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NottinghamPhageLogLikelihoodGrowth.m
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function [likely, timeOut] = ...
NottinghamPhageLogLikelihoodGrowth(theta, ...
fixedVals, simTimes, obsData, dataNoise, simMode, compMode, fitAll)
% Calculate the log likelihood of getting the observed data from theta.
%
% Run the simulation with the candidate theta and determine how likely it
% is that the observed data could have arisen if these where the true
% parameters, given the differences between the observed and simulated data
% and the expected noise of the system.
%
% function likely = NottinghamPhageLogLikelihoodGrowth(theta, ...
% fixedVals, simTimes, obsData, sigmaData, simMode)
%
% logLikely - The log likelihood of getting these data if these were
% the true parameters.
%
% theta - Parameters for the simulation
% fixedVals - Values that are not varied
% simTimes - Time points for which we have observed data
% obsData - The observed data
% sigmaData - How noisy do we believe the data to be?
% simMode - Which version of the model to use
% compMode - How should simulated and observed data be compared?
% fitAll - Should all data sets be fitted? If False do not fit the 2
% predator data set
% Version Author Date Affiliation
% 1.00 J K Summers 02/05/17 Kreft Lab - School of Biosciences -
% University of Birmingham
%
[initVals, thetaODE] = NottinghamPhageSetup(theta, fixedVals, simMode);
% E. coli only simulation
if simMode == 1
% full model
initSpecies(1:5) = initVals(1:5); % Substrate & prey species
initSpecies(6:9) = zeros(4, 1); % predators
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PIIVIIODE, simTimes, ...
initSpecies, thetaODE);
if ~timeOut
% Total of all bacterial prey species
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4) + predVals(:, 5);
end
elseif simMode == 2
% simplified model
initSpecies(1:3) = initVals(1:3); % Substrate & prey bacteria
initSpecies(4:7) = zeros(4, 1); % Predators
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PreyPropPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total prey species
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
end
elseif simMode == 3
% mixed model
% Substrate & prey
initSpecies(1:3) = initVals(1:3);
% Predators
initSpecies(4:7) = zeros(4, 1);
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
end
elseif simMode == 4
% Simplified model, but with Bdellovibrio phenotypic persistence
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:8) = zeros(4, 1); % Predators
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVII, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + predVals(:, 4);
end
elseif (simMode == 5 || simMode == 7)
% Simplified model, but with ability to develop Bdellovibrio phenotypic
% persistence
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:8) = zeros(4, 1); % Predators
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + predVals(:, 4);
end
elseif simMode == 6
% As mode 5, but Bdellovibrio now has a Holling type I functional
% response
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:8) = zeros(4, 1); % Predators
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PreyPropIGPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + predVals(:, 4);
end
else
% Simplified model, but with ability to develop Bdellovibrio phenotypic
% persistence
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:8) = zeros(4, 1); % Predators
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + predVals(:, 4);
end
end
if ~timeOut
oData = obsData(:, 1); % Prey bacteria
% Remove NaNs
compVals(isnan(oData)) = [];
compVals(compVals < 1) = 1;
oData(isnan(oData)) = [];
likely = compareData(compVals, oData, dataNoise, compMode);
%(-0.5 / (sigmaData^2)) * sum((compVals - oData).^2);
end
if ~timeOut
% E. coli and Bdellovibrio simulation
if simMode == 1
initSpecies(1:6) = initVals(1:6); % Substrate, Prey & Bdellovibrio
initSpecies(7:9) = zeros(3, 1); %Bdelloplasts, phage, infectedcells
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
%Total prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4) + predVals(:, 5);
% Bdellovibrio + bdelloplasts
compVals(:, 2) = predVals(:, 6) + predVals(:, 7);
end
elseif simMode == 2
initSpecies(1:4) = initVals(1:4); % Substrate, Prey & Bdellovibrio
initSpecies(5:7) = zeros(3, 1); %Bdelloplasts, phage, infectedcells
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PreyPropPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
% Bdellovbirio + bdelloplast
compVals(:, 2) = predVals(:, 4) + predVals(:, 5);
end
elseif simMode == 3
initSpecies(1:4) = initVals(1:4);
initSpecies(5:7) = zeros(3, 1);
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
compVals(:, 2) = predVals(:, 4) + predVals(:, 5);
end
elseif simMode == 4
initSpecies(1:5) = initVals(1:5); % Substrate, prey & Bdellovibrio
initSpecies(6:8) = zeros(3, 1); % Bdelloplast, phage, infected cell
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVII, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
end
elseif (simMode == 5 || simMode == 7)
initSpecies(1:5) = initVals(1:5); % Substrate, prey & Bdellovibrio
initSpecies(6:8) = zeros(3, 1); % Bdelloplast, phage, infected cell
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
end
elseif simMode == 6
initSpecies(1:5) = initVals(1:5); % Substrate, prey & Bdellovibrio
initSpecies(6:8) = zeros(3, 1); % Bdelloplast, phage, infected cell
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PreyPropIGPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
end
