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Highlights from
ProcessNetwork/ProcessNetwork_Software

  • plot_modwt_wvar_ci_compar...
    plot_modwt_wvar_ci_comparison -- Plot MODWT wavelet variance and confidence intervals calculated via different methods.
  • modwt_plot_comparison_wva...
    modwt_plot_comparison_wvar_ci -- Plot wavelet variance and various confidence interval methods for MODWT wavelet coefficients.
  • AdjMatrices(T,SigThreshT,...
    COMPUTES AN ADJACENCY MATRIX A
  • DoProduction(T)
  • GetEvenBinEdgesGlobal(nBi...
  • GetShannonBits(C,nCounts)
    Get Marginal and Joint Shannon Entropies in terms of bits (log 2), given probability matrices
  • GetUniformBinEdges(sample...
    make nodata entries NaN, because min and max function ignores them...
  • IAAFTsur(xV,nsur)
  • MU_assert_error(expected_...
    MU_assert_error -- Assert that expected and actual error message ids are equal.
  • MU_assert_expression(expr...
    MU_assert_expression -- Assert that expression is true.
  • MU_assert_fuzzy_diff(expe...
    MU_assert_fuzzy_diff -- Assert that expected and actual values are equal within fuzzy diff tolerance.
  • MU_assert_isempty(actual_...
    MU_assert_isempty -- Assert that actual value is empty.
  • MU_assert_isequal(expecte...
    MU_assert_isequal -- Assert that expected and actual values are equal.
  • MU_assert_isequalwithequa...
    MU_assert_isequalwithequalnans -- Assert that expected and actual values are equal with equal NaNs.
  • MU_assert_isnotempty(actu...
    MU_assert_isnotempty -- Assert that actual value is not emtpy.
  • MU_assert_istrue(actual_v...
    MU_assert_istrue -- Assert that actual value is Boolean true.
  • MU_assert_numsigdig_diff(...
    MU_assert_numsigdig_diff -- Assert that expected and actual values are equal within number of significant digits.
  • MU_fail(msg)
    MU_fail -- Throw error for a failed assertion.
  • MU_fail_line(funcname, li...
    MU_fail_line -- Encode function name, line number and message of failure into error message string and call MU_fail.
  • MU_lookup_mode_num_by_nam...
    MU_lookup_mode_num_by_name -- Return the numeric mode code by mode name.
  • MU_lookup_tresult_status_...
    MU_lookup_tresult_status_by_name -- Return the numeric test result status code by test result status name.
  • MU_print_tcase_summary(tc...
    MU_print_tcase_summary -- Print a test case summary.
  • MU_print_tresults(tresult...
    MU_print_tresults -- Print test case results.
  • MU_print_tresults_report(...
    MU_print_tresults_report.m -- Print test case results.
  • MU_print_tsensemble_summa...
  • MU_print_tsuite_summary(t...
    MU_print_tsuite_summary -- Print summary for a test suite.
  • MU_summarize_tresults(tc,...
    MU_summarize_tresults -- Summarize a set of test results.
  • MU_summarize_ts_results(t...
    MU_summarize_ts_results -- Summarize the test suite results.
  • MU_summarize_ts_summaries...
  • MU_tcase_add_test(tc, tfh...
    MU_tcase_add_test -- Add a test to test case.
  • MU_tcase_create(tcase)
    MU_tcase_create -- Create and load a tcase.
  • MU_tcase_list_tests(tc)
    MU_tcase_list_tests_run -- List the tests in a test case.
  • MU_tcase_new(name)
    MU_tcase_new -- Creates a new (empty) test case struct.
  • MU_tcase_run(tc, mode, te...
  • MU_tcase_run_test(tc, tfh...
    MU_tcase_run_test -- Run specified test within a test case.
  • MU_tresult_create(tcname,...
    MU_tresult_create -- Create a new test result struct (tresult_s).
  • MU_tsensemble_add_tsensem...
  • MU_tsensemble_add_tsuite(...
  • MU_tsensemble_create(tsen...
    Verify that tsensemble function file exists current path
  • MU_tsensemble_new(name)
  • MU_tsuite_add_tcase(ts, tc)
    MU_tsuite_add_tcase -- Add a test case struct to test suite struc.
  • MU_tsuite_create(tsuite)
    MU_tsuite_create -- Create and load a test tsuite.
  • MU_tsuite_list_tcases(ts)
    MU_tsuite_list_tests -- List the test cases in a test suite.
  • MU_tsuite_new(name)
    MU_tsuite_new -- Creates a new (empty) test suite structure.
  • MU_tsuite_run(ts, mode, t...
  • NormTheStats(nBinVect,I,T...
    Get size
  • ProcessNetwork(opts)
    % This code contains Version 1.5 of the main ProcessNetwork software,
