From 2f4a634cdc5dc3ff39f45aa379747091948dbab1 Mon Sep 17 00:00:00 2001
From: Mauricio Zambrano-Bigiarini <hzambran@users.noreply.github.com>
Date: Mon, 19 Nov 2012 15:03:22 +0000
Subject: [PATCH] 'plot_NparOF.R and .Rd': new argument 'beh.thr'
---
R/PSO_v2012.R | 7 +------
R/plot_2parOF.R | 5 -----
R/plot_NparOF.R | 46 ++++++++++++++++++++++++++++++++++++------
R/plot_params.R | 8 ++++----
R/read_params.R | 4 ++--
man/ReadPlot_params.Rd | 4 +++-
man/plot_NparOF.Rd | 22 ++++++++++++--------
7 files changed, 64 insertions(+), 32 deletions(-)
diff --git a/R/PSO_v2012.R b/R/PSO_v2012.R
index 0948dfc..a6023b4 100755
--- a/R/PSO_v2012.R
+++ b/R/PSO_v2012.R
@@ -2002,7 +2002,6 @@ hydroPSO <- function(
if (topology != "random") {
nc <- K
- #nc <- npart
if (trunc(K/2) != ceiling(K/2)) {
N <- (K-1)/2
} else N <- K/2
@@ -2020,8 +2019,6 @@ hydroPSO <- function(
X.neighbours[i,j+N+NN] <- neigh.index
} # FOR end
} # FOR end
- #rownames(X.neighbours) <- paste("Part", 1:npart, sep="")
- #colnames(X.neighbours) <- paste("Neigh", 1:nc, sep="")
} # IF end
LocalBest.fit <- rep(fn.worst.value, npart)
@@ -2655,7 +2652,7 @@ hydroPSO <- function(
NormSwarmRadius <- swarm.radius/swarm.diameter
if ( (verbose) & ( iter/REPORT == floor(iter/REPORT) ) )
- message( "iter:", format(iter, width=6, justify="right"),
+ message( "iter:", format(iter, width=nchar(maxit), justify="right"),
" Gbest:", formatC( gbest.fit, format="E", digits=digits, flag=" "),
" Gbest_rate:", format( round(gbest.fit.rate*100, 2), width=6, nsmall=2, justify="left"), "%",
" Iter_best_fit:", formatC(pbest.fit.iter, format="E", digits=digits, flag=" "),
@@ -2917,8 +2914,6 @@ hydroPSO <- function(
# Writing the file 'X.neighbours.txt'
fname <- paste(file.path(drty.out), "/", "Particles_Neighbours.txt", sep="")
- print(X.neighbours)
- print(paste("Neigh", 1:npart, sep=""))
ifelse(topology == "lbest", nc <- K, nc <- npart)
write.table(X.neighbours, file=fname, col.names=paste("Neigh", 1:nc, sep=""), row.names=paste("Part", 1:npart, sep=""), sep=" ", na="", quote=FALSE)
diff --git a/R/plot_2parOF.R b/R/plot_2parOF.R
index fd20afa..31f5887 100755
--- a/R/plot_2parOF.R
+++ b/R/plot_2parOF.R
@@ -89,11 +89,6 @@ plot_2parOF <- function(params,
ifelse(MinMax=="max", decreasing<-FALSE, decreasing<-TRUE)
p <- p[order(p[, gof.name], decreasing = decreasing), ]
- # Define a transformation
- norm_trans <- function(){
- trans_new('norm', function(x) pnorm(x), function(x) qnorm(x))
- }
-
if (type=="sp") {
colnames(p) <- c("x", "y", gof.name)