else
initSpecies(1:5) = initVals(1:5); % Substrate, prey & Bdellovibrio
initSpecies(6:8) = zeros(3, 1); % Bdelloplast, phage, infected cell
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
end
end
end
if ~timeOut
% Prey bacteria
sData = compVals(:, 1);
oData = obsData(:, 2);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
% Bdellovibrio
sData = compVals(:, 2);
oData = obsData(:, 3);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
end
if ~timeOut
% E. coli and halophage simulation
if simMode == 1
initSpecies(1:5) = initVals(1:5);
initSpecies(6) = 0;
initSpecies(7) = initVals(7);
initSpecies(8:9) = zeros(2, 1);
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4) + predVals(:, 5);
compVals(:, 2) = predVals(:, 8) + predVals(:, 9);
end
elseif simMode == 2
initSpecies(1:3) = initVals(1:3);
initSpecies(4) = 0;
initSpecies(5) = initVals(5);
initSpecies(6:7) = zeros(2, 1);
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PreyPropPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
compVals(:, 2) = predVals(:, 6) + predVals(:, 7);
end
elseif simMode == 3
initSpecies(1:3) = initVals(1:3);
initSpecies(4:5) = zeros(2, 1);
initSpecies(6:7) = initVals(6:7);
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
compVals(:, 2) = predVals(:, 6) + predVals(:, 7);
end
elseif simMode == 4
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:6) = zeros(2, 1); % Bdellovibrio & Bdelloplast
initSpecies(7:8) = initVals(7:8); % Bacteriophage & Infected cells
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVII, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% All prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Phage + infected cells
compVals(:, 2) = predVals(:, 7) + predVals(:, 8);
end
elseif (simMode == 5 || simMode == 7)
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:6) = zeros(2, 1); % Bdellovibrio & Bdelloplast
initSpecies(7:8) = initVals(7:8); % Bacteriophage & Infected cells
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% All prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Phage + infected cells
compVals(:, 2) = predVals(:, 7) + predVals(:, 8);
end
elseif simMode == 6
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:6) = zeros(2, 1); % Bdellovibrio & Bdelloplast
initSpecies(7:8) = initVals(7:8); % Bacteriophage & Infected cells
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PreyPropIGPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% All prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Phage + infected cells
compVals(:, 2) = predVals(:, 7) + predVals(:, 8);
end
else
initSpecies(1:4) = initVals(1:4); % Substrate & prey
initSpecies(5:6) = zeros(2, 1); % Bdellovibrio & Bdelloplast
initSpecies(7:8) = initVals(7:8); % Bacteriophage & Infected cells
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% All prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Phage + infected cells
compVals(:, 2) = predVals(:, 7) + predVals(:, 8);
end
end
end
if ~timeOut
% Prey bacteria
sData = compVals(:, 1);
oData = obsData(:, 4);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
% Bacteriophage & infected cells
sData = compVals(:, 2);
oData = obsData(:, 5);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
end
if fitAll && ~timeOut
% E. coli, Bdellovibrio and Halophage simulation
if simMode == 1;
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4) + predVals(:, 5);
compVals(:, 2) = predVals(:, 6) + predVals(:, 7);
compVals(:, 3) = predVals(:, 8) + predVals(:, 9);
end
elseif simMode == 2
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PreyPropPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
compVals(:, 2) = predVals(:, 4) + predVals(:, 5);
compVals(:, 3) = predVals(:, 6) + predVals(:, 7);
end
elseif simMode == 3
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN2PIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
compVals(:, 1) = predVals(:, 2) + predVals(:, 3);
compVals(:, 2) = predVals(:, 4) + predVals(:, 5);
compVals(:, 3) = predVals(:, 6) + predVals(:, 7);
end
elseif simMode == 4
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVII, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
% Phages & infected cells
compVals(:, 3) = predVals(:, 7) + predVals(:, 8);
end
elseif (simMode == 5 || simMode == 7)
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
% Phages & infected cells
compVals(:, 3) = predVals(:, 7) + predVals(:, 8);
end
elseif simMode == 6
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3PreyPropIGPIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
% Phages & infected cells
compVals(:, 3) = predVals(:, 7) + predVals(:, 8);
end
else
[~, predVals, timeOut] = ...
NottinghamPhageSim(@NottinghamPhageN3IGPIIVIODE, ...
simTimes, initSpecies, thetaODE);
if ~timeOut
% Total of all prey bacteria
compVals(:, 1) = predVals(:, 2) + predVals(:, 3) + ...
predVals(:, 4);
% Bdellovibrio & bdelloplasts
compVals(:, 2) = predVals(:, 5) + predVals(:, 6);
% Phages & infected cells
compVals(:, 3) = predVals(:, 7) + predVals(:, 8);
end
end
if ~timeOut
% Prey bacteria
sData = compVals(:, 1);
oData = obsData(:, 6);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
% Bdellovibrio & Bdelloplasts
sData = compVals(:, 2);
oData = obsData(:, 7);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
% Phages & infected cells
sData = compVals(:, 3);
oData = obsData(:, 8);
sData(isnan(oData)) = [];
sData(sData < 1) = 1;
oData(isnan(oData)) = [];
likely = likely + compareData(sData, oData, dataNoise, compMode);
end
end
if ~timeOut
likely = sum(likely);
else
likely = 0;
end
end