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INPUT_persons_datapartners_concepts INPUT_persons_datapartners_concepts.sql LDA_arrayify_input LDA_arrayify_input.sql INPUT_persons_datapartners_concepts->LDA_arrayify_input OUTPUT_topic_descriptions OUTPUT_topic_descriptions.sql INPUT_persons_datapartners_concepts->OUTPUT_topic_descriptions coherences_w_stats coherences_w_stats.py INPUT_persons_datapartners_concepts->coherences_w_stats person_all_facts person_all_facts.sql person_all_facts->INPUT_persons_datapartners_concepts dev_filter_patients_for_2x2 dev_filter_patients_for_2x2.sql person_all_facts->dev_filter_patients_for_2x2 epoch_topic_stat_features epoch_topic_stat_features.sql person_all_facts->epoch_topic_stat_features all_person_facts_epoch_analysis all_person_facts_epoch_analysis.sql person_all_facts->all_person_facts_epoch_analysis days_plot_epoch_stats days_plot_epoch_stats.R person_all_facts->days_plot_epoch_stats index_dates_vs_age index_dates_vs_age.R person_all_facts->index_dates_vs_age index_dates_vs_bmi index_dates_vs_bmi.R person_all_facts->index_dates_vs_bmi pre_post_conditions pre_post_conditions.R person_all_facts->pre_post_conditions condition_era_full_clean condition_era_full_clean.sql condition_era_full_clean->INPUT_persons_datapartners_concepts condition_era_with_epochs condition_era_with_epochs.py condition_era_full_clean->condition_era_with_epochs full_condition_history_stats full_condition_history_stats.sql condition_era_full_clean->full_condition_history_stats median_condition_history median_condition_history.sql condition_era_full_clean->median_condition_history gen_vocabulary gen_vocabulary.py LDA_arrayify_input->gen_vocabulary vectorize_concepts vectorize_concepts.py LDA_arrayify_input->vectorize_concepts OUTPUT_person_topic_assignment OUTPUT_person_topic_assignment.sql topic_weight_totals topic_weight_totals.sql OUTPUT_person_topic_assignment->topic_weight_totals person_topics_arrayify_long person_topics_arrayify_long.sql person_topics_arrayify_long->OUTPUT_person_topic_assignment topic_names topic_names.sql person_topics_arrayify_long->topic_names topic_names->OUTPUT_person_topic_assignment topic_description_decoded_unzipped topic_description_decoded_unzipped.sql topic_names->topic_description_decoded_unzipped topic_names_w_stats topic_names_w_stats.R topic_names->topic_names_w_stats OUTPUT_person_topic_assignment_epochs OUTPUT_person_topic_assignment_epochs.sql topic_names->OUTPUT_person_topic_assignment_epochs OUTPUT_topic_descriptions->coherences_w_stats renamed_OUTPUT_topic_descriptions renamed_OUTPUT_topic_descriptions.sql OUTPUT_topic_descriptions->renamed_OUTPUT_topic_descriptions topic_correlations topic_correlations.R OUTPUT_topic_descriptions->topic_correlations top_terms top_terms.sql OUTPUT_topic_descriptions->top_terms fishers_results_top_topics fishers_results_top_topics.sql OUTPUT_topic_descriptions->fishers_results_top_topics concept_lda_pin concept_lda_pin.sql concept_lda_pin->OUTPUT_topic_descriptions exclude_concepts exclude_concepts.sql concept_lda_pin->exclude_concepts covid_tests covid_tests.sql concept_lda_pin->covid_tests positive_words positive_words.sql concept_lda_pin->positive_words topic_description_decoded_unzipped->OUTPUT_topic_descriptions coherence_by_dp_topic coherence_by_dp_topic.sql masked_coherence_by_dp_topic masked_coherence_by_dp_topic.py coherence_by_dp_topic->masked_coherence_by_dp_topic coherences_w_stats->coherence_by_dp_topic coherence_by_topic coherence_by_topic.sql coherences_w_stats->coherence_by_topic coherence_by_topic->topic_names_w_stats topic_coherence_histogram topic_coherence_histogram.R coherence_by_topic->topic_coherence_histogram person_topic_assignment