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William Jones
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Tidied up comments and licenses.
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‎DATA_COVID_JHU.m

+1-5
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% Karl Friston
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% $Id: DATA_COVID_JHU.m 8001 2020-11-03 19:05:40Z karl $
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% get data
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% TODO: Implement websave in Octave. For now, files have been predownloaded.
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% IF you need to reaquire these files, you'll need to strip all commas and
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% quotes from fields for compatibility with octaves import functions
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# SPDX-License-Identifier: GPL-2.0
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%--------------------------------------------------------------------------
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% defaults
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%--------------------------------------------------------------------------

‎DEM_COVID.m

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% Karl Friston
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% $Id: DEM_COVID.m 7868 2020-06-02 16:39:02Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% F: -1.5701e+04 social distancing based upon P(infected)
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% F: -1.5969e+04 social distancing based upon P(symptomatic)
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% F: -1.5909e+04 social distancing based upon P(waiting)
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% F = 0; for i = 1:numel(DCM), F = F + DCM{1}.F; end, disp(F)
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% Flush octave outputs immediately
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if exist ('OCTAVE_VERSION', 'builtin');
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page_screen_output(0);

‎DEM_COVID_tests.m

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% 0: print nothing but end result
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% 1: output details of test results to console
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% 2: output logs of failed comparisons to text file
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%
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%__________________________________________________________________________
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# Copyright (C) 2021 Embecosm Limited
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# Contributor: William Jones <william.jones@embecosm.com>
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# SPDX-License-Identifier: GPL-2.0
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function DEM_COVID_tests(verbosity)
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if nargin < 1

‎README.md

+1-1

‎octave_importglobal.m

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% Function to import time series CSV files for COVID data. Should work well on
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% the following specific files:
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% Function to import time series CSV files for COVID data. Written for the
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% following specific files:
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% - 'time_series_covid19_confirmed_global.csv'
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% - 'time_series_covid19_deaths_global.csv'
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% from:
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% 'https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_time_series/'
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% and probably won't work well on anything else.
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%__________________________________________________________________________
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# Copyright (C) 2021 Embecosm Limited
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# Contributor: William Jones <william.jones@embecosm.com>
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# SPDX-License-Identifier: GPL-2.0
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function out = octave_importglobal(filename, delim)
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if (nargin < 2)
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delim = ',';

‎octave_importpop.m

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% Function to import time series CSV files for COVID data. Should work well on
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% the following specific files:
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% Function to import time series CSV files for COVID data. Written to import the
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% specific file
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% - 'population.csv'
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% and probably won't work well on much else
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%
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%__________________________________________________________________________
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# Copyright (C) 2021 Embecosm Limited
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# Contributor: William Jones <william.jones@embecosm.com>
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# SPDX-License-Identifier: GPL-2.0
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function out = octave_importpop(filename, delim)
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if (nargin < 2)

‎octave_websave.m

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% A simple websave function for Octave.
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%__________________________________________________________________________
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# Copyright (C) 2021 Embecosm Limited
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# Contributor: William Jones <william.jones@embecosm.com>
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# SPDX-License-Identifier: GPL-2.0
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function S = octave_websave(filename, url)
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txt = urlread(url);
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fid = fopen(filename,'w');

‎spm_COVID.m

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% Karl Friston
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% $Id: spm_COVID.m 7866 2020-05-30 09:57:38Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% Gaussian priors over model parameters
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%--------------------------------------------------------------------------

‎spm_COVID_B.m

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% Karl Friston
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% $Id: spm_COVID_B.m 7942 2020-09-10 22:00:08Z spm $
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# SPDX-License-Identifier: GPL-2.0
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% setup
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%==========================================================================
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‎spm_COVID_PV.m

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@@ -9,7 +9,7 @@ function spm_COVID_PV(DCM,i,T)
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% Karl Friston
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% $Id: spm_COVID_PV.m 7866 2020-05-30 09:57:38Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% use priors from parametric empirical Bayes
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%--------------------------------------------------------------------------
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pE = DCM{i}.M.pE;

‎spm_COVID_ci.m

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% Karl Friston
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% $Id: spm_COVID_ci.m 7871 2020-06-11 08:37:38Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% default: number of outcomes to evaluate
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%--------------------------------------------------------------------------
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if nargin < 4, U = 1:3; end

‎spm_COVID_gen.m

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% Karl Friston
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% $Id: spm_COVID_gen.m 7929 2020-08-16 13:43:49Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% The generative model:
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%==========================================================================

‎spm_COVID_plot.m

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% Karl Friston
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% $Id: spm_COVID_plot.m 7891 2020-07-07 16:34:13Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% Plot outcomes
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%==========================================================================
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% https://www.england.nhs.uk/statistics/statistical-work-areas/critical-care-capacity/

‎spm_COVID_priors.m

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% Karl Friston
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% $Id: spm_COVID_priors.m 7929 2020-08-16 13:43:49Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% sources and background
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%--------------------------------------------------------------------------
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% https://jamanetwork.com/journals/jama/fullarticle/2761044

‎spm_Ce.m

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% Karl Friston
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% $Id: spm_Ce.m 7203 2017-11-08 12:49:15Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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%-Defaults (and backward compatibility with spm_Ce(v,a) == spm_Ce('ar',v,a))
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%--------------------------------------------------------------------------

‎spm_Ncdf.m

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% Andrew Holmes
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% $Id: spm_Ncdf.m 7548 2019-03-20 10:08:49Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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%-Format arguments, note & check sizes
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%--------------------------------------------------------------------------

‎spm_axis.m

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# SPDX-License-Identifier: GPL-2.0
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function varargout = spm_axis(varargin)
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% AXIS Control axis scaling and appearance.
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‎spm_cat.m

