Method pest/mcmcPlot


  MCMCPLOT.M - Tool to visualise results of a MCMC sampling.
 
  DESCRIPTION:  Simple tool that plots results from mcmc pest objects.
                Plots the traces of the chains and th PDFs of the
                parameters.
 
  CALL: 
        >> mcmcPlot(pest_obj,pl)
 
        >> pest_obj.mcmcPlot(pl)
 
 
  PARAMETERS: - pest_obj: pest object
              - pl:       plist
 
     EXAMPLE: - mcmcPlot(p,plist('plotmatrix',true,'burnin',5000,'pdfs',[2 4 5]))
 
 ParametersDescription
 
  Nikos Oct 2011
 
 
Method Details
Access public
Defining Class pest
Sealed 0
Static 0

Parameter Description

Default

no description
Key Default Value Options Description
mcmcPlot
CHAINS [] none Insert an array containing the parameters to plot. If left empty,then by default will plot the chains of every parameter. If set to zero then no chains are plotted. (note: The loglikelihood is stored in the first column)
CHAIN COLOR [0.16700000000000001 0.56399999999999995 0.98799999999999999 ...] none A 3x1 vector defining the color of the chains.
FACE COLOR [0.16700000000000001 0.56399999999999995 0.98799999999999999 ...] none A 3x1 vector defining the color of the faces of the bar graphs. It also applies to plotmatrix.
EDGE COLOR [0.16700000000000001 0.56399999999999995 0.98799999999999999 ...] none A 3x1 vector defining the color of the edges. It also applies to plotmatrix.
BURNIN 1 none Number of samples (of the chains) to be discarded for the computation of the PDFs of the parameters. Also usedfor producing the plotmatrix figure.
NBINS 25 none Number of bins of the pdf histogram computed for every parameter (used again for the computation of the PDFs of the parameters)
PLOTMATRIX 0
  • 0
  • 1
Flag to determine if a plotmatrix is desired
TICKS 0
  • 0
  • 1
In case where the 'PLOTMATRIX' is set to true, and the dimensionality is high, sometimes it is convenient to not draw the x and y-ticks. This flag takes care of this.
PDFS 0 none Determine if a plot of the PDFs of each parameter is desired. The same as the 'CHAINS' option but for plotting the PDFs of the paramters.
PLOT FIT CURVES 1
  • 1
  • 0
Set to true to attempt to plot Gaussian fit curves to parameters histograms.
PARAM NAMES [] none Cell array of names of the parameters to be assigned to each plot. If left empty the default values from the pest object will be used. If the 'NAMES' field of the pest object is empty, some default names will be used.
TRUE VALUES [] none If the parameter values are known and provided, they will be drawn on the histogram plots.
HIST TYPE 'hist'
  • 'hist'
  • 'stairs'
The histogram type.
PLOT ELLIPSOID 0
  • 0
  • 1
True false flag, to plot ellipsoids at different confidence levels, intead of the data. Applies if 'Plotmatrix' is set to true.
COLORPDFS 'r-' none Choose a color for the fitted Gaussians on the PDFs. Used also to point the estimated parameters on the PDFs.
ERROR COLOR 'r--' none Choose a color for the estimated errors on the PDFs.
COLORMAP '' none Choose a colormap for the PDF histograms (as a string). By default colormaps are not used. Note: For best results it is recomended to use this option with less than 25 'NBINS'. For the available colormaps type 'doc colormap'in the terminal.
RESULTS 0
  • 0
  • 1
Set to "true" if a table of the results of the estimated parameters is desired.The results are printed on screen in 2 columns: the 1st contains the mean valueand the second the sigma.
FONTSIZE 10 none The font size for all the cases of the plots.
PLOT CUMSUM 1
  • 1
  • 0
True-False flag to plot hte cumulative mean of the chains.
PYTHON CORNER PLOT, PY CPLOT 0
  • 0
  • 1
A flag to enable/disable the python corner plot. Works only if the 'triangle' python module has been imported. Saves the figure under the name 'triangle_plot' in current directory.
SHOW PROVENANCE 1
  • 1
  • 0
A flag to enable/disable the provenance text patch.

Example

plist('CHAINS', [[]], 'CHAIN COLOR', [[0.16700000000000001 0.56399999999999995 0.98799999999999999]], 'FACE COLOR', [[0.16700000000000001 0.56399999999999995 0.98799999999999999]], 'EDGE COLOR', [[0.16700000000000001 0.56399999999999995 0.98799999999999999]], 'BURNIN', [1], 'NBINS', [25], 'PLOTMATRIX', [false], 'TICKS', [false], 'PDFS', [0], 'PLOT FIT CURVES', [true], 'PARAM NAMES', [[]], 'TRUE VALUES', [[]], 'HIST TYPE', 'hist', 'PLOT ELLIPSOID', [false], 'COLORPDFS', 'r-', 'ERROR COLOR', 'r--', 'COLORMAP', '', 'RESULTS', [false], 'FONTSIZE', [10], 'PLOT CUMSUM', [true], 'PYTHON CORNER PLOT', [false], 'SHOW PROVENANCE', [true])

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Some information of the method pest/mcmcPlot are listed below:
Class name pest
Method name mcmcPlot
Category Helper
Package name ltpda
VCS Version 967b0eec0dece803a81af8ef54ad2f8c784b20b2
Min input args 1
Max input args -1
Min output args 1
Max output args -1
Can be used as modifier 1
Supported numeric types {'double'}




©LTP Team