ReadPlot_out: Reading/Plotting the 'Model_out.txt' output file of hydroPSO

Description

This function reads the values of the objective function/model output for each particle and iteration with optional plot

Usage

read_out(file="Model_out.txt", modelout.cols=NULL, nsim=NULL, obs, MinMax=NULL, 
     beh.thr=NA,verbose=TRUE,plot=TRUE,ptype=c("corr","ts","ecdf","quant2ecdf"), 
     ftype="dm", FUN=mean, weights=NULL, byrow=TRUE,
     quantiles.desired= c(0.05,0.5,0.95), 
     quantiles.labels= c("Q5", "Q50", "Q95"), main=NULL, ylab="Probability", 
     col="blue", leg.cex=1.2, leg.pos="bottomright", 
     cex.axis=1.2, cex.main=1.2, cex.lab=1.2, do.png=FALSE, png.width=1500, 
     png.height=900, png.res=90, png.fname="ModelOut_vs_Obs.png")
plot_out(sim, obs, dates=NULL, ptype=c("corr","ts","ecdf","quant2ecdf"), 
     MinMax=NULL, ftype="o", FUN=mean, verbose=TRUE, weights=NULL, byrow=TRUE, 
     quantiles.desired= c(0.05,0.5,0.95), quantiles.labels=c("Q5","Q50","Q95"), 
     main=NULL, ylab="Probability", col="blue", leg.cex=1.2, 
     leg.pos="bottomright", cex.axis=1.2, cex.main=1.2, cex.lab=1.2, 
     do.png=FALSE, png.width=1500, png.height=900, png.res=90, 
     png.fname="ModelOut_vs_Obs.png")

Arguments

file

character, name (including path) of the output file with the values of the model / objective function for each particle and iteration

modelout.cols

numeric, column number in file that store the outputs that have to be read/plotted, without counting the first three that correspond to iteration, particle and goodness-of-fit value. If modelout.cols=NULL, all the columns in

nsim

OPTIONAL. number simulated equivalent values of the model / objective function to be compared against observations. It is only useful when the model to be calibrated returns NA instead of the simulated values for some parameter set(s) (e.g.,

sim

numeric or zoo vector, simulated equivalent values of the model / objective function to be compared against observations

obs

OPTIONAL. numeric or zoo vector, observations to be compared against the best simulated value. If obs is not provided, its values are read from the output Observations.txt file in the results directory (by default PSO

dates

OPTIONAL. character or Date object used to assign time stamps to each element of sim and obs. If sim and/or obs already have a time stamp, it is over-written by dates It must have the same

MinMax

OPTIONAL. character, indicates whether the optimum value corresponds to the minimum or maximum of the the objective function. It is used to filter out model outputs with a non-acceptable performance Valid values are in: c('min', 'max')

beh.thr

OPTIONAL. numeric, used for selecting only the behavioural parameter sets, i.e. those with a goodness-of-fit value larger/lower than beh.th, depending on the value of MinMax It is used for drawing a horizontal line used for sepa

verbose

logical, if TRUE, progress messages are printed

plot

logical, indicates if a plot with the convergence measures has to be produced

ptype

character, type of plot. Valid values are: -) corr: Scatterplot between the observed values and its best simulated counterpart -) ts: Only possible for observed values of zoo type. A graphical comparison between observed values and

ftype

OPTIONAL. Only used when plot=TRUE and ptype=="ts".See ggof

FUN

OPTIONAL. Only used when plot=TRUE and ptype=="ts".See ggof

weights

numeric vector, values of the weights to be used for computing the quantiles. See quant2ecdf Omitting the weights argument or specifying NULL or a zero-length vector will resu

byrow

logical, indicates whether the computations have to be made for each column or for each row of x. See quant2ecdf When the simulated equivalents are stored in columns, byrow must

quantiles.desired

numeric vector, quantiles to be computed for model outputs. Default values are c(.025, .5, .975) ( => 2.5%, 50%, 97.5% ). See quant2ecdf

quantiles.labels

OPTIONAL. Only used when plot=TRUE character vector, names to quantiles.desired. Default value is c("Q5", "Q50", "Q95"). See quant2ecdf

main

OPTIONAL. Only used when plot=TRUE title for the plot

ylab

OPTIONAL. Only used when plot=TRUE title for the y axis. See plot

col

OPTIONAL. Only used when plot=TRUE specification for the default plotting colour. See par

leg.cex

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

leg.pos

OPTIONAL. Only used when plot=TRUE keyword to be used to position the legend. See legend

cex.axis

OPTIONAL. Only used when plot=TRUE numeric, magnification to be used for the axis annotation relative to 'cex'. See par

cex.main

OPTIONAL. Only used when plot=TRUE numeric, representing the magnification to be used for main titles relative to the current setting of cex

cex.lab

OPTIONAL. Only used when plot=TRUE numeric, representing the magnification to be used for x and y labels relative to the current setting of 'cex'. See par

do.png

logical, indicates if the plot with the comparison between model outputs and observations has to be saved into a PNG file instead of the screen device

png.width

OPTIONAL. Only used when do.png=TRUE numeric, width of the device. See png

png.height

OPTIONAL. Only used when do.png=TRUE numeric, height of the device. See png

png.res

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

png.fname

OPTIONAL. Only used when do.png=TRUE character, name of the output PNG file. See png

Value

list with three elements:
model.valuesmatrix/data.frame (or numeric) with the values of the model / objective function for each particle and iteration
model.gofsnumeric vector with the goodness-of-fit value for each row (or value) in model.values
model.bestnumeric with the best model / objective function value. In order to be computed, the user has to provide a valid value for MinMax
model.obsnumeric with the observed values used during the optimisation. See obs

Examples

Run this code

# Setting the user home directory as working directory
setwd("~")

# Number of dimensions to be optimised
D <- 5

# 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, topology="gbest", write2disk=TRUE, plot=TRUE)  
        )

# Reading the convergence measures got by running hydroPSO
setwd("PSO.out")
read_out(MinMax="min") # each particle in a different pannel

Run the code above in your browser using DataLab

Description

Usage

Arguments

Value

See Also

Examples