X-Git-Url: https://git.auder.net/?a=blobdiff_plain;f=pkg%2FR%2Fplot.R;h=95dc0f77abf6aba1a925ae409a99152b47a31d6f;hb=98e958cab563866f8e00886b54336018a2e8bc97;hp=b720e9a16fe588f492cb6a77af54516115b94bda;hpb=469529710f56c790ae932b45d13fed2e34bcabf2;p=talweg.git

diff --git a/pkg/R/plot.R b/pkg/R/plot.R
index b720e9a..95dc0f7 100644
--- a/pkg/R/plot.R
+++ b/pkg/R/plot.R
@@ -1,120 +1,35 @@
-#' @title plot curves
+#' Plot curves
 #'
-#' @description Plot a range of curves in data
+#' Plot a range of curves in data
 #'
 #' @param data Object of class Data
 #' @param indices Range of indices (integers or dates)
 #'
 #' @export
-plotCurves <- function(data, indices)
+plotCurves <- function(data, indices=seq_len(data$getSize()))
 {
-	yrange = range( sapply( indices, function(i) {
-		serie = c(data$getCenteredSerie(i))
-		if (!all(is.na(serie)))
-			range(serie, na.rm=TRUE)
-		c()
-	}) )
+	series = data$getSeries(indices)
+	yrange = quantile(series, probs=c(0.05,0.95), na.rm=TRUE)
 	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
 	for (i in seq_along(indices))
 	{
-		plot(data$getSerie(indices[i]), type="l", ylim=yrange,
+		plot(series[,i], type="l", ylim=yrange,
 			xlab=ifelse(i==1,"Temps (en heures)",""), ylab=ifelse(i==1,"PM10",""))
-		if (ii < length(indices))
+		if (i < length(indices))
 			par(new=TRUE)
 	}
 }
 
-#' @title plot measured / predicted
+#' Plot error
 #'
-#' @description Plot measured curve (in black) and predicted curve (in red)
+#' Draw error graphs, potentially from several runs of \code{computeForecast}
 #'
-#' @param data Object return by \code{getData}
-#' @param pred Object as returned by \code{getForecast}
-#' @param index Index in forecasts
-#'
-#' @export
-plotPredReal <- function(data, pred, index)
-{
-	horizon = length(pred$getSerie(1))
-	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5, lwd=3)
-	measure = data$getSerie(pred$getIndexInData(index)+1)[1:horizon]
-	yrange = range( pred$getSerie(index), measure )
-	plot(measure, type="l", ylim=yrange, xlab="Temps (en heures)", ylab="PM10")
-	par(new=TRUE)
-	plot(pred$getSerie(index), type="l", col="#0000FF", ylim=yrange, xlab="", ylab="")
-}
-
-#' @title Plot filaments
-#'
-#' @description Plot similar days in the past + "past tomorrow", as black as distances are small
-#'
-#' @param data Object as returned by \code{getData}
-#' @param index Index in data
-#' @param limit Number of neighbors to consider
-#'
-#' @export
-plotFilaments <- function(data, index, limit=60)
-{
-	index = dateIndexToInteger(index, data)
-	ref_serie = data$getCenteredSerie(index)
-	if (any(is.na(ref_serie)))
-		stop("plotFilaments requires a serie without NAs")
-	L = length(ref_serie)
-	first_day = ifelse(length(data$getCenteredSerie(1)<L), 2, 1)
-	distances = sapply(first_day:(index-1), function(i) {
-		sqrt( sum( (ref_serie - data$getCenteredSerie(i))^2 ) / L )
-	})
-	# HACK to suppress NA effect while keeping indexation
-	distances[is.na(distances)] = max(distances,na.rm=TRUE) + 1
-	indices = sort(distances, index.return=TRUE)$ix[1:min(limit,index-first_day)]
-	yrange = range( ref_serie, sapply( indices, function(i) {
-		index = i - first_day + 1
-		serie = c(data$getCenteredSerie(index), data$getCenteredSerie(index+1))
-		if (!all(is.na(serie)))
-			return (range(serie, na.rm=TRUE))
-		c()
-	}) )
-	grays = gray.colors(20, 0.1, 0.9) #TODO: 20 == magic number
-	colors = c(
-		grays[ floor( 20.5 * distances[indices] / (1+max(distances[indices])) ) ], "#FF0000")
-	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5, lwd=2)
-	for (i in seq_len(length(indices)+1))
-	{
-		ind = ifelse(i<=length(indices), indices[i] - first_day + 1, index)
-		plot(c(data$getCenteredSerie(ind),data$getCenteredSerie(ind+1)),
-			ylim=yrange, type="l", col=colors[i],
-			xlab=ifelse(i==1,"Temps (en heures)",""), ylab=ifelse(i==1,"PM10 centré",""))
-		if (i <= length(indices))
-			par(new=TRUE)
-	}
-}
-
-#' @title Plot similarities
-#'
-#' @description Plot histogram of similarities (weights)
-#'
-#' @param pred Object as returned by \code{getForecast}
-#' @param index Index in forecasts (not in data)
-#'
-#' @export
-plotSimils <- function(pred, index)
-{
-	weights = pred$getParams(index)$weights
-	if (is.null(weights))
-		stop("plotSimils only works on 'Neighbors' forecasts")
-	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
-	hist(pred$getParams(index)$weights, nclass=20, xlab="Poids", ylab="Effectif")
-}
-
-#' @title Plot error
-#'
-#' @description Draw error graphs, potentially from several runs of \code{getForecast}
-#'
-#' @param err Error as returned by \code{getError}
+#' @param err Error as returned by \code{computeError}
 #' @param cols Colors for each error (default: 1,2,3,...)