person_topic_assignment.py person_topic_assignment->person_topics_arrayify_long top_1000_terms_per_topic top_1000_terms_per_topic.sql renamed_OUTPUT_topic_descriptions->top_1000_terms_per_topic topic_names_w_stats->renamed_OUTPUT_topic_descriptions topic_clouds_1 topic_clouds_1.R top_1000_terms_per_topic->topic_clouds_1 topic_clouds_2 topic_clouds_2.R top_1000_terms_per_topic->topic_clouds_2 topic_clouds_3 topic_clouds_3.R top_1000_terms_per_topic->topic_clouds_3 topic_clouds_4 topic_clouds_4.R top_1000_terms_per_topic->topic_clouds_4 topic_clouds_5 topic_clouds_5.R top_1000_terms_per_topic->topic_clouds_5 topic_clouds_6 topic_clouds_6.R top_1000_terms_per_topic->topic_clouds_6 topic_clouds_7 topic_clouds_7.R top_1000_terms_per_topic->topic_clouds_7 topic_clouds_8 topic_clouds_8.R top_1000_terms_per_topic->topic_clouds_8 topic_description_decoded_zipped topic_description_decoded_zipped.sql topic_description_decoded_zipped->topic_description_decoded_unzipped topic_description_decoded topic_description_decoded.py topic_description_decoded->topic_description_decoded_zipped topic_weight_totals_nodps topic_weight_totals_nodps.py topic_weight_totals->topic_weight_totals_nodps jensen_shannon jensen_shannon.R topic_weight_totals->jensen_shannon gen_vocabulary->topic_description_decoded gen_vocabulary->vectorize_concepts vectorize_concepts_epochs vectorize_concepts_epochs.py gen_vocabulary->vectorize_concepts_epochs lda_model lda_model.py lda_model->person_topic_assignment topic_description_raw topic_description_raw.py lda_model->topic_description_raw person_topic_assignment_epochs person_topic_assignment_epochs.py lda_model->person_topic_assignment_epochs vectorize_concepts->person_topic_assignment vectorize_concepts->lda_model masked_data_partner_cdms masked_data_partner_cdms.py topic_data_partner_usage_nodps topic_data_partner_usage_nodps.R masked_data_partner_cdms->topic_data_partner_usage_nodps manifest_lda_pin manifest_lda_pin.sql manifest_lda_pin->masked_data_partner_cdms last_reasonable_date last_reasonable_date.sql manifest_lda_pin->last_reasonable_date masked_topic_weight_totals_nodps masked_topic_weight_totals_nodps.py masked_topic_weight_totals_nodps->topic_data_partner_usage_nodps topic_weight_totals_nodps->masked_topic_weight_totals_nodps datapartner_topic_usage_entropy datapartner_topic_usage_entropy.R topic_weight_totals_nodps->datapartner_topic_usage_entropy topic_description_raw->topic_description_decoded datapartner_topic_usage_entropy->topic_names_w_stats topic_correlations->jensen_shannon concept_pre_post_patients concept_pre_post_patients.sql better_fisher_tests better_fisher_tests.R concept_pre_post_patients->better_fisher_tests dev_filter_patients_for_2x2->concept_pre_post_patients condition_era_with_epochs->concept_pre_post_patients epoch_stats_long epoch_stats_long.sql condition_era_with_epochs->epoch_stats_long condition_era_with_epochs_epoch_analysis condition_era_with_epochs_epoch_analysis.sql condition_era_with_epochs->condition_era_with_epochs_epoch_analysis top_terms->concept_pre_post_patients OUTPUT_person_topic_assignment_epochs->dev_filter_patients_for_2x2 OUTPUT_person_topic_assignment_epochs->epoch_topic_stat_features filtered_dps filtered_dps.sql filtered_dps->dev_filter_patients_for_2x2 filtered_dps->epoch_topic_stat_features epoch_stats_long->dev_filter_patients_for_2x2 epoch_stats_long->epoch_topic_stat_features epoch_stats_wide epoch_stats_wide.sql epoch_stats_long->epoch_stats_wide group_topic_stats group_topic_stats.sql epoch_topic_stat_features->group_topic_stats model_tests_covid_gapplyCollect model_tests_covid_gapplyCollect.R epoch_topic_stat_features->model_tests_covid_gapplyCollect condition_era_lda_pin condition_era_lda_pin.sql