and the histograms of the two input variables.
 #'
-#' Plot 2-dimensional kernel density plots and the histograms of the two input variables.
+#' Plot a 2-dimensional kernel density plot and the histograms of the two input variables.
 #'
 #' @param var1 vector with data for one variable.
 #' @param var2 vector with data for another variable.
@@ -16,21 +16,21 @@
 #' @return Plot with the 2-dimensional kernel densities and historgrams for the input variables.
 #' @details The two-dimensional kernel density estimation is done with the function kde2d in package MASS.
 #' @import MASS RColorBrewer
-#' @export plot.kde2d.hist
+#' @export plotFun.kde2d.hist
 #' @author Ana Casanueva, 13.12.2018
 #' @examples \dontrun{
 #' # Generate data
 #' tas <- rnorm(1000, mean=15, sd=2)
 #' td <- rnorm(1000, mean=8, sd=1)
-#' # Plot "-Dim Kernel density with histograms
-#' plot.kde2d.hist(var1=td, var2=tas, xlab="Dew point temp.", ylab="Air temperature", 
+#' # Plot 2-Dim Kernel density with histograms
+#' plotFun.kde2d.hist(var1=td, var2=tas, xlab="Dew point temp.", ylab="Air temperature", 
 #' n.bins=25, add.contours=FALSE, title="2D density plot", cex.main=2)
 #' # add contours for the density values
-#' plot.kde2d.hist(var1=td, var2=tas, xlab="Dew point temp.", ylab="Air temperature", 
+#' plotFun.kde2d.hist(var1=td, var2=tas, xlab="Dew point temp.", ylab="Air temperature", 
 #' n.bins=25, add.contours=TRUE, title="2D density plot with contours", cex.main=2)
 #' }
 
-plot.kde2d.hist <- function(var1, var2, xlim=range(var1, na.rm=T), ylim=range(var2, na.rm=T), breaks.den=NULL, title=NULL, cex.main=1.5, xlab=NULL, ylab=NULL, n.bins=25, add.contours=TRUE){
+plotFun.kde2d.hist <- function(var1, var2, xlim=range(var1, na.rm=T), ylim=range(var2, na.rm=T), breaks.den=NULL, title=NULL, cex.main=1.5, xlab=NULL, ylab=NULL, n.bins=25, add.contours=TRUE){
 
 
 	# *** Build data frame with input variables and histograms ***
@@ -90,7 +90,7 @@ plot.kde2d.hist <- function(var1, var2, xlim=range(var1, na.rm=T), ylim=range(va
 
 	# add color bar
 	par(mar=c(3,0.6,3,4.5))
-	plot.colorbar(round(breaks.den,4), palette=cols, " ", 1, 1.3)
+	plotFun.colorbar(round(breaks.den,4), palette=cols, " ", 1, 1.3)
 
 	# plot title
 	par(mar=c(0.1,2,0.2,0.5))