 #'
-#' @seealso \code{\link{plotPredReal}}, \code{\link{plotFilaments}}, \code{\link{plotSimils}}
-#'   \code{\link{plotFbox}}
+#' @seealso \code{\link{plotCurves}}, \code{\link{plotPredReal}},
+#'   \code{\link{plotSimils}}, \code{\link{plotFbox}},
+#'   \code{\link{computeFilaments}, }\code{\link{plotFilamentsBox}}, \code{\link{plotRelVar}}
 #'
 #' @export
 plotError <- function(err, cols=seq_along(err))
@@ -123,7 +38,7 @@ plotError <- function(err, cols=seq_along(err))
 		err = list(err)
 	par(mfrow=c(2,2), mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5, lwd=2)
 	L = length(err)
-	yrange = range( sapply(1:L, function(index) ( err[[index]]$abs$day ) ), na.rm=TRUE )
+	yrange = range( sapply(1:L, function(i) ( err[[i]]$abs$day ) ), na.rm=TRUE )
 	for (i in seq_len(L))
 	{
 		plot(err[[i]]$abs$day, type="l", xlab=ifelse(i==1,"Temps (heures)",""),
@@ -131,7 +46,7 @@ plotError <- function(err, cols=seq_along(err))
 		if (i < L)
 			par(new=TRUE)
 	}
-	yrange = range( sapply(1:L, function(index) ( err[[index]]$abs$indices ) ), na.rm=TRUE )
+	yrange = range( sapply(1:L, function(i) ( err[[i]]$abs$indices ) ), na.rm=TRUE )
 	for (i in seq_len(L))
 	{
 		plot(err[[i]]$abs$indices, type="l", xlab=ifelse(i==1,"Temps (jours)",""),
@@ -139,7 +54,7 @@ plotError <- function(err, cols=seq_along(err))
 		if (i < L)
 			par(new=TRUE)
 	}
-	yrange = range( sapply(1:L, function(index) ( err[[index]]$MAPE$day ) ), na.rm=TRUE )
+	yrange = range( sapply(1:L, function(i) ( err[[i]]$MAPE$day ) ), na.rm=TRUE )
 	for (i in seq_len(L))
 	{
 		plot(err[[i]]$MAPE$day, type="l", xlab=ifelse(i==1,"Temps (heures)",""),
@@ -147,7 +62,7 @@ plotError <- function(err, cols=seq_along(err))
 		if (i < L)
 			par(new=TRUE)
 	}
-	yrange = range( sapply(1:L, function(index) ( err[[index]]$MAPE$indices ) ), na.rm=TRUE )
+	yrange = range( sapply(1:L, function(i) ( err[[i]]$MAPE$indices ) ), na.rm=TRUE )
 	for (i in seq_len(L))
 	{
 		plot(err[[i]]$MAPE$indices, type="l", xlab=ifelse(i==1,"Temps (jours)",""),
@@ -157,39 +72,181 @@ plotError <- function(err, cols=seq_along(err))
 	}
 }
 
-#' @title Functional boxplot
+#' Plot measured / predicted
+#'
+#' Plot measured curve (in black) and predicted curve (in blue)
+#'
+#' @param data Object return by \code{getData}
+#' @param pred Object as returned by \code{computeForecast}
+#' @param index Index in forecasts (integer or date)
+#'
+#' @export
+plotPredReal <- function(data, pred, index)
+{
+	horizon = length(pred$getSerie(1))
+	measure = data$getSerie( pred$getIndexInData(index)+1 )[1:horizon]
+	prediction = pred$getSerie(index)
+	yrange = range(measure, prediction)
+	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5, lwd=3)
+	plot(measure, type="l", ylim=yrange, xlab="Temps (en heures)", ylab="PM10")
+	par(new=TRUE)
+	plot(prediction, type="l", col="#0000FF", ylim=yrange, xlab="", ylab="")
+}
+
+#' Plot similarities
+#'
+#' Plot histogram of similarities (weights)
+#'
+#' @param pred Object as returned by \code{computeForecast}
+#' @param index Index in forecasts (integer or date)
+#'
+#' @export
+plotSimils <- function(pred, index)
+{
+	weights = pred$getParams(index)$weights