  • QChisq(p, nu)
    % computes the abscissae y for given probability p (upper tail)
  • QGauss(x)
    % computes the abscissae y for given probability x
  • ShannonBitsWrapper(classi...
  • XXX_tcase
    XXX_tcase -- munit test case to test XXX.
  • XXX_tsensemble
    XXX_tsensemble -- munit test suite to test XXX.
  • XXX_tsuite
    XXX_tsuite -- munit test suite to test XXX.
  • advance_scaling_filter(wt...
    advance_scaling_filter -- Calculate the value to advance scaling filter at jth level for a given wavelet.
  • advance_time_series_filte...
    advance_time_series_filter -- Calculate the advance of the time series or filter for a given wavelet.
  • advance_wavelet_filter(wt...
    advance_wavelet_filter -- Calculate the advance of the wavelet filter at jth level for a given wavelet.
  • argterr(func, arg, dataty...
    argterr - Check the data type and size of a function argument.
  • argterr_tcase
    verify_data_tcase -- munit test case to test argterr.
  • assert_tcase
    assert_tcase -- munit test case to test assert functions.
  • classifySignal(sampleMat,...
  • colorspecname2rgb(colorsp...
    colorspecname2rgb -- Look up RGB value by ColorSpec name.
  • columnize(X)
    columnize -- Convert array in to a column vector.
  • compare_struct_fieldnames...
    compare_struct_fieldnames -- Compare two structs for match of fieldnames.
  • compare_struct_fieldvalue...
    compare_struct_fieldvalues -- Compare two structs for match of fieldvalues.
  • couplingLagPlot(R,popts)
  • createSurrogates(opts,Dat...
    Create the surrogate data for statistical testing
  • data_tsuite
    data_tsuite -- munit test suite to test data.
  • dhm(s_X, Z)
    dhm -- Generate simulation of stationary process using Davies-Harte method.
  • display_figures(figure_li...
    display_figures -- Display figure scripts to screen or write to file
  • dwt(X, wtf, nlevels, boun...
    dwt -- Compute the (partial) discrete wavelet transform (DWT).
  • dwt2vector(WJ, VJ, att)
    dwt2vector -- Convert DWT coefficient cell array to vector representation.
  • dwt_equivalent_filter(wtf...
    dwt_equivalent_filter -- Calculate DWT equivalent filter for J levels.
  • dwt_filter(wtfname)
    dwt_filter -- Define the DWT filter coefficients.
  • dwt_filter_tcase
    dwt_filter_tcase -- munit test case to test dwt_filter.
  • dwt_functionality_tcase
    dwt_functionality_tcase -- munit test case to test dwt functionality.
  • dwt_scaling_sgf(f, wtfnam...
    dwt_scaling_sgf -- Calculate squared gain function for DWT scaling filter.
  • dwt_scaling_transfer_func...
    dwt_scaling_transfer_function -- Calculate transfer function for specified DWT scaling filter.
  • dwt_toolbox_tsensemble
  • dwt_verification_tcase
    dwt_verification_tcase -- munit test case to verify results of dwt transform.
  • dwt_wavelet_sgf(f, wtfnam...
    dwt_wavelet_sgf -- Calculate squared gain function for DWT wavelet filter.
  • dwt_wavelet_transfer_func...
    dwt_wavelet_transfer_function -- Calculate transfer function for specified DWT wavelet filter.
  • dwtjm(Vin, h, g, j)
    dwtjm -- Calculate jth level DWT coefficients (MATLAB implementation).
  • encode_errmsg(err_id, err...
    encode_errmsg -- Encode error message for specified err_id.
  • entropyFunction(classifie...
    INITIALIZE PARALLEL OUTPUTS OF THE SHANNON BIT FUNCTION
  • equivalent_filter_width(L...
    equivalent_filter_width -- Calculate width of the equivalent wavelet or scaling filter.
  • error_func(number)
    error('This is an error in error_func');
  • example1_tcase_1
  • example1_tcase_2
  • example1_tcase_error
  • example1_tcase_fail
  • example1_tcase_pass
  • example1_tsuite
  • external_test(varargin)
  • figure_datestamp(filename...
    figure_datestamp -- Print a datestamp in footer area of a figure.
  • figure_footer(str, hfigure)
    figure_footer -- Print the string in the footer text area of a figure.
  • filter_autocorrelation_wi...
    filter_autocorrelation_width - Calculate autocorrelation width of scaling filter.
  • filter_center_of_energy(a)
    filter_center_of_energy -- Calculate filter center of energy.
  • flipvec(x)
  • flipvec_tcase
    modwt_case -- munit test case for flipvec.
