Passing matrix to another function, storing element - matlab

Question

I am having a problem, I have a function popmesh1 that calculates a matrix P( , ). I then use sens_analysis to store a element of that matrix and continue. How do I output P( , ) so that it is kept track of? I keep getting that the matrix is size (0,0). Also, how do I pass the matrix into another function? Sorry to post whole code, I want to concrete and clear, I'm pretty new to MATLAB
function pdemeshpop(varargin)
global par;
global re;
global P;
global par_n;
global a1;
clc
clear
%INIITIALIZE MESH:- Can change time and age for refining of mesh
time=linspace(0,800,4000);
age=linspace(0,time(end),4000);
dt=time(2)-time(1);
dtao=dt;
P=zeros(length(time),9); % State matrix over time.
P1=zeros(length(time),length(age)); % Mesh for population of P1mod.
prodrev=zeros(length(time),length(age));
p1tot=zeros(length(time));
p2tot=zeros(length(time));
f=zeros(length(time));
A_1=zeros(length(time),1);
%Parameters
G=log(2)/30; %This growth rate had been set to nthroot(2,20), but I think it should be log(2)/20 for a doubling time of 20 mins. Units 1/min
R=.75; %Reduction in growth rate due to viral production, range from 0.5-0.75
global A_s; %Number of virus produced each minute from one cell? Units 1/min
A_s = 35; %Source for this?
global re;
re = varargin(1); %Reduction in efficiency of virus production in P1mod
c=1.5e9; %Concentration of cells in saturated culture. Units 1/cm^3 Source: http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=100984&ver=2
K=3e-11; %Adsorption rate. Units cm^3/min. Source: Tzagoloff, H., and D. Pratt. 1964. The initial steps in infection with coliphage M13. Virology 24:372?380.
i = 1; %Is flipping of switch induced or not induced? if i==1 then switch is induced.
if i==1
S_i=0.5; %S_i is probability that a switch will flip during a timestep in a p1ori cell. Units pure number (a probablility). Ranges from 0 to 1.
elseif i==0
S_i= 0.005;
end
%IC and BC implementation for the 9 dependent variables <<<10?
P0=zeros(9,1);
P0(1)=100; %Initial concentration of senders. Units: cells/ml.
P0(2)=10000; %Initial concentration of primary receivers. Units: cells/ml.
P0(3)=10000; %Initial concentration of secondary receivers. Units: cells/ml.
%The loop below covers the initial conditions and BC of t=0,all ages
for i=1:9
P(1,i)=P0(i);
end
%Iterative solution
for m=1:length(time)-1 % m is timestep
%Simplifications
p1tot(m)=P(m,2)+P(m,4)+P(m,6);
p2tot(m)=P(m,3)+P(m,5)+P(m,7);
f(m)=1-(P(m,1)+p1tot(m)+p2tot(m))/c;
%Senders
P(m+1,1)=dt*(P(m,1)*G*R*f(m))+P(m,1);
%Primary Receivers
P(m+1,2)=dt*((P(m,2)*G*f(m))-K*(P(m,8)+P(m,9))*P(m,2))+P(m,2);
%Secondary Receivers
P(m+1,3)=dt*((P(m,3)*G*f(m))-K*(P(m,8)+P(m,9))*P(m,3))+P(m,3);
%Primary Original
P(m+1,4)=dt*((P(m,4)*G*f(m))+K*P(m,8)*P(m,2)-S_i*P(m,4))+P(m,4);
%Secondary Original
P(m+1,5)=dt*((P(m,5)*G*f(m))+K*P(m,8)*P(m,3))+P(m,5);
for n=1:m
t=(m-1)*dt; %Why not t=m*dt?
tao=(n-1)*(dtao);%Determines current age basket
prodrev(m,n)=rate(t-tao); %Calculates corresponding rate of production of phage (reversed)
%Primary Modified
if n==1
P1(m+1,n)=dt*(K*P(m,2)*P(m,9)+S_i*P(m,4)); %Left hand side boundary (New cells at age zero)
else
P1(m+1,n)=dt*(-((P1(m,n)-P1(m,n-1))/dtao)+P1(m,n)*G*R*f(m))+P1(m,n);
end
end
P(m+1,6)=sum(P1(m+1,:)); %phi1mod
%Secondary Modified
P(m+1,7)=dt*((P(m,7)*G*f(m))+K*P(m,9)*P(m,3))+P(m,7);
%Original
P(m+1,8)=dt*(A_s*P(m,1))+P(m,8);
if m<2
A_1(m)=0;
else
convolution(m,:)=prodrev(m,:).*P1(m,:);
%A_1(m)=dtao*trapz(conv(prod1(m,:), P1(m,:)));
A_1(m)=dtao*trapz([convolution(m,:) 0]);
%A_1 obtained by convolving the discrete vectors of P1 and prod1
%then finding the area under the curve
end
%Modified
P(m+1,9)=dt*A_1(m)+P(m,9);
end
P1;
end
function prod=rate(tao)
%Function generates production rate values of the infected cells based on their age
global A_s;
global re;
a=re*A_s; %Max production rate
ageofcell=tao;
if ageofcell<=10
prod=0;
elseif ageofcell<=50
prod=(a/40)*(ageofcell-10);
else
prod=a;
end
end
and my other code that calls the above function, and that I want to pass P(time(length),7) to:
function sens_analysis
global par;
global re;
global par_n;
global P;
time=linspace(0,800,4000);
pdemeshpop_final_re_sens;
re_0 = re;
par = re;
s_nom_ss = a1;
delta = 0.05;
par_n = par*(1+delta);
pdemeshpop_final_re_sens_par(par_n); % similar to pdemeshpop_final_re_sens
s_pert_ss = P(length(time),7);
abs_sens = (s_pert_ss - s_nom_ss)/(delta*re_0);
rel_sens = abs_sens*(re_value/s_nom_ss);
end
Again, sorry to post whole code, felt it was a necessary evil. The global variables might also be unnecessary. Could be something obvious. I might need to store P first somehow. Can someone please explain this carefully? Thank you!

Answer 1

At the beginning of function pdemeshpop you have a clear statement which is erasing from your workspace the variables declared by the global statements. Comment out that clear statement and you'll circumvent that problem.

Answer 2

The first thing I noticed in your code is that you use global variables. In general this is not recommended if it can be avoided. Consider giving them as input to your functions instead, either separately or in a struct.
Of course the clear is removing your variables, but in general if you want to see what is happening, try placing some breakpoints in your code. That allows you to inspect all existing variables. With f10 you can then step through the code and see how everything goes on.
Furthermore, I would always recommend you to use dbstop if error, this way you can efficiently deal with the errors that you will encounter.