How do you add demographic stochasticity to a stage structure population model?
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Hi, I have a 3x3 transition matrix and need to incorporate demographic stochasticity. I tried using binornd(n,p)/n to get a random proportion of stage 1 individuals transitioning each year, but it doesn't appear to be working. It doesn't look like the plot is calling this every year.
Thanks in adance
if true
% code
end
% The demographic parameters
m33 = .98 ;
P21_g = 0.908 ; P21_b = 0.908 ; P21 = 0.908 ;
P22_g = 0.944*0.75 ; P22_b = 0.944*0.75 ; P22 = 0.944*0.75 ;
P32_g = 0.944*0.25 ; P32_b = 0.944*0.25 ; P32 = 0.944*0.25 ;
P33_g = 0.97 ; P33_b = 0.97*m33 ; P33 = 0.97 ;
F3 = 0.5*P33*0.044 ; % 0.5 probability of calf being female * survivability of mature * survivability of mother * fecundity (0.044, from pace)
n1 = 16 ; n2 = 30 ; n3 = 140 ; % the initial condition
N0 = [n1 n2 n3]' ; % note that N0 is written as a column vector to allow matrix calculations
% The three projection matrices i am considering for environmental
% stochasticity (A_g = good year, no mortality event; A_b = bad year,
% mortality event)
A_g = [0 0 F3 ;
binornd(16, P21_g)/16 P22_g 0 ;
0 P32_g P33_g] ;
A_b = [0 0 F3 ;
binornd(16, P21_b)/16 P22_b 0 ;
0 P32_b P33_b] ;
A = [0 0 F3 ;
binornd(16, P21)/16 P22 0 ;
0 P32 P33] ;
% ===== Plotting the population time series and population growth rates for 40 years
% ===== assuming a stable (deterministic) and average environment
N_ts = zeros(3, 21) ; % a matrix that will contain the number of individuals in each age class (columns) over time (rows)
N_ts_total = zeros(1, 21) ; % a vector that will contain the total population size as a function of timee
lambda = zeros(1, 21) ; % a vector that will contain the annual population growth rates as a function of time
N_ts(:, 1) = N0 ; % the initial condition is written into the first column of N_ts
N_ts_total(1, 1) = sum(N0) ; % the initial total population size is the sum of the initial abundances in all age classes
% Project the population 40 years into the future using matrix projections
for i = 2 : 21
N_ts(:, i) = A * N_ts(:, i-1) ; % update the population vector by one year
N_ts_total(1, i) = sum(N_ts(:, i)) ; % sum all individuals in the four age classes in a year to get total pop size
lambda(1, i) = N_ts_total(1, i) / N_ts_total(1, i-1) ; % annual pop growth rate is the the population size in one year, divided by the size in previous year
end
% time series - stage class
figure(1)
plot(0 : 20, N_ts)
hold on
legend ('calves','imm. females','mat. females')
xlabel('\it_t')
ylabel('abundance')
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