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% Karl Friston
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% $Id: spm_cat.m 8045 2021-02-02 18:46:28Z karl $
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# SPDX-License-Identifier: GPL-2.0
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%error('spm_cat.c not compiled - see Makefile')
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‎spm_check_version.m

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% Darren Gitelman
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% $Id: spm_check_version.m 6156 2014-09-05 17:34:53Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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%-Detect software used
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%==========================================================================

‎spm_cross.m

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% Karl Friston
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% $Id: spm_cross.m 7838 2020-04-23 17:40:45Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% handle single inputs
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%--------------------------------------------------------------------------
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if nargin < 2

‎spm_dcm_bma.m

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% Will Penny
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% $Id: spm_dcm_bma.m 7679 2019-10-24 15:54:07Z spm $
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# SPDX-License-Identifier: GPL-2.0
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% defaults
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%--------------------------------------------------------------------------
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if nargin < 4 || isempty(Nsamp)

‎spm_dcm_bmr_all.m

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% Karl Friston, Peter Zeidman
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% $Id: spm_dcm_bmr_all.m 8045 2021-02-02 18:46:28Z karl $
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# SPDX-License-Identifier: GPL-2.0
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%-specification of null prior covariance
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%--------------------------------------------------------------------------

‎spm_dcm_bpa.m

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% Will Penny & Klaas Enno Stephan
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% $Id: spm_dcm_bpa.m 7866 2020-05-30 09:57:38Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% Preiminaries
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%--------------------------------------------------------------------------

‎spm_dcm_peb.m

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% Karl Friston
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% $Id: spm_dcm_peb.m 8024 2020-11-28 12:09:53Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% get filenames and set up
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%==========================================================================

‎spm_diag.m

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% Guillaume Flandin
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% $Id: spm_diag.m 7809 2020-03-31 11:55:09Z karl $
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# SPDX-License-Identifier: GPL-2.0
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try
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X = varargin{1};

‎spm_diff.m

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% Karl Friston
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% $Id: spm_diff.m 7977 2020-10-07 15:29:54Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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% step size for numerical derivatives
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%--------------------------------------------------------------------------

‎spm_dx.m

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% Karl Friston
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% $Id: spm_dx.m 7975 2020-10-06 14:46:56Z spm $
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# SPDX-License-Identifier: GPL-2.0
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% defaults
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%--------------------------------------------------------------------------
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nmax = 512; % threshold for numerical approximation

‎spm_en.m

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% Karl Friston
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% $Id: spm_en.m 3901 2010-05-27 16:14:36Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% detrend
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%--------------------------------------------------------------------------

‎spm_expm.m

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% Karl Friston
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% $Id: spm_expm.m 5691 2013-10-11 16:53:00Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% % standard [eigen]solution
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% %--------------------------------------------------------------------------
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% [V,D] = eig(full(J));

‎spm_fieldindices.m

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% Karl Friston
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% $Id: spm_fieldindices.m 7031 2017-02-27 19:46:48Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% if varargin is a vector simply return fieldnames
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%--------------------------------------------------------------------------

‎spm_figure.m

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% Andrew Holmes
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% $Id: spm_figure.m 7833 2020-04-17 10:43:06Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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%==========================================================================
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% - FORMAT specifications for embedded CallBack functions

‎spm_find_pC.m

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% Karl Friston
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% $Id: spm_find_pC.m 8024 2020-11-28 12:09:53Z karl $
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# SPDX-License-Identifier: GPL-2.0
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%-parse input arguments
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%--------------------------------------------------------------------------
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if nargin > 2

‎spm_funcheck.m

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% Karl Friston
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% $Id: spm_funcheck.m 6481 2015-06-16 17:01:47Z karl $
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# SPDX-License-Identifier: GPL-2.0
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%-Create function handle
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%==========================================================================

‎spm_hist_smooth.m

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% Karl Friston
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% $Id: spm_hist_smooth.m 8000 2020-11-03 19:04:17Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% remove negative values
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%--------------------------------------------------------------------------
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x = x(:);

‎spm_inv.m

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% Karl Friston
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% $Id: spm_inv.m 7143 2017-07-29 18:50:38Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% check A
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%--------------------------------------------------------------------------
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[m,n] = size(A);

‎spm_invNcdf.m

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% Andrew Holmes
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% $Id: spm_invNcdf.m 6859 2016-08-24 16:46:16Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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%-Format arguments, note & check sizes
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%--------------------------------------------------------------------------

‎spm_kron.m

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% Karl Friston
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% $Id: spm_kron.m 7814 2020-04-06 11:47:47Z guillaume $
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# SPDX-License-Identifier: GPL-2.0
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% Deal with cell arrays
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%--------------------------------------------------------------------------

‎spm_length.m

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% Karl Friston
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% $Id: spm_length.m 6233 2014-10-12 09:43:50Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% vectorise numerical arrays
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%--------------------------------------------------------------------------

‎spm_log_evidence.m

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% Karl Friston
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% $Id: spm_log_evidence.m 6856 2016-08-10 17:55:05Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% Compute reduced log-evidence
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%==========================================================================
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‎spm_log_evidence_reduce.m

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% Karl Friston
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% $Id: spm_log_evidence_reduce.m 6849 2016-07-31 12:34:33Z karl $
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# SPDX-License-Identifier: GPL-2.0
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% Compute reduced log-evidence
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%==========================================================================

‎spm_logdet.m

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% Karl Friston and Ged Ridgway
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% $Id: spm_logdet.m 7975 2020-10-06 14:46:56Z spm $
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# SPDX-License-Identifier: GPL-2.0
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% Note that whether sparse or full, rank deficient cases are handled in the
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% same way as in spm_logdet revision 4068, using svd on a full version of C

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