The function read_particles
reads the ‘Particles.txt’ output file, which stores all the parameter sets tested during the optimisation along with their corresponding goodness-of-fit values
The function plot_particles
takes the parameter sets and their corresponding goodness-of-fit value, read by read_particles
, and produces the following plots:
1) Dotty plots
2) Histograms
3) Boxplots
4) Correlation matrix (optional)
5) Empirical CDFs
6) Parameter values vs Number of Model Evaluations
7) (pseudo) 3D dotty plots
read_particles(file="Particles.txt", verbose=TRUE, plot=TRUE,
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, do.pairs=FALSE,
dp3D.names="auto", GOFcuts="auto",
colorRamp= colorRampPalette(c("darkred", "red", "orange", "yellow",
"green", "darkgreen", "cyan")), alpha=1, points.cex=0.7,
legend.pos="topleft", do.png=FALSE, png.width=1500,
png.height=900, png.res=90,
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")
plot_particles(params, 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, do.pairs=FALSE,
weights=NULL, byrow=FALSE, leg.cex=1.5,
dp3D.names="auto", GOFcuts="auto",
colorRamp= colorRampPalette(c("darkred", "red", "orange", "yellow",
"green", "darkgreen", "cyan")), alpha=1, points.cex=0.7,
legend.pos="topleft", verbose=TRUE,
do.png=FALSE, png.width=1500, png.height=900, png.res=90,
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")
read_velocities(file="Velocities.txt", ... )
character, name (including path) of the output file with the position and fitness value of each particle and for each iteration
data.frame whose rows represent the values of different parameter sets
OPTIONAL. numeric with the values of goodness-of-fit values for each parameter in params
(in the same order!)
logical, if TRUE, progress messages are printed
logical, indicates if the following figures has to be produced: dotty plots, histograms, empirical CDFs, Parameter Values Against Number of Model Evaluations, and 3D dotty plots of Parameter Values
character, name to be given to the goodness-of-fit values in all the plots
OPTIONAL. character, indicates if the optimum value in params
corresponds to the minimum or maximum of the the objective function. Only used to identify the optimum in the plot
Valid values are in: c('min', 'max')
numeric, used for selecting only the behavioural parameter sets, i.e. those with a goodness-of-fit value greater/less than or equal to beh.thr
, depending on the value of MinMax
By default beh.thr=NA
and all the parameter sets are considered for the subsequent anlysis
OPTIONAL. Only used when plot=TRUE
character, colour for drawing a horizontal line for separating behavioural from non behavioural parameter sets
OPTIONAL. Only used when plot=TRUE
numeric, line type for drawing a horizontal line for separating behavioural from non behavioural parameter sets
OPTIONAL. Only used when plot=TRUE
numeric, width for drawing a horizontal line for separating behavioural from non behavioural parameter sets
OPTIONAL. Only used when plot=TRUE
numeric, number of rows to be used in the plotting window
If nrows
is set to auto, the number of rows is automatically computed depending on the number of columns of params
OPTIONAL. Only used when plot=TRUE
character, colour for drawing the points of the dotty plots
OPTIONAL. Only used when plot=TRUE
character, label for the 'y' axis
OPTIONAL. Only used when plot=TRUE
character, title for the plot
OPTIONAL. Only used when plot=TRUE
numeric, type of symbol to be used for drawing the points of the dotty plots (e.g., 1: white circle)
OPTIONAL. Only used when plot=TRUE
numeric, values controlling the size of text and points with respect to the default
OPTIONAL. Only used when plot=TRUE
numeric, magnification for main titles relative to the current setting of cex
OPTIONAL. Only used when plot=TRUE
numeric, magnification for axis annotation relative to the current setting of cex
OPTIONAL. Only used when plot=TRUE
numeric, magnification for x and y labels relative to the current setting of cex
OPTIONAL. Only used when plot=TRUE
further arguments passed to the plot command or from other methods
OPTIONAL. Only used when plot=TRUE
breaks for plotting the histograms of the parameter sets. See hist
OPTIONAL. Only used when plot=TRUE
logical, if TRUE, the histogram graphic is a representation of frequencies, the counts component of the result; if FALSE, probability densities, component density, are plotted (so that the histogram has a total area of one). Defaults to TRUE if and only if breaks are equidistant (and probability is not specified). See hist
OPTIONAL. Only used when plot=TRUE
logical, indicates whether a correlation matrix among parameters has to be plotted. If the number of parameter sets tried during the optimisation is large, it may require some time.
OPTIONAL. Only used when plot=TRUE
numeric vector, values of the weights to be used for computing the empirical CDFs. See params2ecdf
OPTIONAL. Only used when plot=TRUE
logical, indicates whether the computations have to be made for each column or for each row of params
. See params2ecdf
OPTIONAL. Only used when plot=TRUE
character expansion factor *relative* to current 'par("cex")'. Used for text, and provides the default for 'pt.cex' and 'title.cex'. Default value = 1.2
character, name of all the parameters (usually only the most sensitive ones) that will be used for plotting pseudo-3D plots
If dp3D.names='auto'
half the number of parameters in file
are chosen randomly for plotting. See plot_NparOF
numeric, specifies at which values of the objective function gof.name
the colours of the plot have to change. See plot_NparOF
R function defining the colour ramp to be used for colouring the pseudo-3D dotty plots of Parameter Values, OR character representing those colours. See plot_NparOF
numeric between 0 and 1 representing the transparency level to apply to the colors of the pseudo-3D dotty plots. See plot_NparOF
size of the points to be plotted
not used yet ...
logical, indicates if the plot with the convergence measures has to be saved into a PNG file instead of the screen device
OPTIONAL. Only used when do.png=TRUE
numeric, width of the device. See png
OPTIONAL. Only used when do.png=TRUE
numeric, height of the device. See png
OPTIONAL. Only used when do.png=TRUE
numeric, nominal resolution in ppi which will be recorded in the PNG file, if a positive integer of the device. See png
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the dotty plots of the parameter values
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the histograms of the parameter values
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the boxplots of the parameter values
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the empirical CDFs of the parameter values
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the parameter values vs the number of model evaluations
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the pseudo-3D plots of all the parameters defined in dp3D.names
OPTIONAL. Only used when do.png=TRUE
character, filename used to store the PNG file with the correlation matrix among the parameters and goodness-of-fit values in params
and gofs
. See plot_params
and hydropairs
read_particles
returns a list with four elements:
numeric or matrix/data.frame with the parameter values for each particle and iteration
numeric vector with the goodness-of-fit value for each particle and iteration
numeric with the parameter values of the best particle. In order to be computed, the user has to provide a valid value for MinMax
numeric with the best godness-of-fit value among all the particles. In order to be computed, the user has to provide a valid value for MinMax
# NOT RUN {
# Setting the user home directory as working directory
setwd("~")
# Number of dimensions to be optimised
D <- 4
# Boundaries of the search space (Sphere test function)
lower <- rep(-100, D)
upper <- rep(100, D)
# Setting the seed
set.seed(100)
# Runing PSO with the 'Sphere' test function, writting the results to text files
hydroPSO(fn=sphere, lower=lower, upper=upper,
control=list(maxit=100, write2disk=TRUE, plot=TRUE) )
# reading the 'Particles.txt' output file of hydroPSO, and plotting dotty plots,
# histograms, eCDFs, ...
setwd("PSO.out")
particles <- read_particles()
# reading only the particles in 'Particles.txt' with a goodness-of-fit value
# lower than 'beh.thr'
particles <- read_particles(beh.thr=1000, MinMax="min")
# }
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