+	if (is.null(weights))
+		stop("plotSimils only works on 'Neighbors' forecasts")
+	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
+	hist(pred$getParams(index)$weights, nclass=20, xlab="Poids", ylab="Effectif")
+}
+
+#' Functional boxplot
 #'
-#' @description Draw the functional boxplot on the left, and bivariate plot on the right
+#' Draw the functional boxplot on the left, and bivariate plot on the right
 #'
 #' @param data Object return by \code{getData}
-#' @param fiter Optional filter: return TRUE on indices to process
+#' @param indices integer or date indices to process
+#' @param plot_bivariate Should the bivariate plot appear?
 #'
 #' @export
-plotFbox <- function(data, filter=function(index) TRUE)
+plotFbox <- function(data, indices=seq_len(data$getSize()))
 {
 	if (!requireNamespace("rainbow", quietly=TRUE))
 		stop("Functional boxplot requires the rainbow package")
 
-	start_index = 1
-	end_index = data$getSize()
-	if (length(data$getCenteredSerie(1)) < length(data$getCenteredSerie(2)))
+	series_matrix = data$getSeries(indices)
+	# Remove series with NAs
+	no_NAs_indices = sapply( 1:ncol(series_matrix),
+		function(i) all(!is.na(series_matrix[,i])) )
+	series_matrix = series_matrix[,no_NAs_indices]
+
+	series_fds = rainbow::fds(seq_len(nrow(series_matrix)), series_matrix)
+	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
+	rainbow::fboxplot(series_fds, "functional", "hdr", xlab="Temps (heures)", ylab="PM10",
+		plotlegend=FALSE, lwd=2)
+	rainbow::fboxplot(series_fds, "bivariate", "hdr", plotlegend=FALSE)
+}
+
+#' Compute filaments
+#'
+#' Get similar days in the past, as black as distances are small
+#'
+#' @param data Object as returned by \code{getData}
+#' @param index Index in data (integer or date)
+#' @param limit Number of neighbors to consider
+#' @param plot Should the result be plotted?
+#'
+#' @return A list with
+#' \itemize{
+#'   \item index : index of the current serie ('today')
+#'   \item neighb_indices : indices of its neighbors
+#'   \item colors : colors of neighbors curves (shades of gray)
+#' }
+#'
+#' @export
+computeFilaments <- function(data, index, limit=60, plot=TRUE)
+{
+	ref_serie = data$getCenteredSerie(index)
+	if (any(is.na(ref_serie)))
+		stop("computeFilaments requires a serie without NAs")
+
+	# Determine indices of no-NAs days followed by no-NAs tomorrows
+	fdays = getNoNA2(data, 1, dateIndexToInteger(index,data)-1)
+	# Series + tomorrows in columns, ref_serie first
+	centered_series = data$getCenteredSeries(fdays)
+
+	# Obtain neighbors (closest for euclidian norm)
+	L = length(ref_serie)
+	distances = sqrt( colSums( (centered_series - ref_serie)^2 / L ) )
+	sorted_distances = sort(distances, index.return=TRUE)
+
+	# Compute colors for each neighbor (from darkest to lightest)
+	nn = min(limit, length(distances))
+	min_dist = min(sorted_distances$x[1:nn])
+	max_dist = max(sorted_distances$x[1:nn])
+	color_values = floor( 19.5 * (sorted_distances$x[1:nn]-min_dist) / (max_dist-min_dist) ) + 1
+	colors = gray.colors(20,0.1,0.9)[color_values] #TODO: 20 == magic number
+
+	if (plot)
 	{
-		# Shifted start (7am, or 1pm, or...)