  • fuzzy_diff(a, b, fuzzy_to...
    fuzzy_diff -- Find differences in two arrays exceeding fuzzy_tolerance.
  • getCountMat(tupleMat,nBin...
    This function takes only classified signals, where the signal has already
  • imodwt(WJt, VJt, att)
    imodwt -- Calculate the inverse (partial) maximal overlap discrete wavelet transform (IMODWT).
  • imodwt_details(WJt, wtfname)
    imodwt_details -- Calculate details via inverse maximal overlap discrete wavelet transform (IMODWT).
  • imodwt_mra(WJt, VJt, w_att)
    imodwt_mra -- Calculate MODWT multi-resolution details and smooths from wavelet coefficients via IMODWT transform.
  • imodwt_mra_verification_t...
    imodwt_mra_verification_tcase -- munit test case to verify results of imodwt_mra transform.
  • imodwt_smooth(VJt, wtfnam...
    imodwt_smooth -- Calculate smooths at J0 level via inverse maximal overlap discrete wavelet transform (IMODWT).
  • imodwt_tcase
    imodwt_tcase -- munit test case to test imodwt function.
  • infomsg(msg_str, verbosit...
    infomsg -- Display an informative message based on global VERBOSITY setting.
  • intializeOutput(nDataFile...
    Determine size of 3rd dimension for statistical tests depending on
  • iswtf(wtf)
    iswtf -- Determine if input is a valid wtf struct.
  • linesegment(xstart, ystar...
    linesegment -- Plot a set of line segments as specified by their start and end points.
  • linesegment_plot(x1, y1, ...
    linesegment_plot -- Plot a series of line segments on current plot axes.
  • list2struct(list)
    liststruct -- Convert a list (cell array) of name-value pairs to a struct.
  • list2struct_tcase
    list2struct_tcase -- munit test case to test list2struct.
  • list_tcase(tcase, logfile)
    list_tcase -- List the tests in a MUnit test case.
  • list_tsuite(tsuite, logfile)
    list_tsuite -- List the test cases in a MUnit test suite.
  • load_16pt_d4_modwt
    load_16pt_d4_modwt -- Load MODWT coefficients (D4 filter) for 16pt times series.
  • load_16pta
    load_16pt -- Load 16pt series in left-hand plot of Figure 42.
  • load_atomic_clock
    load_atomic_clock -- Load atomic clock time differences times series.
  • load_datasets_tcase
    load_datasets_tcase -- munit test case to test load_datasets.
  • load_ecg
    load_ecg -- Load ecg times series.
  • load_ecg_c6_dwt
    load_ecg_c6_dwt -- Load DWT coefficients (C6 filter) for ecg times series.
  • load_ecg_d4_dwt
    load_ecg_d4_dwt -- Load DWT coefficients (D4 filter) for ecg times series.
  • load_ecg_haar_dwt
    load_ecg_haar_dwt -- Load DWT coefficients (Haar filter) for ecg times series.
  • load_ecg_la8_dwt
    load_ecg_la8_dwt -- Load DWT coefficients (LA8 filter) for ecg times series.
  • load_ecg_la8_modwt
    load_ecg_la8_modwt -- Load MODWT coefficients (LA8 filter) for ecg times series.
  • load_ecg_la8_modwt_mra
    load_ecg_la8_modwt_mra -- Load MODWT MRA coefficients (LA8 filter) for ecg times series.
  • load_epic_cov_ts
    load_epic_cov_ts -- Load EPIC covariance time series source data.
  • load_msp
    load_msp -- Ocean shear series.
  • load_msp_4096
    load_msp_4096 -- Ocean shear series.
  • load_msp_d6_sdf
    load_msp_d6_sdf -- Load MODWT SDF (D6) for ocean shear (msp) times series.
  • load_msp_d6_wvar
    load_msp_d6_wvar -- Load MODWT WVAR (D6) for ocean shear (msp) times series.
  • load_msp_d6_wvar_edof1
    load_msp_d6_wvar_edof1 -- Load MODWT WVAR EDOF (LA8 filter) for ocean shear (msp) times series.
  • load_msp_d6_wvar_edof3
    load_msp_d6_wvar_edof1 -- Load MODWT WVAR EDOF (LA8 filter) for ocean shear (msp) times series.
  • load_nile
    load_nile -- Load Nile River times series.
  • load_nile_haar_modwt
    load_nile_haar_modwt -- Load MODWT coefficients (Haar filter) for Nile River times series.
  • load_nile_wvar_622_715
    load_nile_wvar_622_715 -- Load MODWT WVAR for Nile time series for period 622-715.
  • load_nile_wvar_716_1284
    load_nile_wvar_716_1284 -- Load MODWT WVAR for Nile time series for period 716-1284.
  • load_nmr
    load_nmr -- Load atomic clock time differences times series.
  • load_solar_magnetic
    load_solar_magnetic -- Load solar magnetic field magnitude time series.
  • load_subtidal
