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summary_stats_birth_death.m
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% This code runs, collates, and saves the data from the lattice simulations N_runs times.
function summary_stats(fName, s_pos, s_del, mu, N_muts_necessary, bx_size, weights_matrix, total_weight_sum, weights_matrix_bx, total_weight_sum_bx)
N_runs = 200; % Change this for more or less runs
mut_probs_tested = mu;
tEnd= 600; % Stop saving data at time = 600.
time_step = 1;
times_vec = time_step:time_step:tEnd ;
N_times = length(times_vec);
shannon_indices_runs = cell(N_runs,length(mut_probs_tested));
simpson_indices_runs = cell(N_runs,length(mut_probs_tested));
moranI_time_series_runs = cell(N_runs,length(mut_probs_tested));
gearyC_time_series_runs = cell(N_runs,length(mut_probs_tested));
fpi0_vals = cell(N_runs,length(mut_probs_tested));
fpi_vals = cell(N_runs,length(mut_probs_tested));
fpi2_vals = cell(N_runs,length(mut_probs_tested));
fpi3_vals = cell(N_runs,length(mut_probs_tested));
mpi_pos_vals = cell(N_runs,length(mut_probs_tested));
mpi_tot_vals = cell(N_runs,length(mut_probs_tested));
lattice_erpos_runs = cell(N_runs,length(mut_probs_tested));
lattice_ki67_runs = cell(N_runs,length(mut_probs_tested));
time_of_cancer_occurrence_measure1_runs = cell(N_runs,length(mut_probs_tested));
time_of_cancer_occurrence_measure2_runs = cell(N_runs,length(mut_probs_tested));
biopsy_types_of_mutants_runs = cell(N_runs,length(mut_probs_tested));
biopsy_shannon_indices_runs = cell(N_runs,length(mut_probs_tested));
biopsy_simpson_indices_runs = cell(N_runs,length(mut_probs_tested));
biopsy_moranI_runs = cell(N_runs,length(mut_probs_tested));
biopsy_gearyC_runs = cell(N_runs,length(mut_probs_tested));
fpi0_bx_vals = cell(N_runs,length(mut_probs_tested));
fpi_bx_vals = cell(N_runs,length(mut_probs_tested));
fpi2_bx_vals = cell(N_runs,length(mut_probs_tested));
fpi3_bx_vals = cell(N_runs,length(mut_probs_tested));
mpi_pos_bx_vals = cell(N_runs,length(mut_probs_tested));
mpi_tot_bx_vals = cell(N_runs,length(mut_probs_tested));
biopsy_erpos_runs = cell(N_runs,length(mut_probs_tested));
biopsy_ki67_runs = cell(N_runs,length(mut_probs_tested));
scraping_types_of_mutants_runs = cell(N_runs,length(mut_probs_tested));
scraping_shannon_indices_runs= cell(N_runs,length(mut_probs_tested));
scraping_simpson_indices_runs = cell(N_runs,length(mut_probs_tested));
scraping_erpos_runs = cell(N_runs,length(mut_probs_tested));
scraping_ki67_runs = cell(N_runs,length(mut_probs_tested));
types_of_mutants_time_series_runs = cell(N_runs,length(mut_probs_tested));
for j=1:length(mut_probs_tested)
parfor i=1:N_runs % Parallel loop
i % Just to keep track
[shannon_indices, simpson_indices, moranI_time_series, gearyC_time_series, fpi0, fpi, fpi2, fpi3,mpi_pos,mpi_tot, lattice_erpos_time_series, lattice_ki67_time_series,...
biopsy_shannon_indices, biopsy_simpson_indices, biopsy_moranI_series, biopsy_gearyC_series, fpi0_bx, fpi_bx, fpi2_bx, fpi3_bx,mpi_pos_bx,mpi_tot_bx, biopsy_erpos_time_series, biopsy_ki67_time_series,...
