Error: Index in position 1 is invalid. Array indices must be positive integers or logical values?

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Ameer Fahmi
Ameer Fahmi on 18 Jul 2019
Commented: Walter Roberson on 19 Jul 2019
I'm trying to use the below described code of bayesian time-varying VAR. The complete package of the code can be found here.
I have issues in estimating the TVP-VAR model with more than one lag, my data has two variables with 268 observations and the optima lag is set at 6 as indicated by information criteria.
clear; clc;
load USdata1.csv;
Y0 = USdata1(1:3,:);
shortY = USdata1(4:end,:);
[T n] = size(shortY);
Y = reshape(shortY',T*n,1);
p = 6; % no. of lags
q = n^2*p+n; % dim of states
Tq = T*q; Tn = T*n; q2 = q^2; nnp1 = n*(n+1);
nloop = 11000; burnin = 1000;
%% initialize for storage
store_Omega11 = zeros(nloop-burnin,n,n);
store_Omega22 = zeros(nloop-burnin,q);
store_beta = zeros(nloop-burnin,Tq);
%% initialize the Markov chain
Omega11 = cov(USdata1);
Omega22 = .01*ones(q,1); % store only the diag elements
invOmega11 = Omega11\speye(n);
invOmega22 = 1./Omega22;
beta = zeros(Tq,1);
%% prior
nu01 = n+3; S01 = eye(n);
nu02 = 3; S02 = .005*ones(q,1);
Vbeta = 5*ones(q,1);
%% construct and compute a few thigns
X = zeros(T,n*p);
for i=1:p
X(:,(i-1)*n+1:i*n) = [Y0(3-i+1:end,:); shortY(1:T-i,:)];
end
bigG = SURform([ones(n*T,1) kron(X,ones(n,1))]);
H = speye(Tq,Tq) - sparse(q+1:Tq,1:(T-1)*q,ones(1,(T-1)*q),Tq,Tq);
newnu1 = nu01 + T;
newnu2 = nu02 + (T-1)/2;
disp('Starting MCMC.... ');
disp(' ' );
start_time = clock;
for loop = 1:nloop
%% sample beta
invS = sparse(1:Tq,1:Tq,[1./Vbeta; repmat(invOmega22,T-1,1)]');
K = H'*invS*H;
GinvOmega11 = bigG'*kron(speye(T),invOmega11);
GinvOmega11G = GinvOmega11*bigG;
invP = K + GinvOmega11G;
C = chol(invP); % so that C'*C = invP
betahat = C\(C'\(GinvOmega11*Y));
beta = betahat + C\randn(Tq,1); % C is upper triangular
%% sample Omega11
e1 = reshape(Y-bigG*beta,n,T);
newS1 = S01 + e1*e1';
invOmega11 = wishrnd(newS1\speye(n),newnu1);
Omega11 = invOmega11\speye(n);
%% sample Omega22
e2 = reshape(H*beta,q,T);
newS2 = S02 + sum(e2(:,2:end).^2,2)/2;
invOmega22 = gamrnd(newnu2,1./newS2);
Omega22 = 1./invOmega22;
if loop>burnin
i=loop-burnin;
store_beta(i,:) = beta';
store_Omega11(i,:,:) = Omega11;
store_Omega22(i,:) = Omega22';
end
if ( mod( loop, 2000 ) ==0 )
disp( [ num2str( loop ) ' loops... ' ] )
end
end
disp( ['MCMC takes ' num2str( etime( clock, start_time) ) ' seconds' ] );
disp(' ' );
%% compute posterior means
betahat = mean(store_beta)';
Omega11hat = squeeze(mean(store_Omega11));
Omega22hat = mean(store_Omega22);
tempbetahat = reshape(betahat,nnp1,T)';
gamhat1 = tempbetahat(:,1:n+1);
gamhat2 = tempbetahat(:,(n+1)+1:2*(n+1));
The code gives no error when one lag is used, but when more than 1 lag is used, an error occurs reffering to the matrix "X" in line 28. The matrix X is basically constructed to include all the lags, in case of 6 lags the X matrix should have 12 columns with non-zero values, but when I use 6 lags, the Matrix "X" is having columns with zero values which generates the following error
Index in position 1 is invalid. Array indices must be positive integers or logical values.
The extended X matrix is genertated with the lines below, thus something has to be done here to avoid the error
for i=1:p
X(:,(i-1)*n+1:i*n) = [Y0(3-i+1:end,:); shortY(1:T-i,:)];
end
But I don't know what should be done here, could anyone please help me with this issue?
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Answers (1)

Geoff Hayes
Geoff Hayes on 18 Jul 2019
Ameer - if the lag p is 6, then in this code
for i=1:p
X(:,(i-1)*n+1:i*n) = [Y0(3-i+1:end,:); shortY(1:T-i,:)];
end
when i is 4 (since iterating from 1 to 6), then
3 - i + 1 = 3 - 4 + 1 = 0
and so you are using an invalid index into Y0 and the error message makes sense. You need to adjust your code to handle this situation. Does Y0 need to be defined differently?
Y0 = USdata1(1:6,:);
And then adjust the 3 at
[Y0(3-i+1:end,:); shortY(1:T-i,:)];
?
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