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Mauricio Zambrano-Bigiarini authoredMauricio Zambrano-Bigiarini authored
plot_particles.R 13.81 KiB
# File plot_particles.R
# Part of the hydroPSO R package, http://www.rforge.net/hydroPSO/ ;
# http://cran.r-project.org/web/packages/hydroPSO
# Copyright 2011-2012 Mauricio Zambrano-Bigiarini & Rodrigo Rojas
# Distributed under GPL 2 or later
################################################################################
# 'plot_particles' #
# Author : Mauricio Zambrano-Bigiarini & Rodrigo Rojas #
# Started: 08-Nov-2011, #
# Updates: 02-Feb-2012 ; 17-Feb-2012 ; 09-Mar-2012 #
################################################################################
# This function plots the contents of the 'Particles.txt' ouput file of #
# hydroPSO, with the position and fitness value of all the particles in the #
# swarm for all the iterations. #
# The following plots are produced: #
# 1) Dotty Plots of Parameter Values #
# 2) Histograms of Parameter Values #
# 3) Empirical CDFs of Parameter Values #
# 4) Parameter Values Against Number of Model Evaluations #
# 5) Plotting pseudo-3D dotty plots of Parameter Values #
################################################################################
plot_particles <- function(#####################################################
#### 'plotparam' parameters ####
params, #parameter values
gofs,
gof.name="GoF",
MinMax=NULL,
beh.thr=NA,
beh.col="red",
beh.lty=1,
beh.lwd=2,
nrows="auto",
col="black",
ylab=gof.name,
main=NULL,
pch=19,
cex=0.5,
cex.main=1.5,
cex.axis=1.5,
cex.lab=1.5,
#...,
breaks="Scott",
freq=TRUE,
#####################################################
# For ECDFs of parameter values ('params2ecdf')
weights=NULL,
byrow=FALSE,
leg.cex=1.5,
#####################################################
# Parameters for the 3D dotty plots ('plot_NparOF') ##
dp3D.names="auto",
GOFcuts="auto",
colorRamp= colorRampPalette(c("darkred", "red", "orange", "yellow", "green", "darkgreen", "cyan")),
alpha=1,
points.cex=0.7,
legend.pos="topleft", # not used yet,but included for avoiding warnings from 'plot_results'
verbose=TRUE,
#####################################################
#### PNG options
do.png=FALSE,
png.width=1500,
png.height=900,
png.res=90,
#png.drty="pngs",
dotty.png.fname="Params_DottyPlots.png", hist.png.fname="Params_Histograms.png",
bxp.png.fname="Params_Boxplots.png",
ecdf.png.fname="Params_ECDFs.png",
runs.png.fname="Params_ValuesPerRun.png",
dp3d.png.fname="Params_dp3d.png",
pairs.png.fname="Params_Pairs.png"
) {
# Checking that 'params' exists
if ( missing(params) ) stop( "Missing argument: 'params'" )
# Checking that 'gofs' exists
if ( missing(gofs) ) stop( "Missing argument: 'gofs'" )
# number of parameters
nparam <- ncol(params)
# Parameter names
param.names <- colnames(params)
# Adding the GoF to the used data.frame
z <- cbind(params, gofs)
colnames(z)[nparam+1] <- gof.name
##############################################################################
# 1) Plotting Dotty Plots of Parameter Values
if (verbose) message( " ")
msg <- "[ Plotting dotty plots for parameter values"
if (do.png) msg <- paste(msg, " into '", basename(dotty.png.fname), sep="")
msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
plot_params(params=params,
gofs=gofs,
ptype="dottyplot",
param.cols=1:nparam,
param.names=param.names,
#of.col=ncol(z),
of.name=gof.name,
MinMax=MinMax,
beh.thr=beh.thr,
beh.col=beh.col,
beh.lty=beh.lty,
beh.lwd=beh.lwd,
nrows=nrows,
col=col,
ylab=ylab,
main=main,
pch=pch,
cex=cex,
cex.main=cex.main,
cex.axis=cex.axis,
cex.lab=cex.lab,
#...,
breaks=breaks,
freq=freq,
verbose=FALSE,
# PNG options
do.png=do.png,
png.width=png.width,
png.height=png.height,
png.res=png.res,
png.fname=dotty.png.fname
)
#############################################################################
# 2) Plotting Histograms of Parameter Values
msg <- "[ Plotting histograms for parameter values"
if (do.png) msg <- paste(msg, " into '", basename(hist.png.fname), sep="") msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
if (!do.png) x11()
plot_params(params=params,
gofs=gofs,
ptype="histogram",
param.cols=1:nparam,
param.names=param.names,
#of.col=ncol(z),
of.name=gof.name,
MinMax=MinMax,
beh.thr=beh.thr,
beh.col=beh.col,
beh.lty=beh.lty,
beh.lwd=beh.lwd,
nrows=nrows,
col=col,
ylab=ylab,
main=main,
pch=pch,
cex=cex,