    load_subtidal -- Load subtidal sea level times series.
  • load_table333
    load_table333 -- Load data from table333
  • logwrite(msg,vout)
    Appends a message to the processLog, which is a cell of strings
  • make(target, opts)
    make.m -- Make-like utility for compiling wmtsa C functions.
  • make(target, opts)
    make.m -- Make-like utility for compiling wmtsa C functions.
  • modwt(X, wtf, nlevels, bo...
    modwt -- Compute the (partial) maximal overlap discrete wavelet transform (MODWT).
  • modwt_choose_nlevels(choi...
    modwt_choose_nlevels -- Select J0 based on choice, wavelet filter and data series length.
  • modwt_cir_shift(WJt, VJ0t...
    modwt_cir_shift -- Circularly shift (advance) MODWT coefficients for alignment with original time series.
  • modwt_cir_shift_mra_bdry(...
    modwt_cir_shift_mra_bdry -- Calculate bounds of MODWT MRA coefficents affected by circular shift.
  • modwt_cir_shift_mra_bdry_...
    modwt_cir_shift_mra_bdry_indices - Return indices of the MODWT MRA influenced by circularity conditions.
  • modwt_cir_shift_scoef_bdr...
    modwt_cir_shift_scoef_bdry -- Calculate circular shift boundaires for MODWT scaling coefficients at level J0.
  • modwt_cir_shift_scoef_bdr...
    modwt_cir_shift_scoef_bdry_indices - Return indices of the MODWT scaling coefficients at boundaries affected by circularity conditions.
  • modwt_cir_shift_wcoef_bdr...
    modwt_cir_shift_wcoef_bdry -- Calculate bounds of MODWT wavelet coefficients affected by circular shift.
  • modwt_cir_shift_wcoef_bdr...
    modwt_cir_shift_wcoef_bdry_indices - Return indices of the MODWT wavelet coefficients influenced by circularity conditions.
  • modwt_cum_level_cum_wav_s...
    modwt_cum_level_cum_wav_svar -- Calculate cumulative level of cumulative sample variance of MODWT wavelet coefficients.
  • modwt_cum_level_wcov(wcov...
    modwt_cum_level_wcov -- Compute cumulative level wavelet covariance.
  • modwt_cum_level_wcov_tcase
    modwt_cum_level_wcov_tcase -- munit test case to test modwt_cum_level_wcov.
  • modwt_cum_level_wvar_tcase
    modwt_cum_level_wvar_tcase -- munit test case to test modwt_cum_level_wvar.
  • modwt_cum_wav_svar(WJt, w...
    modwt_cum_wav_svar -- Calculate cumulative sample variance of MODWT wavelet coefficients.
  • modwt_equivalent_filter(w...
    modwt_equivalent_filter -- Calculate MODWT equivalent filter for J levels.
  • modwt_filter(wtfname)
    modwt_filter -- Define the MODWT filter coefficients.
  • modwt_filter_tcase
    modwt_filter_tcase -- munit test case to test modwt_filter.
  • modwt_functionality_tcase
    modwt_functionality_tcase -- munit test case to test modwt functionality.
  • modwt_inv_cir_shift(TWJt,...
    modwt_inv_cir_shift -- Inverse circularly shift (advance) MODWT coefficients.
  • modwt_mra(X, wtf, nlevels...
    modwt_mra -- Calculate MODWT multi-resolution details and smooths of a time series (direct method).
  • modwt_mra_functionality_t...
    modwt_mra_functionality_tcase -- munit test case to test modwt_mra functionality.
  • modwt_mra_verification_tcase
    modwt_mra_verification_tcase -- munit test case to verify results of modwt_mra transform.
  • modwt_num_nonboundary_coe...
    modwt_num_nonboundary_coef -- Calculate number of nonboundary MODWT coefficients for jth level.
  • modwt_rot_cum_wav_svar(WJ...
    modwt_rot_cum_wsvar -- Calculate the rotated wavelet sample variance from MODWT wavelet coefficients.
  • modwt_running_wcov(TWJtX,...
    modwt_running_wcov -- Calculate running wavelet covariance of circularly-shifted MODWT wavelet coefficients.
  • modwt_running_wvar(TWJt, ...
    modwt_running_wvar -- Calculate running wavelet variance of circularly-shifted MODWT wavelet coefficients.
  • modwt_scaling_sgf(f, wtfn...
    modwt_scaling_sgf -- Calculate squared gain function for MODWT scaling filter.
  • modwt_scaling_transfer_fu...
    modwt_scaling_transfer_function -- Calculate transfer function for specified MODWT scaling filter.
  • modwt_tsuite
    modwt_tsuite -- munit test suite to test modwt and inverse transforms.
  • modwt_utils_tsuite
    modwt_utils_tsuite -- munit test suite to test modwt_utils.
  • modwt_verification_tcase