diff --git a/R/plot_NparOF.R b/R/plot_NparOF.R
index 4bfa571..7ab0c3b 100755
--- a/R/plot_NparOF.R
+++ b/R/plot_NparOF.R
@@ -7,15 +7,15 @@
################################################################################
# 'plot_NparOF' #
################################################################################
-# Author : Mauricio Zambrano Bigarini #
+# Author : Mauricio Zambrano Bigiarini #
# Started: Nov 30th, 2010 #
# Updates: 17-Jan-2011 ; 28-Jan-2011 ; 09-Mar-2011 #
-# 17-Feb-2012 ; 21-Feb-2012 ; 09-Mar-2012 ; 23-Mar-2012 #
+# 17-Feb-2012 ; 21-Feb-2012 ; 09-Mar-2012 ; 23-Mar-2012 ; 19-Nov-2012 #
################################################################################
# Purpose: For 'n' user-defined parameters, it produces 'sum(1:(npar-1))' #
-# 'plot_2parOF' plots, with the values of the objective funtion in #
+# 'plot_2parOF' plots, with the values of the objective function in #
# a 2D box, where the boundaries of each parameter are used as axis. #
-# The 'sum(1:(npar-1)) plots corresponds to all the posible #
+# The 'sum(1:(npar-1)) plots corresponds to all the possible #
# combinations of 2 parameters among all the 'n' parameters provided #
################################################################################
# nrows : numeric, with the amount of rows to be used in the plotting window.
@@ -26,6 +26,7 @@ plot_NparOF <- function(params,
gofs,
param.names=colnames(params),
MinMax=c("min", "max"),
+ beh.thr=NA,
nrows="auto",
gof.name="GoF",
main=paste(gof.name, "Surface"),
@@ -38,6 +39,10 @@ plot_NparOF <- function(params,
) {
+ ##############################################################################
+ # 1) Checkings #
+ ##############################################################################
+
# Checking 'params'
if (missing(params))
stop("Missing argument: 'params' must be provided !!" )
@@ -57,7 +62,7 @@ plot_NparOF <- function(params,
# Number of parameters that will be analysed
npar <- length(param.names)
- # creating the varaible that will store the position of the selected parameters within 'params'
+ # creating the variable that will store the position of the selected parameters within 'params'
par.pos <- numeric(npar)
# Checking 'param.names'
@@ -66,7 +71,32 @@ plot_NparOF <- function(params,
stop("Invalid argument: The field '", param.names[i], "' doesn't exist in 'params'")
par.pos[i] <- which(colnames(params) == param.names[i])
- } # FOR end
+ } # FOR end
+
+
+ ##############################################################################
+ # 2) Computations #
+ ##############################################################################
+
+ # Filtering out those parameter sets above/below a certain threshold
+ if (!is.na(beh.thr)) {
+ # Checking 'beh.thr'
+ mx <- max(gofs, na.rm=TRUE)
+ if (beh.thr > mx)
+ stop("Invalid argument: 'beh.thr' must be lower than ", mx ,"!!")
+
+ # Computing the row index of the behavioural parameter sets
+ ifelse(MinMax=="min", beh.row.index <- which(gofs <= beh.thr),
+ beh.row.index <- which(gofs >= beh.thr) )
+
+ # Removing non-behavioural parameter sets & gofs
+ params <- params[beh.row.index, ]
+ gofs <- gofs[beh.row.index]
+
+ # Amount of behavioural parameter sets
+ nbeh <- nrow(params)
+ if (verbose) message( "[ Number of behavioural parameter sets: ", nbeh, " ]" )
+ } # IF end
# If the user didn't provide 'GOFcuts', the 5 quantiles are used
if (length(GOFcuts) == 1){
@@ -74,6 +104,10 @@ plot_NparOF <- function(params,
GOFcuts <- unique( quantile( as.numeric(gofs),
probs=c(0, 0.25, 0.5, 0.75, 0.9, 0.95, 1), na.rm=TRUE) )
} # IF end
+
+ ##############################################################################
+ # 3) Plotting #
+ ##############################################################################
# Number of plots that will be drawn
nplots <- sum(1:(npar-1))
diff --git a/R/plot_params.R b/R/plot_params.R
index f5cc551..592e56c 100755
--- a/R/plot_params.R
+++ b/R/plot_params.R
@@ -17,7 +17,7 @@
# corresponding objective function value (usually for plotting the
# efficiencies of different parameter sets)
-# params : data.frame, whose colums represents the behavioural parameter
+# params : data.frame, whose columns represents the behavioural parameter
# sets and the goodness of fit of each one of them
# of.name: character, with the name of the column that contains the values
# of the objective function for each parameter set
@@ -156,9 +156,9 @@ plot_params.default <- function(params,
} # IF end
##############################################################################
- # 2) Plotting #
+ # 3) Plotting #
##############################################################################
- # Ploting ALL the PARAMETER SETS
+ # Plotting ALL the PARAMETER SETS
if (verbose) message( " ")
if (verbose) message( "[ Plotting ... ]")
@@ -181,7 +181,7 @@ plot_params.default <- function(params,
old.par <- par(no.readonly=TRUE)
if (!do.png) on.exit(par(old.par))
- # Plotting the distribution of all the parameter sampled with LH, not only the behaviourals
+ # Plotting the distribution of all the parameter sampled with LH, not only the behavioural ones
MinMax.colour <- "coral"
par(mfrow=c(lnr, ncol))
par(mar=c(5,4.5,1,2)+0.1) # Default: par(mar=c(5,4,4,2)+0.1)
