Search Results:

Showing results 1 to 10 of 15.


Function parseHdr [FITSio v2.1-0]
keywords
files
title
Parse FITS header
description
Parse FITS header to extract keyword = variable pairs. Mostly useful for finding values given keyword name.
Function find.package [base v3.5.2]
keywords
files
title
Find Packages
description
Find the paths to one or more packages.
Function read.vcf [gaston v1.4.9]
keywords
vcf files
title
Create a bed.matrix from VCF files
description
Create a bed.matrix from a .vcf file.
Function verification [hydroPSO v0.4-1]
keywords
files
title
verification
description
Run the model and get a goodness-of-fit value by comparing the simulated values against observations for the optimum parameter set found by optimisation
Function ReadPlot_GofPerParticle [hydroPSO v0.4-1]
keywords
files
title
plotParticlesGof
description
This function reads/plots the parameter values of each particle and the objective function against the iteration number
Function ReadPlot_particles [hydroPSO v0.4-1]
keywords
files
title
Reading/Plotting the 'Particles.txt' output file
description
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
Function ReadPlot_results [hydroPSO v0.4-1]
keywords
files
title
Reading/Plotting all the output files generated by ‘hydroPSO’
description
The function read_results reads the following output files of hydroPSO: 1) ‘BestParameterSet.txt’: best parameter set and its corresponding goodness-of-fit found during the optimisation 2) ‘Particles.txt’: parameter values and their corresponding goodness-of-fit value for all particles and iterations 3) ‘Velocities.txt’: velocity values and their corresponding goodness-of-fit value for all particles and iterations 4) ‘Model_out.txt’: values of the objective function/model output for each particle and iteration 5) ‘ConvergenceMeasures.txt’: convergence measures summarizing performance of hydroPSO 6) ‘Particles_GofPerIter.txt’: goodness-of-fit only for all the particles during all the iterations The function plot_results takes the outputs of the read_results function and then produces the following plots: 1) Dotty plots of parameter values 2) Histograms of parameter values 3) Boxplots of parameter values 4) Correlation matrix among parameter values (optional) 5) Empirical CDFs of parameter values 6) Parameter values vs Number of Model Evaluations 7) (pseudo) 3D dotty plots of (selected) parameter values 8) GoF for each particle against Number of Model Evaluations 9) Velocity values vs Number of Model Evaluations 10a) Scatterplot between Best Simulated values and Observations (OPTIONAL, only if MinMax is provided) 10b) Empirical CDFs for model's output (only produced if obs is NOT a zoo object) 10b) ggof (See ggof) between Best Simulated values and Observations (OPTIONAL, only if obs is a zoo object) 10d) Empirical CDFs for selected quantiles of model's output (OPTIONAL, only if obs is a zoo object) 11) Convergence Measures (Gbest and normSwarmRadius) vs Iteration Number
Function hydroPSO2pest [hydroPSO v0.4-1]
keywords
files
title
Export hydroPSO input files to PEST
description
This function exports the content of the hydroPSO input files ‘ParamRanges.txt’ and ‘ParamFiles.txt’ to PEST, into a single ‘.pst’ files with corresponding ‘.tpl’ and ‘.ins’ files
Function ReadPlot_params [hydroPSO v0.4-1]
keywords
files
title
Reading/Plotting the values of different parameter sets
description
This function reads a file containing different parameter sets and their corresponding goodness-of-fit values The following values of file set default values for header, skip and param.cols: -) modelpara.out, created by the GLUE algorithm of SWAT-CUP, -) modelpara.beh, created by the GLUE algorithm of SWAT-CUP, -) goal.sf2, created by the SUFI-2 algorithm of SWAT-CUP -) goal.pso, created by the PSO algorithm of SWAT-CUP -) ParameterValues.log, created by Nimbus calibration tool (Lisflood model) header and skip are automatically set, in other case, they need to be provided
Function hydroPSO [hydroPSO v0.4-1]
keywords
files
title
Enhanced Particle Swarm Optimisation algorithm
description
State-of-the-art version of the Particle Swarm Optimisation (PSO) algorithm (SPSO-2011 and SPSO-2007 capable). hydroPSO can be used as a replacement for optim, but its main focus is the calibration of environmental and other real-world model codes. Several fine-tuning options and PSO variants are available to customise the PSO engine to different calibration problems.