diff --git a/NEWS b/NEWS
index dc10fc4272b3d3c79e01cdb8394fed988de45cad..97beac6d8398adc914579b1e51e597e32f83445b 100755
--- a/NEWS
+++ b/NEWS
@@ -1,5 +1,5 @@
##############################################################
-# Previous Releases: see old file 'WhatsNew.txt' for details #
+# Previous Releases: see old file 'ChangeLog' for details #
##############################################################
0.1-54 01-Apr-2012
diff --git a/WhatsNew.txt b/WhatsNew.txt
deleted file mode 100755
index b19b29fc93ee344cda7159fd01cbe29a0f6b4a12..0000000000000000000000000000000000000000
--- a/WhatsNew.txt
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@@ -1,246 +0,0 @@
-*) 01-Apr-2012 : 0.1-54
- -) 'params2ecdf' : minor bugfix for png generation ('file' argument changed by 'filename')
- -) 'plot_GofPerParticle' : minor bugfix for png generation ('file' argument changed by 'filename')
- -) 'plot_ParamsPerIter' : minor bugfix for png generation ('file' argument changed by 'filename')
- -) 'plot_convergence' : minor bugfix for png generation ('file' argument changed by 'filename')
- -) 'plot_params' : minor bugfix for png generation ('file' argument changed by 'filename')
- -) 'plot_particles' : minor bugfix for png generation ('file' argument changed by 'filename')
-
-*) 23-Mar-2012 : 0.1-53
- -) 'plot_2parOF' : -) new argument 'MinMax', to allow plotting the "best" points over the rest
- -) new argument 'axis.rot', to allow rotation of axis labels
- -) 'plot_NparOF' : -) new argument 'MinMax', to allow plotting the "best" points over the rest
- -) new argument 'axis.rot', to allow rotation of axis labels
- -) 'plot_out' : -) when 'ptype=="corr"', a lattice grid is added, to make easier the identification of values
- -) when 'ptype=="corr"', the line type for the correlation line between obs and best sim was changed from 1 to 3.
- -) 'plot_params' : -) title for individual figures was removed (with repeating the parameter name presented in the axis) for dottyplots, histograms and boxplots
- -) nicer axis labels
- -) 'plot_ParamsPerIter': -) title for individual figures was removed (with repeating the parameter name presented in the axis)
- -) nicer axis labels
- -) new argument 'verbose'
- -) 'plot_2parOF' : -) less black margins and bold axis labels
- -) 'plot_NparOF' : -) less black margins among figures and bold axis labels
- -) 'hydroPSO' : -) 'of_out.txt' name was changed to 'Model_out.txt'
- -) 'read_out' : -) 'of_out.txt' name was changed to 'Model_out.txt'
- -) contact e-mails were updated
-
-
-*) 09-Mar-2012 : 0.1-52
- -) 'plot_params' : -) default value for 'breaks' argument was changed from "FD" to "Scott" (computation of histograms bins)
- -) default value for 'freq' argument was changed from "FALSE" to "TRUE" (histograms plots)
- -) 'read_params' : -) default value for 'breaks' argument was changed from "FD" to "Scott" (computation of histograms bins)
- -) default value for 'freq' argument was changed from "FALSE" to "TRUE" (histograms plots)
- -) 'plot_particles': -) default value for 'breaks' argument was changed from "FD" to "Scott" (computation of histograms bins)
- -) default value for 'freq' argument was changed from "FALSE" to "TRUE" (histograms plots)
- -) new argument 'alpha' (for allowing transparency of points in 3D-dotty plots)
- -) 'read_particles': -) default value for 'breaks' argument was changed from "FD" to "Scott" (computation of histograms bins)
- -) default value for 'freq' argument was changed from "FALSE" to "TRUE" (histograms plots)
- -) new argument 'alpha' (for allowing transparency of points in 3D-dotty plots)
- -) 'plot_results' : -) default value for 'breaks' argument was changed from "FD" to "Scott" (computation of histograms bins)
- -) default value for 'freq' argument was changed from "FALSE" to "TRUE" (histograms plots)
- -) new argument 'alpha' (for allowing transparency of points in 3D-dotty plots)
- -) 'plot_2parOF' : -) new argument 'alpha' (for allowing transparency of points)
- -) 'plot_NparOF' : -) new argument 'alpha' (for allowing transparency of points)
- -) now the legend is drawn in a window different from the one of the last pair of parameters (much nicer than before !)
