get_synth_mlpcr_data.m_bak

% function [X, Y, ll, bb_to_X, bb, w] = get_synth_mlpcr_data(n,X_dims,w_df,latent_df,nsrY,nsrX,...)
%
% Generates a sample of Y outcomes that depend on X in some latent 
% subspace of X in a hierarchical manner, with hierarchy specified by user 
% supplied group labels.
%
% Input ::
%
%   n           - Number of observations to sample
%
%   lvls        - Number of levels
%
%   grps        - cell array of length lvls, each element is a vector
%                   mapping from elements to group affiliation. First level
%                   should have a unit vector.
%
%   X_dims      - Number of IV. Ignored if 'cov' w also specified.
%
%   w_df        - cell array, length "lvls". Each element specifies number 
%                   of degrees of freedom of your covariance matrix for the
%                   corresponding levels. This defines the number of 
%                   non-noise dimensions in X. 
%                   If supplying custom covariance matrix you may not know
%                   w_df (e.g. if you use an empirical covariance mat). In
%                   that case this becomes a hyperparameter analagous to
%                   the dimensionality hyperparameter in PCR.
%
%   latent_df   - cell array, length "lvls". Number of latent IVs on 
%                  which Y depends from each level
%
%   nsrY        - noise to signal ratio for DV measurements. Noise is
%                   evenly distributed across levels of measurement (e.g. 
%                   with 2 levels, 50% is fixed effects (FE) error, 50% is 
%                   RE error; with 3 levels 33% is FE error, 33% is RE 
%                   error 1 at the 1st level and 33% is RE error at the 2nd
%                   level; etc). We use nsr instead of snr so we can
%                   specify noiseless instances without numerical problems.
%
%   nsrX        - signal to noise ratio for IV measurements.
%
%   covPat      - cell array of length "lvls" - 1 where each element 
%                   specifies a covariance pattern for random effects. 
%                   Options are 'isotropic','diagonal', and 'full'. Custom
%                   random effects covariance pattern specification not
%                   available at this time.
%
% Optional Input ::
%
%   'cov'       - followed by a cell array with user supplied covariance 
%                   matrices of length "lvls". X_dim argument is ignored 
%                   if user supplies covariance matrix.
%                   w_df should be an estimate of the user supplied
%                   matrices df. If in doubt overshoot with w_df.
%
% Output ::
%
%   Y           - observed DVs with normally distributed additive noise.
%
%   X           - n x X_dims multivariate normal matrix of observed IVs 
%                   with w_df degrees of freedom.
%
%   ll          - cell array of length lvls with latent dimensions in X
%
%   ll_to_Y     - true fixed effect regression coefficients mapping ll to Y
%
%   X_to_Y      - true coefficients mapping X to Y
%
%   w           - cell array of length "lvls" containing true covariance 
%                 matrices with latent_df degrees of freedom that were used
%                 to generate the multivariate normal X. If user supplied
%                 covariance matrices, this will just be a copy
%                 of what the user supplied.
%
%   wRE         - lvls-1 cell array of random effects covariances. One
%                   element per random effect level.
%

function [X, Y, ll, X_to_Y, ll_to_Y, w, wRE] = get_synth_mlpcr_data(n,lvls,grps,X_dims,w_df,latent_df,nsrY,nsrX,covPat,varargin)
    %% parse input arguments
    % get covariance matrix for X
    w = cell(lvls,1);
    for i = 1:lvls
        w_chol = randn(X_dims,w_df{i});
        w{i} = w_chol*w_chol';
    end
    for i = 1:length(varargin)
        if ischar(varargin{i})
            switch varargin{i}
                case 'cov'
                    w = varargin{i+1};
                    X_dims = size(w,1);
                otherwise
                    error(['Did not understand ', varargin{i}]);
            end
        end
    end
    
    %% sanity checks
    lvlVars = {grps,w_df,latent_df,w};
    lvlVarNames = {'grps','w_df','latent_df','w'};
    for i = 1:length(lvlVars)
        this_var = lvlVars{i};
        if length(this_var) ~= lvls
            error([ int2str(i) ' lvls specified but only ' int2str(length(this_var)) ' ' lvlVarNames{i}, ' provided']);
        end
    end
    
    if length(covPat) ~= lvls - 1
        error(['covPat has ' int2str(length(covPat)) ' elements, but ' int2str(lvls - 1) ' are needed.']);
    end
    
    if X_dims <= max(cell2mat(w_df))
        error('X_dim must be >= max(w_df) (covariance matrix df).');
    end
    if X_dims <= max(cell2mat(latent_df))
        error('X_dim must be >= max(latent_df) defining X ~ Y relationship.');
    end
    for i = 1:lvls
        if w_df{i} < latent_df{i}
            error(['w_df{' int2str(i) '} (covariance matrix df) must be >= latent_df{' int2str(i) '} defining X ~ Y relationship.']);
        end
    end
    if max(cell2mat(w_df)) > n
        error('max(w_df) (covariance matrix df) must be < n. If you fewer n are desired, simply select a subset post-hoc.');
    end
    
    %% sample noise free instances
    
    % meaningful dimensions are some random subset of non-noise dimensions of X;
    ll_to_Y = cell(lvls,1);
    ll = cell(lvls,1);
    pc = cell(lvls,1);
    yy = 0;
    X_to_Y = zeros(n,1); % initialize to n x 1, will transform to X_dims x 1 later
    xx_tot = zeros(n,X_dims);
    for i = 1:lvls
        ll_to_Y{i} = zeros(min([X_dims,n]) - 1,1);
        ll_to_Y{i}(randperm(w_df{i},latent_df{i})) = rand(latent_df{i},1) - 0.5;
    
        xx{i} = mvnrnd(zeros(X_dims,1),w{i},n);
        xx_tot = xx_tot + xx{i};
        