    modwt_verification_tcase -- munit test case to verify results of modwt transform.
  • modwt_wavelet_sample_vari...
    modwt_wavelet_sample_variance -- Compute sample variance from MODWT wavelet decomposition and orignal data series.
  • modwt_wavelet_sgf(f, wtfn...
    modwt_wavelet_sgf -- Calculate squared gain function for MODWT wavelet filter.
  • modwt_wavelet_transfer_fu...
    modwt_wavelet_transfer_function -- Calculate transfer function for specified MODWT wavelet filter.
  • modwt_wcor(WJtX, WJtY, p)
    modwt_wcor -- Calculate the wavelet correlation of MODWT wavelet coefficients.
  • modwt_wcov(WJtX, WJtY, ci...
    modwt_wcov -- Calculate the wavelet covariance from MODWT wavelet coefficients.
  • modwt_wcov_functionality_...
    modwt_wcov_functionality_tcase -- munit test case to test modwt_wcov.
  • modwt_wvar(WJt, ci_method...
    modwt_wvar -- Calculate wavelet variance of MODWT wavelet coefficients.
  • modwt_wvar_ci(wvar, MJ, c...
    modwt_wvar_ci -- Calculate confidence interval of MODWT wavelet variance.
  • modwt_wvar_ci_functionali...
    modwt_wvar_ci_functionality_tcase -- munit test case to test modwt_wvar_ci.
  • modwt_wvar_ci_verificatio...
    modwt_wvar_ci_verification_tcase -- munit test case to test modwt_wvar_ci.
  • modwt_wvar_functionality_...
    modwt_wvar_functionality_tcase -- munit test case to test modwt_wvar.
  • modwt_wvar_psd(wvar, delt...
    modwt_wvar_psd -- Calculate estimate of band-averaged power spectral density from MODWT wavelet variance.
  • modwt_wvar_psd_tcase
    modwt_wvar_psd_tcase -- munit test case to test modwt_wvar_psd.
  • modwt_wvar_verification_t...
    modwt_wvar_verification_tcase -- munit test case to test modwt_wvar.
  • modwtjm(Vtin, ht, gt, j)
    modwtjm -- Calculate jth level MODWT coefficients (MATLAB implementation).
  • multiCouplingSynchronyPlo...
    % Horizontal bar plot showing the zero-lag coupling statistic (black bar)
  • multi_yoffset_plot(x, y, ...
    multi_yoffset_plot -- Plot series of stacked plots of multiple data series.
  • munit_tsuite
  • nargerr(func, ...
    nargerr -- Check number of arguments to a function.
  • nargerr_tcase
    nargerr_tcase -- munit test case to test nargerr.
  • nsigdig_diff(a, b, nsdig,...
    nsigdig_diff -- Find differences in two arrays exceedning number of significant digits.
  • numsigdig_diff(x, y, nums...
    numsigdig_diff -- Find differences in two arrays exceedning number of significant digits.
  • optsCheck(opts,nVars)
    Checks parameters and settings to run the ProcessNetwork software
  • overplot_imodwt_cir_mra_b...
    overplot_imodwt_cir_mra_bdry -- Plot an overlay of the boundaries of inverse MODWT MRA influenced by circularity conditions.
  • overplot_modwt_cir_shift_...
    overplot_modwt_cir_shift_coef_bdry -- Plot an overlay of the boundaries of shifted MODWT coefficients influenced by circularity conditions.
  • parse_opts(varargin)
    parse_opts -- Parse name-value pair options into a struct.
  • parse_opts_tcase
    parse_opts_tcase -- munit test case to test parse_opts.
  • plot_cum_wcov(wcov, CI_wc...
    plot_cum_wcov -- Plot the cumlative wavelet covariance and (optionally) confidence intervals.
  • plot_dwt_vector(W, NJ, Li...
    plot_dwt_vector -- Plot the vector W of DWT coefficients.
  • plot_equivalent_filter(tr...
    plot_equivalent_filter -- Plot equivalent wavelet filters for J levels.
  • plot_filter_sgf(transform...
    plot_filter_sgf -- Plot squared gain functions for specified transform, wavelet filter, levels and frequencies.
  • plot_imodwt_mra(DJt, SJ0t...
    plot_imodwt_mra -- Plot the inverse MODWT multiresolution analysis detail and smooth coefficients and original time series.
  • plot_modwt_clcwsvar(clcws...
    plot_modwt_clcwsvar -- Plot the cumulative level of cumulative sample variance of MODWT wavelet coefficients.
  • plot_modwt_coef(WJt, VJ0t...
    plot_modwt_coef -- Plot the MODWT wavelet and scaling coefficients and the original time series.
  • plot_modwt_coef2(WJt, VJ0...
    plot_modwt_coef2 -- Plot the MODWT wavelet and scaling coefficients and the original time series (individual subplots version).
  • plot_modwt_cwsvar(cwsvar,...
    function_name -- Plot the cumulative sample variance of the MODWT wavelet coefficients.