-
-*) 24-Feb-2012 : 0.1-51
- -) Start-up message was added, to show the authors of the package and how to cite it
- -) 'hydroPSO' : -) arguments 'model.FUN' and 'model.FUN.args' were moved back from within the 'control' argument up to the main function.
- -) not used message was removed from hydroPSO (showed after each regrouping)
- -) 'lhoat' : -) arguments 'model.FUN' and 'model.FUN.args' were moved back from within the 'control' argument up to the main function.
- -) 'verification' : -) arguments 'model.FUN' and 'model.FUN.args' were moved back from within the 'control' argument up to the main function.
- -) 'read_out' : -) fixed buf when reading results of test functions (introduced in version 0.1-50)
-
-
-*) 23-Feb-2012 : 0.1-50
- -) improved examples in most of the functions
- -) 'lhoat' : -) now it is (partially) able to manage models/objective functions that may return non-finite values as goodness-of-fit values (e.g., MODFLOW when the solver doesn't converge or some cells got dry)
- -) 'verification' : -) arguments were modified in order to allow the analysis of any R function and not only of environmental models ('optim' compatibility)
- -) improved format of output files (digits, GoF before parameter values, etc., ...)
- -) 'read_out' : -) fixed bug that appeared when reading results created by running 'hydroPSO' with some of the test functions
- -) fixed bug that appeared when reading observations that were not zoo objects
- -) name of the argument 'plot.type' was changed to 'ptype'
- -) new argument: 'modelout.cols', to be able to extract only some columns of the model output file.
- -) 'plot_out' : -) new plot.type:' "quant2ecdf"
- -) new argument: leg.pos
- -) name of the argument 'plot.type' was changed to 'ptype'
- -) 'q2ecdf' : -) its name was changed to 'quant2ecdf', in order to make clearer its purpose
- -) its argument 'Qbeh' was changed by 'sim', in order to make avoid explicit reference to streamflows
- -) its argument 'qobs' was changed by 'obs', in order to make avoid explicit reference to streamflows
- -) default value for 'byrow' was changed form FALSE to TRUE, in order to make shorter its call within hydroPSO
- -) new argument: leg.pos
- -) 'params2ecdf' : -) new argument: 'obs'
- -) new argument: leg.pos
- -) now it produces more than 1 plot/PNG of the amount of parameters is larger than 21, in order to avoid figures that be too small
- -) 'plot_results' : -) name of the argument 'modelout.png.fname' was changed by 'modelout.best.png.fname'
- -) new argument: 'GOFcuts'
- -) new argument: 'param.names', in order to plot only some of the calibrated parameters
- -) Default values for params 'cex.main' and 'cex.lab' were slightly increased up to 1.7 and 1.5, respectively
- -) 'plot2parOF' : -) its name was changed to 'plot_2parOF'
- -) new argument: gofs
- -) modified argumet: 'params', which now only includes parameter values, and NOT the goodness-of-fit of each one of them
- -) 'plotNparOF' : -) new argument: gofs
- -) modified argumet: 'params', which now only includes parameter values, and NOT the goodness-of-fit of each one of them
- -) argument 'GOFcuts': default value was changed from missing to "auto"
- -) 'plot_particles' : -) new argument: 'GOFcuts'
- -) now it produces boxplots as well.
- -) new argument: 'bxp.png.fname'
- -) 'read_particles' : -) new argument: 'GOFcuts'
- -) new argument: 'legend.pos' (not used yet, but required...)
- -) new PNG arguments: do.png, png.width, png.height, png.res, dotty.png.fname, hist.png.fname, ecdf.png.fname, runs.png.fname, dp3d.png.fname, pairs.png.fname, 'bxp.png.fname'
- -) 'hydroPSO' : -) minor bugfix in the generation of the 'Observations.txt' files
- -) removed "effective reduction" message after each regrouping
- -) 'plotIterParams' : -) its name was changed to 'plot_ParamsPerIter'
- -) 'read_params' : -) argument 'plot.type' was renamed to 'ptype' (hydroTSM compatibility)
- -) default value for argument 'param.cols' was changed form 'missing' to 'NULL'
- -) default value for argument 'param.names' was changed form 'missing' to 'NULL'
- -) it was transformed into a generic function, with method: default
- -) 'plot_params' : -) argument 'plot.type' was renamed to 'ptype' (hydroTSM compatibility)
- -) it was transformed into a generic function, with methods: default, matrix, data.frame
- -) 'read_GofPerParticle': -) argument 'plot.type' was renamed to 'ptype' (hydroTSM compatibility)
- -) 'read_results' : -) new argument: 'modelout.cols', to be able to extract only some columns of the model output file.
