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Fix Predict #457

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merged 2 commits into from
Oct 27, 2023
Merged

Fix Predict #457

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b00de4b
feat: include new arguments into out_of_sample.stan
NicholasCowie Oct 26, 2023
cc5f19b
bug: accommodating difficulties of netcdf
NicholasCowie Oct 26, 2023
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92 changes: 50 additions & 42 deletions maud/stan/out_of_sample_model.stan
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Original file line number Diff line number Diff line change
Expand Up @@ -65,12 +65,18 @@ data {
array[2, N_experiment_test] vector[N_drain] priors_drain_test;
// configuration
array[N_experiment_test] vector<lower=0>[N_mic - N_unbalanced] conc_init;
real rel_tol;
real abs_tol;
int max_num_steps;
real rel_tol_ode;
real abs_tol_ode;
int max_num_steps_ode;
real rel_tol_alg;
real abs_tol_alg;
int max_num_steps_alg;
real steady_state_threshold_abs;
real steady_state_threshold_rel;
real steady_state_penalty_rel;
int<lower=0, upper=1> likelihood; // set to 0 for priors-only mode
real drain_small_conc_corrector;
real<lower=0> timepoint;
int<lower=0, upper=1> penalize_non_steady;
}
transformed data {
real initial_time = 0;
Expand Down Expand Up @@ -100,19 +106,19 @@ generated quantities {
for (e in 1 : N_experiment_test) {
drain_test[e] = to_vector(normal_rng(priors_drain_test[1, e],
priors_drain_test[2, e]));
conc_pme_test[e] = to_vector(lognormal_rng(log(priors_conc_phos_test[1, e]),
conc_pme_test[e] = to_vector(lognormal_rng(priors_conc_phos_test[1, e],
priors_conc_phos_test[2, e]));
conc_unbalanced_test[e] = to_vector(lognormal_rng(log(priors_conc_unbalanced_test[1, e]),
conc_unbalanced_test[e] = to_vector(lognormal_rng(priors_conc_unbalanced_test[1, e],
priors_conc_unbalanced_test[2, e]));
conc_enzyme_test[e] = to_vector(lognormal_rng(log(priors_conc_enzyme_test[1, e]),
conc_enzyme_test[e] = to_vector(lognormal_rng(priors_conc_enzyme_test[1, e],
priors_conc_enzyme_test[2, e]));
}
// Simulation of experiments
for (e in 1 : N_experiment_test) {
flux_test[e] = rep_vector(0, N_reaction);
vector[N_enzyme] conc_enzyme_experiment = conc_enzyme_test[e];
vector[N_pme] conc_pme_experiment = conc_pme_test[e];
array[1] vector[N_mic - N_unbalanced] conc_balanced_experiment;
vector[N_mic - N_unbalanced] conc_balanced_experiment;
int N_eko_experiment = measure_ragged(enzyme_knockout_test_bounds, e);
int N_pko_experiment = measure_ragged(pme_knockout_test_bounds, e);
if (N_eko_experiment > 0) {
Expand All @@ -128,40 +134,42 @@ generated quantities {
e);
conc_pme_experiment[pko_experiment] = rep_vector(0, N_pko_experiment);
}
conc_balanced_experiment = ode_bdf_tol(dbalanced_dt,
conc_init[e, balanced_mic_ix],
initial_time, {timepoint},
rel_tol, abs_tol, max_num_steps,
conc_unbalanced_test[e],
balanced_mic_ix,
unbalanced_mic_ix,
conc_enzyme_experiment,
dgr_test[e], kcat, km, ki,
transfer_constant,
dissociation_constant, kcat_pme,
conc_pme_experiment,
drain_test[e],
temperature_test[e],
drain_small_conc_corrector, S,
subunits, edge_type,
edge_to_enzyme, edge_to_drain,
ci_mic_ix, sub_km_ix_by_edge_long,
sub_km_ix_by_edge_bounds,
prod_km_ix_by_edge_long,
prod_km_ix_by_edge_bounds,
sub_by_edge_long,
sub_by_edge_bounds,
prod_by_edge_long,
prod_by_edge_bounds, ci_ix_long,
ci_ix_bounds, allostery_ix_long,
allostery_ix_bounds,
allostery_type, allostery_mic,
edge_to_tc,
phosphorylation_ix_long,
phosphorylation_ix_bounds,
phosphorylation_type,
phosphorylation_pme);
conc_test[e, balanced_mic_ix] = conc_balanced_experiment[1];
conc_balanced_experiment = solve_newton_tol(maud_ae_system,
conc_init[e],
rel_tol_alg, abs_tol_alg,
max_num_steps_alg,
rel_tol_ode, abs_tol_ode,
max_num_steps_ode,
conc_unbalanced_test[e],
balanced_mic_ix,
unbalanced_mic_ix,
conc_enzyme_experiment,
dgr_test[e], kcat, km, ki,
transfer_constant,
dissociation_constant, kcat_pme,
conc_pme_experiment,
drain_test[e],
temperature_test[e],
drain_small_conc_corrector, S,
subunits, edge_type,
edge_to_enzyme, edge_to_drain,
ci_mic_ix, sub_km_ix_by_edge_long,
sub_km_ix_by_edge_bounds,
prod_km_ix_by_edge_long,
prod_km_ix_by_edge_bounds,
sub_by_edge_long,
sub_by_edge_bounds,
prod_by_edge_long,
prod_by_edge_bounds, ci_ix_long,
ci_ix_bounds, allostery_ix_long,
allostery_ix_bounds,
allostery_type, allostery_mic,
edge_to_tc,
phosphorylation_ix_long,
phosphorylation_ix_bounds,
phosphorylation_type,
phosphorylation_pme);
conc_test[e, balanced_mic_ix] = conc_balanced_experiment;
conc_test[e, unbalanced_mic_ix] = conc_unbalanced_test[e];
vector[N_edge] edge_flux = get_edge_flux(conc_test[e],
conc_enzyme_experiment,
Expand Down
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