  • plot_modwt_rcwsvar(rcwsva...
    plot_modwt_rcwsvar -- Plot the rotated cumulative sample variance of the MODWT wavelet coefficients.
  • plot_wcor(wcor, CI, ylabe...
    plot_wcor -- Plot the wavelet correlation and (optionally) confidence intervals.
  • plot_wcov(wcov, CI_wcov, ...
    plot_wcov -- Plot the wavelet covariance and confidence intervals.
  • plot_wvar(wvar, CI_wvar, ...
    plot_wvar - Plot the wavelet variance and confidence intervals.
  • plot_wvar_psd(f, CJ, f_ba...
    plot_wvar_psd -- Plot power spectral density (PSD) estimated from wavelet variance.
  • plot_wvar_psd_tcase
    plot_wvar_psd_tcase -- munit test case to test plot_wvar_psd.
  • plot_wvar_tcase
    plot_wvar_tcase -- munit test case to test plot_wvar.
  • preProcess(opts,Data)
    Run the preprocessing options, currently includes data trimming and
  • removePeriodicMean(signal...
    Removes the mean at every timestep from a periodic signal. For example,
  • replace(A, S1, S2)
    REPLACE - Replace Elements
  • rgb2colorspecname(rgb, fo...
    rgb2colorspecname -- Look up ColorSpec name by rgb value.
  • run_tcase(tcase, mode, lo...
    run_tcase -- Run a MUnit test case and print the test results.
  • run_tsensemble(tsensemble...
    Start timer
  • run_tsuite(tsuite, mode, ...
    run_tsuite -- Run a MUnit test suite.
  • runtc(tcase, mode, logfil...
  • runts(tsuite, mode, logfi...
  • sample_tcase
  • sample_tsuite
  • set_axes_prop(haxes, axes...
    set_plot_prop - Set properties of given axes.
  • set_default(var_name, def...
    set_default -- Set default value for a variable in workspace.
  • set_default_tcase
    set_default_tcase -- munit test case to test set_default.
  • set_defaults(defaults, va...
    set_defaults -- Create variables with default values if non-existant in workspace.
  • set_defaults_tcase
    set_defaults_tcase -- munit test case to test set_defaults.
  • set_infomsg_verbosity_lev...
    set_infomsg_verbosity_level -- Set and return numeric value of VERBOSE to the verbose level for informational messages.
  • set_opts_defaults(in_opts...
    set_opts_defaults -- Set default values for opts.
  • suptitle(str)
    SUPTITLE Puts a title above all subplots.
  • tc_summary_tcase
    tc_summary_tcase -- munit test case to test tcase summary functions.
  • tcase_tcase
    tcase_tcase -- munit test case to test tcase functions.
  • test_dwt
    test_dwt -- Test driver for dwt.
  • test_imodwt_mra
    test_modwt -- Test driver for imodwt_mra
  • test_modwt_running_wvar
    test_modwt_running_wvar -- Test driver for test_modwt_running_wvar.
  • test_modwt_wvar
    test_modwt -- Test driver for imodwt_wvar
  • test_modwt_wvar_psd
    test_modwt_wvar_psd -- Test driver for modwt_wvar_psd
  • trimNoData(rawData,NoData...
  • ts_sample_variance(X)
    ts_sample_variance -- Compute the sample variance of a time-series data set (vector or array).
  • tsuite_tcase
    tsuite_tcase -- munit test case to test tsuite functions.
  • utils_tsuite
    utils_tsuite -- munit test suite to test utils.
  • validate_opts(opts, valid...
    validate_opts -- Validate opts fieldnames.
  • verify_datatype(var, data...
    verify_datatype -- Verify the datatype(s) of a variable.
  • verify_datatype_tcase
    verify_data_tcase -- munit test case to test verify_datatype.
  • waveletTransform(rawData,...
    Extract signal variations at a particular scale or set of scales using
  • wavelet_filter(g)
    wavelet_filter -- Compute wavelet filter coefficents from scaling filter coefficients.
  • wmtsa_acvs(X, estimator, ...
    wmtsa_acvs -- Calculate the autocovariance sequence (ACVS) of a data series.
  • wmtsa_acvs_tcase
    wmtsa_acvs_tcase -- munit test case to test wmtsa_acvs.
  • wmtsa_biased_ccvs(X, Y)
    wmtsa_biased_ccvs -- Calculate the biased cross covariance sequence (CCVS) of two data series.
  • wmtsa_ccvs(X, Y, estimato...
    wmtsa_ccvs -- Calculate the cross covariance sequence (CCVS) of a data series.
  • wmtsa_ccvs_tcase
    wmtsa_ccvs_tcase -- munit test case to test wmtsa_ccvs.
  • wmtsa_chi2inv(p, nu)
    wmtsa_chi2inv -- Wrapper function for chi2inv.
  • wmtsa_data(dataset)
    wmtsa_data -- Load a WMTSA dataset.