diff --git a/R/read_params.R b/R/read_params.R
index 379e6da..6be6310 100755
--- a/R/read_params.R
+++ b/R/read_params.R
@@ -31,7 +31,7 @@
# the file format: header is set to TRUE if and only if the first row
# contains one fewer field than the number of columns.
# param.cols: numerical vector, with the column position in 'param.fname' that
-# represent the paramter values used during the calibrations
+# represent the parameter values used during the calibrations
# param.names: character, with the names to be given to each one of the parameters
# stored in the columns represented by 'param.cols' (usually, the
# most sensitive parameters in 'param.fname' )
@@ -41,7 +41,7 @@
# plot : logical, indicating if dotty plots of the parameter sets and its
# objective function have to be plotted or not
# beh.thr: OPTIONAL, only used when 'plot=TRUE'. \cr
-# numeric, with a behavioural threshold to be used for ploting
+# numeric, with a behavioural threshold to be used for plotting
# a horizontal line
# beh.col: OPTIONAL, only used when 'plot=TRUE'. \cr
# color to be used for plotting the horizontal line on 'beh.thr'
diff --git a/man/ReadPlot_params.Rd b/man/ReadPlot_params.Rd
index 4330db4..7856f7d 100755
--- a/man/ReadPlot_params.Rd
+++ b/man/ReadPlot_params.Rd
@@ -123,7 +123,9 @@ Valid values are in: \code{c('min', 'max')}
}
\item{beh.thr}{
OPTIONAL \cr
-numeric, value for drawing a horizontal line for separating behavioural from non behavioural parameter sets
+numeric, threshold value used for selecting parameter sets that have to be used in the analysis (\sQuote{behavioural parameters}, using the GLUE terminology) \cr
+If \code{MinMax='min'}, only parameter sets with a goodness-of-fit value (given by \code{gofs}) less than or equal to \code{beh.thr} will be considered for the subsequent analysis. \cr
+If \code{MinMax='max'}, only parameter sets with a goodness-of-fit value (given by \code{gofs}) greater than or equal to \code{beh.thr} will be considered for the subsequent analysis
}
\item{beh.col}{
OPTIONAL. Only used when \code{plot=TRUE} \cr
diff --git a/man/plot_NparOF.Rd b/man/plot_NparOF.Rd
index 26ba684..b2ff474 100755
--- a/man/plot_NparOF.Rd
+++ b/man/plot_NparOF.Rd
@@ -16,10 +16,10 @@ The \kbd{sum(1:(npar-1))} plots corresponds to all the possible combinations of
}
\usage{
plot_NparOF(params, gofs, param.names=colnames(params), MinMax=c("min", "max"),
- nrows="auto", gof.name="GoF", main=paste(gof.name, "Surface"),
- GOFcuts="auto", colorRamp= colorRampPalette(c("darkred", "red",
- "orange", "yellow", "green", "darkgreen", "cyan")), points.cex=0.7,
- alpha=1, axis.rot=c(0, 0), verbose=TRUE)
+ beh.thr=NA, nrows="auto", gof.name="GoF", main=paste(gof.name, "Surface"),
+ GOFcuts="auto", colorRamp= colorRampPalette(c("darkred", "red",
+ "orange", "yellow", "green", "darkgreen", "cyan")), points.cex=0.7,
+ alpha=1, axis.rot=c(0, 0), verbose=TRUE)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
@@ -34,6 +34,12 @@ character, names for the parameters in \code{params} that have to be plotted (\c
}
\item{MinMax}{
character, indicates whether the optimum value in \code{gofs} corresponds to the minimum or maximum of the objective function. Valid values are in: \code{c('min', 'max')}
+}
+ \item{beh.thr}{
+OPTIONAL \cr
+numeric, threshold value used for selecting parameter sets that have to be used in the analysis (\sQuote{behavioural parameters}, using the GLUE terminology) \cr
+If \code{MinMax='min'}, only parameter sets with a goodness-of-fit value (given by \code{gofs}) less than or equal to \code{beh.thr} will be considered for the subsequent analysis. \cr
+If \code{MinMax='max'}, only parameter sets with a goodness-of-fit value (given by \code{gofs}) greater than or equal to \code{beh.thr} will be considered for the subsequent analysis
}
\item{nrows}{
numeric, number of rows to be used in the plotting window \cr
@@ -88,7 +94,7 @@ Mauricio Zambrano-Bigiarini, \email{mzb.devel@gmail.com}
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{plot_2parOF}}, \code{\link{read_results}}, \code{\link{plot_results}}, \code{\link{plot_GofPerParticle}}, \code{\link{plot_ParamsPerIter}}
+\code{\link{plot_2parOF}}, \code{\link{read_results}}, \code{\link{plot_results}}, \code{\link{plot_GofPerParticle}}, , \code{\link{plot_params}}, \code{\link{plot_ParamsPerIter}}
}
\examples{
# Number of dimensions to be optimised
@@ -103,9 +109,9 @@ setwd("~")
set.seed(100)
# Running PSO with the 'rosenbrock' test function, writing the results to text files
-hydroPSO(fn="rosenbrock",
- lower=rep(-30, nparam), upper=rep(30, nparam),
- control=list(MinMax="min", npart=2*nparam, write2disk=TRUE)
+hydroPSO(fn=rosenbrock,
+ lower=rep(-10, nparam), upper=rep(10, nparam),
+ control=list(write2disk=TRUE)
) # hydroPSO
# reading the 'Particles.txt' output file of hydroPSO
--
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