-		start_index = 2
-		end_index = data$getSize() - 1
+		# Complete series with (past and present) tomorrows
+		ref_serie = c(ref_serie,data$getCenteredSerie(index+1))
+		centered_series = rbind( centered_series, data$getCenteredSeries(fdays+1) )
+		yrange = quantile(cbind(ref_serie,centered_series), probs=c(0.05,0.95), na.rm=TRUE)
+		par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5, lwd=2)
+		for (i in nn:1)
+		{
+			plot(centered_series[,sorted_distances$ix[i]], ylim=yrange, type="l", col=colors[i],
+				xlab=ifelse(i==nn,"Temps (en heures)",""), ylab=ifelse(i==nn,"PM10 centré",""))
+			par(new=TRUE)
+		}
+		# Also plot ref curve, in red
+		plot(ref_serie, ylim=yrange, type="l", col="#FF0000", xlab="", ylab="")
+		abline(v=24, lty=2, col=colors()[56])
 	}
 
-	series_matrix = sapply(start_index:end_index, function(index) {
-		as.matrix(data$getSerie(index))
-	})
-	# Remove NAs. + filter TODO: merge with previous step: only one pass required...
-	nas_indices = seq_len(ncol(series_matrix))[ sapply( 1:ncol(series_matrix),
-		function(index) ( !filter(index) || any(is.na(series_matrix[,index])) ) ) ]
-	series_matrix = series_matrix[,-nas_indices]
+	list("index"=index,"neighb_indices"=fdays[sorted_distances$ix[1:nn]],"colors"=colors)
+}
 
+#' Functional boxplot on filaments
+#'
+#' Draw the functional boxplot on filaments obtained by \code{computeFilaments}
+#'
+#' @param data Object return by \code{getData}
+#' @param fil Output of \code{computeFilaments}
+#'
+#' @export
+plotFilamentsBox = function(data, fil, ...)
+{
+	if (!requireNamespace("rainbow", quietly=TRUE))
+		stop("Functional boxplot requires the rainbow package")
+
+	series_matrix = rbind(
+		data$getSeries(fil$neighb_indices), data$getSeries(fil$neighb_indices+1) )
 	series_fds = rainbow::fds(seq_len(nrow(series_matrix)), series_matrix)
-	par(mfrow=c(1,2), mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
+	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
 	rainbow::fboxplot(series_fds, "functional", "hdr", xlab="Temps (heures)", ylab="PM10",
 		plotlegend=FALSE, lwd=2)
-	rainbow::fboxplot(series_fds, "bivariate", "hdr", plotlegend=FALSE)
+
+	# "Magic" found at http://stackoverflow.com/questions/13842560/get-xlim-from-a-plot-in-r
+	usr <- par("usr")
+	yr <- (usr[4] - usr[3]) / 27
+	par(new=TRUE)
+	plot(data$getSerie(fil$index), type="l", lwd=2, lty=2,
+		ylim=c(usr[3] + yr, usr[4] - yr), xlab="", ylab="")
+}
+
+#' Plot relative conditional variability / absolute variability
+#'
+#' Draw the relative conditional variability / absolute variability based on filaments
+#' obtained by \code{computeFilaments}
+#'
+#' @param data Object return by \code{getData}
+#' @param fil Output of \code{computeFilaments}
+#'
+#' @export
+plotRelVar = function(data, fil, ...)
+{
+	ref_var = c( apply(data$getSeries(fil$neighb_indices),1,sd),
+		apply(data$getSeries(fil$neighb_indices+1),1,sd) )
+	fdays = getNoNA2(data, 1, fil$index-1)
+	global_var = c( apply(data$getSeries(fdays),1,sd), apply(data$getSeries(fdays+1),1,sd) )
+
+	yrange = range(ref_var, global_var)
+	par(mar=c(4.7,5,1,1), cex.axis=1.5, cex.lab=1.5)
+	plot(ref_var, type="l", col=1, lwd=3, ylim=yrange,
+		xlab="Temps (heures)", ylab="Écart-type")
+	par(new=TRUE)
+	plot(global_var, type="l", col=2, lwd=3, ylim=yrange, xlab="", ylab="")
+	abline(v=24, lty=2, col=colors()[56])
 }