        [pc{i},ll{i}] = pca(xx{i},'NumComponents',min([X_dims,n])-1);
        yy = yy + ll{i}*ll_to_Y{i};
        
        X_to_Y = X_to_Y + xx{i}*pinv(pc{i})'*ll_to_Y{i};
    end
    X_to_Y = pinv(xx_tot)*X_to_Y; % this is where we transform to X_dims x 1

    %% add noise
    e = sqrt(nsrY/lvls*var(yy))*randn(n,1);
    Y = yy + e; 
    for i = 2:lvls % iteratively add random effects noise
        this_grp = grps{i};
        uniq_grp_elem = unique(this_grp);
        n_units = length(uniq_grp_elem);
        n_re_betas = length(ll_to_Y{i});
        
        % generate random effects covariance
        wRE = cell(lvls,1);
        
        switch covPat{i - 1}
            case 'full'
                wRE_chol = 1/n_re_betas*randn(n_re_betas);

                % this tmp_wRE will generate random normal unit 
                % vectors
                tmp_wRE = wRE_chol*wRE_chol'; 
                
                % RE IVs have their own amplitude: var(ll{i})
                % note that covariance matrix can be factored as diag(s)*C*diag(s) 
                %   where s are standard eviation of each dimension and C is the
                %   correlation matrix between dimensions. We take advantage of
                %   this implicitly here to normalize by IV amplitudes.
                tmp_wRE = diag(1./std(ll{i}))*tmp_wRE*diag(1./std(ll{i}));
            case 'diagonal'
                tmp_wRE = eye(n_re_betas);
                tmp_wRE(tmp_wRE == 1) = randn(n_re_betas,1).^2;
                
                % this tmp_wRE will generate random normal unit 
                % vectors
                tmp_wRE = 1/sum(diag(tmp_wRE))*tmp_wRE;
                
                % RE IVs have their own amplitude: var(ll{i})
                % note that covariance matrix can be factored as diag(s)*C*diag(s) 
                %   where s are standard eviation of each dimension and C is the
                %   correlation matrix between dimensions. We take advantage of
                %   this implicitly here to normalize by IV amplitudes.
                tmp_wRE = diag(1./std(ll{i}))*tmp_wRE*diag(1./std(ll{i}));
            case 'isotropic'
                tmp_wRE = eye(n_re_betas);
                tmp_wRE(wRE{i} == 1) = randn.^2;
                
                % this will generate unit normal vectors
                tmp_wRE = 1/sum(diag(tmp_wRE))*tmp_wRE;
                
                % normalize for IV amplitudes
                tmp_wRE = 1/mean(var(ll{i}))*tmp_wRE;
            otherwise
                error(['Did not understand covPat{' int2str(i - 1) '}: ' covPat{i} '. Options are full, diagonal or isotropic']);
        end
        
        % signal amplitude is var(yy)
        % fraction of noise allocated to RE: 1/lvls
        wRE{i} = var(yy) * (nsrY/lvls) * tmp_wRE;
        
        % construct each RE block for each instance in grp{i}
        re_blk = cell(n_units,1);
        ii = 0;
        jj = 0;
        for j = 1:n_units
            this_grp_elem = this_grp(uniq_grp_elem(j) == this_grp);
            nn = length(this_grp_elem);
            these_re = mvnrnd(zeros(1,n_re_betas),wRE{i},1)'; % draw random effects with specified covariance structure
            re_blk{j} = repmat(these_re,1,nn);
            ii = ii + size(re_blk{j},1);
            jj = jj + size(re_blk{j},2);
        end
        if jj ~= n
            error(['Something strange is happening with random effects block generation for lvl ' int2str(i)]);
        end
        
        % plug each re_blk into diagonal of re mat
        sparsityLim = 0.1;
        nz = n*n_re_betas;
        sparsity = nz/(ii * jj);
        if sparsity < sparsityLim
            re = spalloc(ii,jj,nz); % preallocate sparse matrix
        else
            re = zeros(ii,jj);
        end
        last_ii = 0;
        last_jj = 0;
        for j = 1:n_units
            if sparsity < sparsityLim
                this_blk = sparse(re_blk{j});
            else
                this_blk = re_blk{j};
            end
            [this_ii, this_jj] = size(this_blk);
            ii_range = (last_ii + 1):(last_ii + this_ii);
            jj_range = (last_jj + 1):(last_jj + this_jj);
            re(ii_range,jj_range) = re_blk{j};
            last_ii = last_ii + this_ii;
            last_jj = last_jj + this_jj;
        end
        
        %add random effects to Y
        if sparsity < sparsityLim
            Y = Y + full(diag(repmat(ll{i},1,n_units)*re));
        else
            Y = Y + diag(repmat(ll{i},1,n_units)*re);
        end
        % the fact that I take the diagonal here means I'm probably messing
        % up my formalism up higher. There should be some matrices Z and u
        % such that Z*u = re, but instead I ended up with some zz and uu
        % such that diag(zz*uu) = re. The repmat() invocation is also 
        % strange. Z shouldn't need replicates like that. Worth revisiting
        % later.
    end
    
    % the true variance is likely a weighted average of diag(w{i})'s, but
    % solving it requires some math. Instead let's approximate it
    % empirically. Note: it might just be sum(diag(w{i}));
    X = zeros(n,X_dims);
    for i = 1:lvls
        X = X + xx{i};
    end
    X = X + repmat(var(X)*nsrX,n,1).*randn(size(X)); % add measurement noise (e.g. physiological noise)
end