cex.main=cex.main,
cex.axis=cex.axis,
cex.lab=cex.lab,
#...,
breaks=breaks,
freq=freq,
verbose=FALSE,
# PNG options
do.png=do.png,
png.width=png.width,
png.height=png.height,
png.res=png.res,
png.fname=hist.png.fname
)
#############################################################################
# 3) Plotting Histograms of Parameter Values
msg <- "[ Plotting boxplots for parameter values"
if (do.png) msg <- paste(msg, " into '", basename(bxp.png.fname), sep="")
msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
if (!do.png) x11()
plot_params(params=params,
gofs=gofs,
ptype="boxplot",
param.cols=1:nparam,
param.names=param.names,
#of.col=ncol(z),
of.name=gof.name,
MinMax=MinMax,
beh.thr=beh.thr,
beh.col=beh.col,
beh.lty=beh.lty,
beh.lwd=beh.lwd,
nrows=nrows,
col=col,
ylab=ylab,
main=main,
pch=pch,
cex=cex,
cex.main=cex.main,
cex.axis=cex.axis,
cex.lab=cex.lab,
#...,
breaks=breaks,
freq=freq,
verbose=FALSE, # PNG options
do.png=do.png,
png.width=png.width,
png.height=png.height,
png.res=png.res,
png.fname=bxp.png.fname
)
#############################################################################
# 4) Plotting Correlation Matrix of Parameter Values (with hydroTSM::hydropairs)
if ( require(hydroTSM) ) {
msg <- "[ Plotting correlation matrix for parameter values"
if (do.png) msg <- paste(msg, " into '", basename(pairs.png.fname), sep="")
msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
if (!do.png) x11()
plot_params(params=params,
gofs=gofs,
ptype="pairs",
param.cols=1:nparam,
param.names=param.names,
#of.col=ncol(z),
of.name=gof.name,
MinMax=MinMax,
beh.thr=beh.thr,
beh.col=beh.col,
beh.lty=beh.lty,
beh.lwd=beh.lwd,
nrows=nrows,
col=col,
ylab=ylab,
main=main,
pch=pch,
cex=cex,
cex.main=cex.main,
cex.axis=cex.axis,
cex.lab=cex.lab,
#...,
breaks=breaks,
freq=freq,
verbose=FALSE,
# PNG options
do.png=do.png,
png.width=png.width,
png.height=png.height,
png.res=png.res,
png.fname=pairs.png.fname
)
} # IF end
#############################################################################
# 5) Empirical CDFs of Parameter Values
msg <- "[ Plotting empirical CDFs for parameter values"
if (do.png) msg <- paste(msg, " into '", basename(ecdf.png.fname), sep="")
msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
if (!do.png) x11()
params2ecdf(params=params,
param.names=param.names,
weights=weights,
byrow=byrow,
plot=TRUE,
nrows=nrows,
ylab="Probability",
main=main,
col=col,
leg.cex=leg.cex,
cex.axis=cex.axis, cex.main=cex.main,
cex.lab=cex.lab,
verbose=FALSE,
#...,
# PNG options
do.png=do.png,
png.width=png.width,
png.height=png.height,
png.res=png.res,
png.fname=ecdf.png.fname
)
#############################################################################
# 6) Parameter Values Against Number of Model Evaluations
msg <- "[ Plotting parameter values vs Number of Model Evaluations"
if (do.png) msg <- paste(msg, " into '", basename(runs.png.fname), sep="")
msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
if (!do.png) x11()
plot_ParamsPerIter(params=params,
param.names=param.names,
main=main,
xlab="Model Evaluations",
nrows=nrows,
cex=cex,
cex.main=cex.main,
cex.axis=cex.axis,
cex.lab=cex.lab,
col=rainbow(ncol(params)),
lty=3,
verbose=FALSE,
#...,
# PNG options
do.png=do.png,
png.width=png.width,
png.height=png.height,
png.res=png.res,
png.fname=runs.png.fname
)
############################################################################
# 7) Plotting 3D dotty plots of Parameter Values
if (length(dp3D.names)==1) {
if (dp3D.names == "auto") {
if (nparam > 5) nparam <- ceiling(nparam/2)
params <- params[,1:nparam]
# Adding the GoF to the used data.frame
z <- cbind(params, gofs)
# number of parameters to be used in 3D dotty plots
nparam <- ncol(params)
colnames(z)[nparam+1] <- gof.name
# Parameter names
dp3D.names <- colnames(params)
} # IF end
} # IF end
msg <- "[ Plotting 3D dotty plots for parameter values"
if (do.png) msg <- paste(msg, " into '", basename(dp3d.png.fname), sep="")
msg <- paste(msg, "' ... ]", sep="")
if (verbose) message(msg)
if (do.png) png(filename=dp3d.png.fname, width=png.width, height=png.height, res=png.res)
else x11()
plot_NparOF(#params=z,
params=params,
gofs=gofs,
param.names=dp3D.names,
nrows=nrows,
gof.name=gof.name, main=main,
GOFcuts=GOFcuts,
colorRamp= colorRamp,
alpha=alpha,
points.cex=points.cex,
verbose=FALSE
)
if (do.png) dev.off()
} # 'plot_particles' END