plot_NparOF: N 2-dimensional plots of Parameter Values against the...
In hydroPSO: Particle Swarm Optimisation, with Focus on Environmental Models

Description Usage Arguments Author(s) See Also Examples

For n user-defined parameters, the function creates sum(1:(npar-1)) 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 possible combinations of 2 parameters among all the n parameters provided

plot_NparOF(params, gofs, param.names=colnames(params), 
         MinMax=c(NULL,"min","max"), 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=0.65, 
         axis.rot=c(0, 0), verbose=TRUE)

`params`	matrix or data.frame with the parameter values
`gofs`	numeric with the values of goodness-of-fit values for each one of the parameters in `params` (in the same order!)
`param.names`	character, names for the parameters in `params` that have to be plotted (`param.names` can be a subset of `params`)
`MinMax`	character, indicates whether the optimum value in `gofs` corresponds to the minimum or maximum of the objective function. It is required when `beh.thr` is provided. Valid values are in: `c(NULL, 'min', 'max')` By default, `MinMax=NULL` which plot particles in the order they are provided in `params` and `gofs` in each one of the output figures If `MinMax='min'` place particles with lower goodness-of-fit values are plotted on top of those with larger values, in each one of the output figures, and vice-versa for `MinMax='max'`.
`beh.thr`	OPTIONAL numeric, threshold value used for selecting parameter sets that have to be used in the analysis (‘behavioural parameters’, using the GLUE terminology) If `MinMax='min'`, only parameter sets with a goodness-of-fit value (given by `gofs`) less than or equal to `beh.thr` will be considered for the subsequent analysis. If `MinMax='max'`, only parameter sets with a goodness-of-fit value (given by `gofs`) greater than or equal to `beh.thr` will be considered for the subsequent analysis
`nrows`	numeric, number of rows to be used in the plotting window If `nrows='auto'` the number of columns is automatically computed depending on the number of parameters in `params`
`gof.name`	character, name of the objective function to be plotted. It has to correspond to the name of one column of `params` It is used as title for the legend of the final figure.
`main`	character, currently not used
`GOFcuts`	numeric, specifies at which values of the objective function given in `gofs` the colours of the plot have to change If `GOFcuts="auto"` and `MinMax=NULL`, the intervals are defined by the (unique values of the) `gofs` quantiles corresponding to the following probabilities: `probs=c(0, 0.1, 0.25, 0.5, 0.75, 0.9, 1)` If `GOFcuts="auto"` and `MinMax='min'`, the intervals are defined by the (unique values of the) `gofs` quantiles corresponding to the following probabilities: `probs=c(0, 0.25, 0.5, 0.85, 0.9, 0.97, 1)` If `GOFcuts="auto"` and `MinMax='max'`, the intervals are defined by the (unique values of the) `gofs` quantiles corresponding to the following probabilities: `probs=c(0, 0.03, 0.1, 0.15, 0.5, 0.75, 1)`
`colorRamp`	R function defining the colour ramp to be used for colouring the pseudo-3D dotty plots of Parameter Values, OR character representing those colours
`points.cex`	size of the points to be plotted
`alpha`	numeric between 0 and 1 representing the transparency level to apply to `colorRamp`, ‘0’ means fully transparent and ‘1’ means opaque
`axis.rot`	numeric vector of length 2 representing the angle (in degrees) by which the axis labels are to be rotated, left/bottom and right/top, respectively.
`verbose`	logical; if TRUE, progress messages are printed

Mauricio Zambrano-Bigiarini, mzb.devel@gmail.com

plot_2parOF, read_results, plot_results, plot_GofPerParticle, plot_params, plot_ParamsPerIter

# Number of dimensions to be optimised
D <- 5

# Boundaries of the search space (Rosenbrock test function)
lower <- rep(-30, D)
upper <- rep(30, D)

## Not run: 
# Setting the user's home directory as working directory
setwd("~")

# Setting the seed
set.seed(100)

# Optimising the 'Rosenbrock' test function, and writing the results to text files
hydroPSO(fn=rosenbrock, lower=lower, upper=upper, control=list(write2disk=TRUE) ) 
  
# reading the 'Particles.txt' output file of hydroPSO
setwd("PSO.out")
particles <- read_particles(plot=FALSE)
               
# plotting the value of each parameter and the objective function against the 
# values of the objective function
plot_NparOF(params=particles[["part.params"]], gofs=particles[["part.gofs"]],
            gof.name="Rosenbrock", alpha=0.5)

## End(Not run)