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Fixed the issue happened when user specifies the RHAS model for mixture finder #20

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merged 1 commit into from
Apr 16, 2025
Merged

Fixed the issue happened when user specifies the RHAS model for mixture finder #20

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13 changes: 9 additions & 4 deletions main/phylotesting.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1486,9 +1486,9 @@ void runModelFinder(Params &params, IQTree &iqtree, ModelCheckpoint &model_info,
iqtree.aln->model_name = best_model.getName();
best_subst_name = best_model.subst_name;
best_rate_name = best_model.rate_name;
bool mix_finder_mode = (params.model_name == "MIX+MF" || params.model_name == "MIX+MFP" || params.model_name == "MF+MIX" || params.model_name == "MFP+MIX");
if (mix_finder_mode)
best_rate_name = best_model.orig_rate_name;
string best_orig_rate_name = best_model.orig_rate_name;
if (under_mix_finder)
CKP_SAVE(best_orig_rate_name); // for mixture finder
// Checkpoint *checkpoint = &model_info;
string best_model_AIC, best_model_AICc, best_model_BIC;
CKP_RESTORE(best_model_AIC);
Expand Down Expand Up @@ -6451,7 +6451,7 @@ CandidateModel runModelSelection(Params &params, IQTree &iqtree, ModelCheckpoint

iqtree.aln->model_name = best_model.getName();
best_subst_name = best_model.subst_name;
best_rate_name = best_model.orig_rate_name; // because the original rate name may include the input parameters
best_rate_name = best_model.rate_name;

Checkpoint *checkpoint = &model_info;
string best_model_AIC, best_model_AICc, best_model_BIC;
Expand Down Expand Up @@ -6539,6 +6539,7 @@ void optimiseQMixModel_method_update(Params &params, IQTree* &iqtree, ModelCheck
params.model_name = "";
bool under_mix_finder = true;
runModelFinder(params, *iqtree, model_info, best_subst_name, best_rate_name, nest_network, under_mix_finder);
string best_orig_rate_name = model_info["best_orig_rate_name"];

// (cancel) Step 2: do tree search for this single-class model
// runTreeReconstruction(params, iqtree);
Expand Down Expand Up @@ -6568,6 +6569,8 @@ void optimiseQMixModel_method_update(Params &params, IQTree* &iqtree, ModelCheck
do_init_tree = false;
model_str = best_subst_name;
do {
if (params.optimize_from_given_params == false)
best_rate_name = best_orig_rate_name;
best_model = runModelSelection(params, *iqtree, model_info, action, do_init_tree, model_str, best_subst_name, best_rate_name, nest_network);
cout << endl << "Model: " << best_subst_name << best_rate_name << "; df: " << best_model.df << "; loglike: " << best_model.logl << "; " << criteria_str << " score: " << best_model.getScore() << ";";
if (params.opt_qmix_criteria == 1) {
Expand Down Expand Up @@ -6601,6 +6604,8 @@ void optimiseQMixModel_method_update(Params &params, IQTree* &iqtree, ModelCheck
model_info.put("best_model_BIC", best_model_pre_BIC);

best_subst_name = model_str;
if (params.optimize_from_given_params == false)
best_rate_name = best_orig_rate_name;
int n_class = getClassNum(model_str);
if (params.opt_rhas_again) {
if (n_class == 1) {
Expand Down