- -) 'hydromod' : -) name of the output object 'sim.values' was changed to 'sim' (for simplicity)
-
-
-*) 13-Feb-2012 : 0.1-49
- -) 'hydromod' : -) call to 'system' was changed by a call to 'system2', in order to have a proper management of 'stdout' and 'stderr' in Windows OS.
- -) 'ignore.stdout' argument was changed by 'stdout' ('system2' compatibility)
- -) new argument 'stderr' ('system2' compatibility)
- -) 'lhoat' : -) arguments were modified in order to allow the analysis of any R function and not only of environmental models ('optim' compatibility)
- -) improved format of output files (digits, GoF before parameter values, etc., ...)
- -) now it is able to manage models/objective functions that may return non-finite values as goodness-of-fit values (e.g., MODFLOW when the solver doesn't converge or some cells got dry)
- -) parameters with RelativeImportance equal to zero now geta Ranking equal to the number of parameter, according to the description in Griensven et al.,2006
- -) 'read_params': -) default plotting colour was changed from 'black' to '#00000030' (semi-transparent black), i order to better distinguish the density of the points in the region close to the "optimum"
- 'plot_params' -) the colour used to plot a vertical and horizontal line on the optimum point found by hydroPSO was changed from 'grey' to 'coral'
- -) new 'plot.type': "pairs" (require the hydroTSM package)
- -) 'hydroPSO' : -) user-defined 'control' parameters are now shown when the algorithm starts
- -) fixed bug in asynchronous update of personal and global best (when some personal bests were NA)
- -) default value for 'control[["npart"]]' was changed from 30 to NA. If the user do not specify a value for that argument, the SPSO-2007 value is used then: 'ceiling(10+2*sqrt(n))'
- -) default value for 'control[["maxit"]]' was changed from 300 to 1000.
- -) default value for 'control[["topology"]]' was changed from 'gbest' to 'random'.
- -) default value for 'control[["use.TVc1"]]' was changed from 'FALSE' to 'TRUE'.
- -) default value for 'control[["TVc1.type"]]' was changed from 'linear' to 'non-linear'.
- -) default value for 'control[["TVc1.exp"]]' was changed from 1 to 1.5
- -) default value for 'control[["TVc2.type"]]' was changed from 'linear' to 'non-linear' (by default 'use.TVc2=FALSE')
- -) default value for 'control[["c1"]]' was changed from 2.05 to 0.5+log(2) (for SPSO-2007 compatibility)
- -) default value for 'control[["c2"]]' was changed from 2.05 to 0.5+log(2) (for SPSO-2007 compatibility)
- -) default value for 'control[["lambda"]]' was changed from 0.5 to 1 (for SPSO-2007 compatibility)
- -) name of the argument 'control[["psoin.drty"]]' was changed to 'control[["drty.in"]]'
- -) name of the argument 'control[["psoout.drty"]]' was changed to 'control[["drty.out"]]'
- -) name of the argument 'control[["useTVvmax"]]' was changed to 'control[["useTVlambda"]]'
- -) name of the argument 'control[["TVvmax.type"]]' was changed to 'control[["TVlambda.type"]]'
- -) name of the argument 'control[["TVvmax.rng"]]' was changed to 'control[["TVlambda.rng"]]'
- -) name of the argument 'control[["TVvmax.exp"]]' was changed to 'control[["TVlambda.exp"]]'
- -) the option 'na.rm=TRUE' was added to the computation of min/max values in the following functions: 'sync.update.pgbests', 'UpdateLocalBest', 'compute.w.aiwf', 'hydroPSO'. This change was necessary in order to allow the correct computation of the best fit per iteration when the fitness of one or more particles was NA.
- -) now the observed values provided provided in 'model.FUN.args' are saved to the output file 'Observations.txt'
- -) 'read_out' : -) improved management of input files with different amount of columns in different rows of the file.