  • wmtsa_data_tcase
    wmtsa_data_tcase -- munit test case to test wmtsa_data.
  • wmtsa_encode_errmsg(err_i...
    wmtsa_encode_errmsg -- Encode error message for given err_id.
  • wmtsa_err_table
    $Id: wmtsa_err_table.m 612 2005-10-28 21:42:24Z ccornish $
  • wmtsa_gen_fd_sdf_acvs(N, ...
    wmtsa_gen_fd_sdf_acvs -- Generate the ACVS from the SDF of fractionally difference (FD) process.
  • wmtsa_ismatrix(x, type)
    wmtsa_ismatrix -- Determine if item is a matrix.
  • wmtsa_ismatrix_tcase
    modwt_case -- munit test case for wmtsa_ismatrix.
  • wmtsa_isscalar(x)
    wmtsa_isscalar -- Determine if item is a point.
  • wmtsa_isscalar_tcase
    modwt_case -- munit test case for wmtsa_isscalar.
  • wmtsa_isvector(x, type)
    wmtsa_isvector -- Determine if item is a vector.
  • wmtsa_isvector_tcase
    modwt_case -- munit test case for wmtsa_isvector.
  • wmtsa_norminv(p)
    wmtsa_norminv -- Wrapper function for norm2inv.
  • wmtsa_qmf(a, inverse)
    wmtsa_qmf -- Calculate quadrature mirror filter (QMF).
  • wmtsa_tsensemble
  • wtfilter(wtfname, transform)
    wtfilter -- Define wavelet transform filter coefficients.
  • wtfilter_tcase
    wtfilter_tcase -- munit test case to test wtfilter.
  • wtfilter_tsuite
    wtfilter_tsuite -- munit test suite to test wtfilter and inverse transforms.
  • wvar_var_fd_sdf_acvs(meth...
    wvar_var_fd_sdf_acvs -- Calculate variance of wavelet variance for a FD process for given wavelet transform filter.
  • yn(x, return_format)
    yn -- Determine Boolean value.
  • yn_tcase
    modwt_case -- munit test case for yn.
  • omodwt.m
  • figure328.m
    figure328 - Display selected portion of vertical shear measurements and
  • figure330.m
    figure330 - Compare 'octave band' PSD (SDF) estimates for vertical
  • figure329.m
    figure329 - Calculate and plot wavelet variances for vertical shear series
  • figure334.m
  • table333.m
    table333 - Compute equivalent degrees of freedom and number of
  • MUnit.m
  • GenerateToyData.m
    Ben Ruddell - UIUC - Noisy Data Generator - 19JAN2007
  • startup.m
    startup.m - Startup file for WMTSA package
  • figure331.m
    figure331 - Display leakage of Haar wavelet variance
  • figure195.m
    figure195 - Calculate and plot MODWT expanded view of MRA of ocean shear to replicate Figure 195 of WMTSA.
  • figure194.m
    figure194 - Calculate and plot MODWT MRA of ocean shear to replicate Figure 194 of WMTSA.
  • figure190.m
    figure190 - Calculate and plot rotated cumulative variance of subtidal sea level variations to replicate Figure 190 of WMTSA.
  • figure187.m
    figure187 - Calculate and plot expanded view of MODWT MRA for Crescent City subtidal variations to replicate Figure 187 of WMTSA.
  • figure186.m
    figure186 - Calculate and plot MODWT MRA for Crescent City subtidal variations to replicate Figure 186 of WMTSA.
  • config_runscript_Toy.m
    Setup file to run the ProcessNetwork software, and a couple plotting
  • config_runscript_ChaosWit...
    Setup file to run the ProcessNetwork software, and a couple plotting
  • config_runscript_Bondville.m
    Setup file to run the ProcessNetwork software, and a couple plotting
  • ChaosDataWithResolutions.m
  • canonical_type_graph.m
  • figure184.m
    figure184 - Calculate and plot MODWT MRA of ECG time series to replicate Figure 184 of WMTSA.
  • figure183.m
    figure183 - Calculate and plot MODWT coefficients of ECG time series to replicate Figure 183 of WMTSA.
  • figure126.m
    figure126 - Calculate and plot partial DWT coefficients W of level J0 = 6 for
  • figure099.m
    figure099 - Calculate and plot squared gain functiosn of DWT LA(8) filters.
  • figure098b.m
    figure098b - Calculate and plot equivalent LA(8) wavelet and scaling filters.
  • figure098a.m
    figure098a - Calculate and plot equivalent D(4) wavelet and scaling filters.
  • MUnit_Variables.m
  • MUnit_Templates.m
  • MUnit_Structures.m
  • modwtj.m
    modwtj -- Compute MODWT coefficients for jth level.
  • imodwtj.m
    imodwtj -- Compute inverse MODWT for jth level.
  • DWT_Structures.m
  • MUnit_Library.m
  • MUnit_Introduction.m
  • MUnit_Errors.m
  • MUnit_Applications.m
  • MUnit_API.m
  • View all files