scraping_shannon_indices, scraping_simpson_indices, scraping_erpos_time_series, scraping_ki67_time_series,...
time_of_cancer_occurrence_measure1, time_of_cancer_occurrence_measure2, types_of_mutants_time_series, biopsy_types_of_mutants, scraping_types_of_mutants]=...
new_model2d_birth_death(N_muts_necessary,s_pos, s_del,mut_probs_tested(j), bx_size, times_vec,weights_matrix,total_weight_sum,weights_matrix_bx,total_weight_sum_bx);
shannon_indices_runs{i,j} = shannon_indices;
simpson_indices_runs{i,j} = simpson_indices;
moranI_time_series_runs{i,j} = moranI_time_series;
gearyC_time_series_runs{i,j} = gearyC_time_series;
fpi0_vals{i,j} = fpi0;
fpi_vals{i,j} = fpi;
fpi2_vals{i,j} = fpi2;
fpi3_vals{i,j} = fpi3;
mpi_pos_vals{i,j} = mpi_pos;
mpi_tot_vals{i,j} = mpi_tot;
lattice_erpos_runs{i,j} = lattice_erpos_time_series;
lattice_ki67_runs{i,j} = lattice_ki67_time_series;
time_of_cancer_occurrence_measure1_runs{i,j} = time_of_cancer_occurrence_measure1;
time_of_cancer_occurrence_measure2_runs{i,j} = time_of_cancer_occurrence_measure2;
biopsy_types_of_mutants_runs{i,j} = biopsy_types_of_mutants;
biopsy_shannon_indices_runs{i,j} = biopsy_shannon_indices;
biopsy_simpson_indices_runs{i,j} = biopsy_simpson_indices;
biopsy_moranI_runs{i,j} = biopsy_moranI_series;
biopsy_gearyC_runs{i,j} = biopsy_gearyC_series;
fpi0_bx_vals{i,j} = fpi0_bx;
fpi_bx_vals{i,j} = fpi_bx;
fpi2_bx_vals{i,j} = fpi2_bx;
fpi3_bx_vals{i,j} = fpi3_bx;
mpi_pos_bx_vals{i,j} = mpi_pos_bx;
mpi_tot_bx_vals{i,j} = mpi_tot_bx;
biopsy_erpos_runs{i,j} = biopsy_erpos_time_series;
biopsy_ki67_runs{i,j} = biopsy_ki67_time_series;
scraping_types_of_mutants_runs{i,j} = scraping_types_of_mutants;
scraping_shannon_indices_runs{i,j}= scraping_shannon_indices;
scraping_simpson_indices_runs{i,j} = scraping_simpson_indices;
scraping_erpos_runs{i,j} = scraping_erpos_time_series;
scraping_ki67_runs{i,j} = scraping_ki67_time_series;
types_of_mutants_time_series_runs{i,j} = types_of_mutants_time_series;
end
end
save(fName, 'shannon_indices_runs','simpson_indices_runs','moranI_time_series_runs','gearyC_time_series_runs','fpi0_vals','fpi_vals','fpi2_vals','fpi3_vals','mpi_pos_vals','mpi_tot_vals',...
'lattice_erpos_runs','lattice_ki67_runs','time_of_cancer_occurrence_measure1_runs','time_of_cancer_occurrence_measure2_runs',...
'biopsy_shannon_indices_runs','biopsy_simpson_indices_runs','biopsy_moranI_runs','biopsy_gearyC_runs','fpi0_bx_vals','fpi_bx_vals','fpi2_bx_vals','fpi3_bx_vals','mpi_pos_bx_vals','mpi_tot_bx_vals',...
'biopsy_erpos_runs','biopsy_ki67_runs','scraping_shannon_indices_runs','scraping_simpson_indices_runs','scraping_erpos_runs','scraping_ki67_runs','types_of_mutants_time_series_runs','biopsy_types_of_mutants_runs','scraping_types_of_mutants_runs');
end