- -) new arguments: 'beh.thr', 'MinMax'
- -) 'read_particles' : -) fixed error produced when 'beh.thr' is lower than the minimum gof of all the parameter sets
- -) 'read_params' : -) fixed error produced when 'beh.thr' is lower than the minimum gof of all the parameter sets
- -) 'read_convergence': -) improved management of 'beh.thr' when this function is called from 'red_results' or 'plot_results'
- -) 'plot_particles' : -) new argument 'png.drty'
- -) new argument 'pairs.png.fname'
- -) 'read_results' : -) name of the argument 'psoout.drty' was changed to 'drty.out'
- -) 'plot_results' : -) name of the argument 'psoout.drty' was changed to 'drty.out'
- -) new argument 'pairs.png.fname'
- -) new function: 'plot_out'
-
-
-*) 22-Ene-2012 : 0.1-48
- -) fixed bug in regrouping for minimisation cases
- -) fixed bug in methods 'fips' and 'wfips' for 'topology==random'
- -) default value for control[["REPORT"]] was changed from 10 to 100
- -) 'read_results': now -when the function is finished- leaves the user in the same directory of the initial call
- -) improved .Rd files
- -) added checkings for 'maxit < REPORT' and 'lambda' out of [0,1]
- -) 'read_params': -) the argument 'beh.thr' is now used for discarding non behavioural parameter sets
- -) improved management of the parameter names
- -) the output of the function is not a single data.frame with parameter sets and goodness-of-fit measures, but a list of two elements: i) a data.frame with the parameter sets, and ii) anumeric vector with the goodness-of-fit measures separated
- -) 'plot_params': -) the argument 'beh.thr' is now used for discarding non behavioural parameter sets
- -) improved management of the parameter names
- -) the argument 'of.col' was removed.
- -) new argument 'gofs' which is used instead of 'of.col'
- -) 'cex.main', 'cex.lab' and 'cex.axis' were changed, in all the plotting functions, from 1.2 to 1.5 in order to have font size better suited for "final" plots
-
-*) 16-Ene-2012 : 0.1-47
- -) name of the main function ('PSO') was changed to 'hydroPSO'
- -) name of the 'n.particles' parameter was changed to 'npart'
- -) name of the 'n.gbest' parameter was changed to 'ngbest'
- -) in the 'fn' argument of the 'hydroPSO' function, 'hydromod' was changed as valid character for the argument by the character 'model', in order to avoid confusion with the 'hydromod' function
- -) all the arguments but c(par, fn, method, lower, upper) where removed form the call to the function and they were replaced by the new argument 'control' (towards 'optim' compatibility)
- -) new 'dumping' boundary condition
- -) fixed bug in LHS introduced in v0.1-46 (formula restored to the one of v0.1-45)
- -) fixed bug in the 'reflecting' boundary condition introduced in v0.1-46 (formula restored to the one of v0.1-45)
- -) parameter 'par' is not longer required (different to 'optim'). If provided, the dimension of the solution space is taken from it, and if not it is taken from 'lower' and 'upper'.
- -) 'lower' & 'upper' must be vectors with the dimension of the solution space (different to 'optim').
- -) the name of the 'read.convergence' function was changed to 'read_convergence'
- -) the name of the 'plot.convergence' function was changed to 'plot_convergence'
- -) the name of the 'read.results' function was changed to 'read_results'
- -) the name of the 'plot.best' function was changed to 'plot_results'
- -) the name of the 'read.particles' function was changed to 'read_particles'
- -) the name of the 'plot.particles' function was changed to 'plot_particles'
- -) the name of the 'read.best' function was changed to 'read_best'
- -) the name of the 'read.out' function was changed to 'read_out'
- -) the name of the 'read.param' function was changed to 'read_params'
- -) the name of the 'plotparam' function was changed to 'plot_params'
- -) improved documentation
- -) added 'ByteCompile' option to the package DESCRIPTION (by default set it to TRUE)
-
-*) 29-Nov-2011 : 0.1-46
- -) 'UpdateLocalBest': added 'LocalBest.pos' variable
- -) fixed bug in 'compute.veloc' function for 'lbest' topology
- -) fixed bugs in some test functions
- -) parameter 'of.name' was changed to 'fn' (towards 'optim' compatibility), and now it can accept any R function
- -) parameter 'n.iter' was changed to 'maxit' (towards 'optim' compatibility)
- -) parameter 'stop.tol' was changed to 'reltol' (towards 'optim' compatibility)
- -) parameter 'X.Boundaries' was changed by 'lower' & 'upper' (towards 'optim' compatibility)
- -) parameter 'Xini' was changed to 'par' (towards 'optim' compatibility)
- -) new parameter 'abstol' (towards 'optim' compatibility)
- -) new parameter 'algorithm', which can be in c("canonical", "ipso", "fips"), in order to clearly separate topologies from improved PSO algorithms
- -) new parameter 'maxfn' with the maximum number of function evaluations (towards 'psoptim' compatibility)
- -) the following test functions are now exported and can be used as any R function: rosenbrock, sphere, rastrigrin, griewank, schafferF6, ackley.