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ProcessNetwork/Proc​essNetwork_Software

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29 Apr 2013 (Updated )

Functions for the delineation of Dynamical Process Networks using Information Theory

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Description

Attribution
The ProcessNetwork software was written between 2005 and 2008 at the University of Illinois at Urbana-Champaign, in the Department of Civil Engineering, funded 2006-2008 by a NASA fellowship #NNX06AF71H , and then continued development has occurred at Arizona State University, funded 2013-2015 by a grant from the NSF’s Macrosystems Biology program BIO-1241960. Dr. Benjamin L. Ruddell is the primary author of the software, but many collaborators have contributed to its ongoing development. The work is that of the author, and its accuracy and implications are not necessarily supported by the funding and employing organizations. Those using the software are requested to cite the software using the following three citations, and to communicate with the author regarding modifications, extensions, and applications of the software.

Current Citation for the software:

Ruddell, B.L., C. Sturtevant, M. Kang, and R. Yu (2008), ProcessNetwork Software, version 1.5, accessed at (INSERT URL OR SOURCE HERE) on (INSERT DATE HERE).

Citations for the methods employed in the software:

Ruddell, B. L.*, and P. Kumar (2009a), Ecohydrologic process networks: 1. Identification, Water Resour. Res., 45, W03419, doi:10.1029/2008WR007279.

Ruddell, B. L.*, and P. Kumar (2009b), Ecohydrologic process networks: 2. Analysis and characterization, Water Resour. Res., 45, W03420, doi:10.1029/2008WR007280.

Ruddell, B.L.*, N. Oberg, P. Kumar, and M. Garcia (2010), Using Information-Theoretic Statistics in MATLAB to Understand How Ecosystems Affect Regional Climates, MATLAB Digest Academic Edition, February 2010, www.mathworks.com/academia.

Sturtevant, C., et al. (2015), Identifying scale-emergent, non-linear, asynchronous processes of wetland methane exchange, Journal of Geophysical Research.

Acknowledgements:

Dr. Praveen Kumar, for advising and co-authorship of publications at the University of Illinois
Dr. Ricky Robertson, for important histogram algorithm advice at the University of Illinois
Numerous students and colleagues who provided help with MATLAB coding
Cove Sturtevant and Dennis Baldocchi of the University of California, Berkeley for redevelopment of the MATLAB code in Version 1.5 to improve the processing speed of individual functions and add a wavelet transformation module, IAAFT surrogate data generation, and plotting functions.
Minseok Kang and Rong Yu for contributions to code versions 1.2 through 1.4

Introduction

The purpose of this software is to delineate Dynamical Process Networks based on observations of information flow between discrete vector variables using information theory, including the Transfer Entropy statistic. The software also computes Shannon Entropy, Mutual Information, Relative Entropy, and many other information theoretic statistics. The software is valid for all kinds of data, but the typical application is to Dynamical information flow and Shannon Entropy, and the typical dataset a multivariate timeseries. The software is written for the MATLAB® scientific computing environment. This basic version of the software does not contain any GUI features and there are limited plotting scripts, but more of these features may be available separately. The basic version of the software contains a small set of preprocessing functions and filters, but others may also be useful.

Required Products MATLAB Distributed Computing Server
Parallel Computing Toolbox
Simulink
Simulink Verification and Validation
Statistics and Machine Learning Toolbox
MATLAB
DO Qualification Kit
MATLAB release MATLAB 8.4 (R2014b)
Other requirements Supports multiple-core and parallel toolbox calculation of the Matlab 2014b release, but this is not required.
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Updates
20 Oct 2015 1.1

Version 1.4 contains bug fixes and added features compared with the last release from April 2013, version 1.0.

21 Mar 2016 1.5

2 August 2015 Cove Sturtevant, Benjamin L. Ruddell [RELEASE VERSION 1.5]

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