marshmat.m

function marshmat
datatitle='Marsh Creek Spring/Summer Chinook';
code = 'MarshCr';

p = .4815; 
s1 = .018; 
s2 = .044; so = .8; b3 = 0; b4 = .216; b5 = 1; m = 2747;
themat = [ 0 0 0 0  p*s1*m; 
   	 s2 0 0 0 0 ; 
   	 0 so*(1-b3) 0 0 0 ; 
   	 0 0 so*(1-b4) 0 0 ;
    0 so*b3 so*b4 so*b5 0 ];
    
stochplace = [ 0 0 0 0 1; 2 0 0 0 0; 0 3 0 0 0; 0 0 4 0 0; 0 3 4 5 0]; %this sez where to put what evar params
    
[tmpa tmpb] = eig(themat);
stableagestruc = tmpa(:,1)/sum(tmpa(:,1));
%pulse
pulseagestruc=stableagestruc;
pulseagestruc(1)=0;
 
evarstream=[.13 .08];
evarocean=[.05 .05 .05]; %level of environmental variance; log(normal(0,evar))
ecorr=.8; %correlation between the evars when the survivorships are chosen from a multivariate normal; applies to evar 3+

 %weight based on age of return
 %weight=cumsum(fliplr([0  0 0  .284 .716]));
 %weight based on % that become spawners
 weight=[0.0238 0.5396 0.6746 0.8 1];

obsstage = 5; %what stage is observed; in this case spawners
mrt=sum((2:6).*[0 0 0 .0061/.0238 .0177/.0238]);
save marshmat datatitle code themat stochplace stableagestruc pulseagestruc evarstream evarocean ecorr weight obsstage mrt;