- -) arguments 'MinMax', 'topology', 'algorithm', 'best.update', 'boundary.wall', 'Xini.type', 'Vini.type', 'IW.type', 'TVc1.type', 'TVc2.type', 'TVvmax.type' are now get by using 'match.arg' function
- -) clear distinction between "topology" (gbest, lbest) and "method" (canonical pso, ipso)
- -) new topology 'vonNeumann' (particular case of lbest with 4 neighbours)
- -) new topology 'random', based on SPSO 2007, described in Clerc 2005
- -) new methods 'fips' & 'wfips'
- -) new 'convergence', 'message' and 'counts' ( function.calls, iterations, regrouping ) fields added to the output of hydroPSO
- -) name of the output element 'Best.Parameter.Values' was changed to 'par' (towards 'optim' compatibility)
- -) name of the output element 'Global.Best.Value' was changed to 'value' (towards 'optim' compatibility)
- -) name of the output element 'Global.Best.Position' was changed to 'best.particle' (towards 'optim' compatibility)
- -) Velocity is now initialized as in SPSO 2007 (Vini= [ U(lower, upper) - Xini] / 2 )
-
-
-*) 11-Nov-2011 : 0.1-45
- -) Added scientific notation for simulated values in 'of_out.txt"
- -) New read.convergence & plot.convergence functions
- -) New read.particles & plot.particles functions
- -) New read.velocities
- -) New read.sim function for reading the output model simulated values
- -) New read.best function
- -) New read_results function, a wrapper to several reading functions for reading all the results produced by hydroPSO
- -) New plot_results function, a wrapper to several plotting functions for reading all the results produced by hydroPSO
- -) New 'read_convergence' and 'plot_convergence' functions
- -) 'plotparam': thanks to Rodrigo Rojas'collaboration, this function was greatly improved, in order to get (almost) journal quality by default
- -) 'of-out.txt' changed to 'of_out.txt', in order to avoid problems with the symbol '-'
- -) 'PSO-logfile.txt' changed to 'PSO_logfile.txt', in order to avoid problems with the symbol '-'
- -) Particles.txt : GoF is now writen as third column instead of as the last one
- -) Velocities.txt : GoF is now writen as third column instead of as the last one
- -) 'XtFitness.txt' was renamed to 'Particles_GofPerIter.txt'
- -) 'plotParticlesGof' was renamed to 'read.GofPerParticle'
-
--) 28-Oct-2011 : 0.1-44. Added scientific notation for output files
--) 17-Oct-2011 : 0.1-43. Improved documentation to the PSO algorithm and small changes in the name of some control variables
--) 08-Oct-2011 : 0.1-42. Added documentation to the PSO algorithm
--) 05-Sep-2011 : 0.1-41. Added main title for 'plotparam', 'plotNparLines'
--) 01-Sep-2011 : 0.1-40.'plotparam': changed default columns and names for parameters
--) 24-Jun-2011 : parallel implementation with multi-core running with PSO and a hydrological model
--) May-2011 : Shuffling Evolution PSO working with generic hydromodel and generic goodness-of-fit function calls ('model.FUN' and 'model.FUN.args')
--) Apr-2011 : PSO
--) 29-Dec-2010 : new method: IPSO
--) ~ 23-Dec-2010: Shuffling Evolution PSO working with test functions
--) Dec-2010 : Shuffling Evolution PSO idea
--) Nov-2010 : PSO working with hydrological models
--) 2009-Oct2010: hydroPSO hibernation :(
--) Jul-2008 : canonical PSO working with some test functions
--) its name was changed to 'plot_NparOF'