condition_era_lda_pin->condition_era_full_clean condition_era_lda_pin->filtered_dps fishers_results_cleaned fishers_results_cleaned.R fishers_results_top_topics->fishers_results_cleaned better_fisher_tests->fishers_results_top_topics analysis_r_code analysis_r_code.R analysis_r_code->model_tests_covid_gapplyCollect coherence_results_correlation coherence_results_correlation.R model_tests_covid_pvals model_tests_covid_pvals.R model_tests_covid_pvals->coherence_results_correlation covid_plot_1 covid_plot_1.R model_tests_covid_pvals->covid_plot_1 figure_4_plots figure_4_plots.R model_tests_covid_pvals->figure_4_plots figure_5_plots figure_5_plots.R model_tests_covid_pvals->figure_5_plots overall_plot_1 overall_plot_1.R model_tests_covid_pvals->overall_plot_1 pasc_plot_1 pasc_plot_1.R model_tests_covid_pvals->pasc_plot_1 volcano_plot volcano_plot.R fishers_results_cleaned->volcano_plot model_tests_covid_gapplyCollect->model_tests_covid_pvals LDA_arrayify_input_epochs LDA_arrayify_input_epochs.sql LDA_arrayify_input_epochs->vectorize_concepts_epochs prep_epoch_model_input prep_epoch_model_input.sql prep_epoch_model_input->LDA_arrayify_input_epochs person_topics_arrayify_long_epochs person_topics_arrayify_long_epochs.sql person_topics_arrayify_long_epochs->OUTPUT_person_topic_assignment_epochs all_person_facts_epoch_analysis->OUTPUT_person_topic_assignment_epochs all_person_facts_epoch_analysis->condition_era_with_epochs_epoch_analysis condition_era_with_epochs_epoch_analysis->prep_epoch_model_input person_topics_arrayify_epochs person_topics_arrayify_epochs.py person_topics_arrayify_epochs->person_topics_arrayify_long_epochs person_topic_assignment_epochs->person_topics_arrayify_epochs vectorize_concepts_epochs->person_topic_assignment_epochs cohort_and_idx2 cohort_and_idx2.sql index_dates index_dates.sql cohort_and_idx2->index_dates u07_ip_ed u07_ip_ed.sql u07_ip_ed->cohort_and_idx2 person_union person_union.sql u07_ip_ed->person_union u07_any u07_any.sql u07_any->cohort_and_idx2 u07_any->person_union lab_pos lab_pos.sql lab_pos->cohort_and_idx2 lab_pos->person_union mis_c mis_c.sql mis_c->cohort_and_idx2 mis_c->person_union u099 u099.sql u099->cohort_and_idx2 u099->person_union person_union->cohort_and_idx2 exclude_concepts->condition_era_full_clean covid_tests->lab_pos concept_set_members_lda_pin concept_set_members_lda_pin.sql concept_set_members_lda_pin->exclude_concepts concept_set_members_lda_pin->covid_tests ed_concepts ed_concepts.sql concept_set_members_lda_pin->ed_concepts first_longcovid_clinic_visit first_longcovid_clinic_visit.sql concept_set_members_lda_pin->first_longcovid_clinic_visit first_positive_antibody_test first_positive_antibody_test.sql concept_set_members_lda_pin->first_positive_antibody_test concept_set_members_lda_pin->positive_words ed_concepts->u07_ip_ed epoch_stats_wide->person_all_facts first_b94_etc first_b94_etc.sql first_b94_etc->index_dates condition_occurrence_lda_pin condition_occurrence_lda_pin.sql condition_occurrence_lda_pin->u07_ip_ed condition_occurrence_lda_pin->u07_any condition_occurrence_lda_pin->mis_c condition_occurrence_lda_pin->u099 condition_occurrence_lda_pin->first_b94_etc first_longcovid_clinic_visit->index_dates codeset_ids codeset_ids codeset_ids->first_longcovid_clinic_visit codeset_ids->first_positive_antibody_test observation_lda_pin observation_lda_pin.sql observation_lda_pin->first_longcovid_clinic_visit first_positive_antibody_test->index_dates measurement_lda_pin measurement_lda_pin.sql measurement_lda_pin->lab_pos measurement_lda_pin->first_positive_antibody_test full_condition_history_stats->person_all_facts index_dates_fix_yr10k index_dates_fix_yr10k.py index_dates->index_dates_fix_yr10k last_reasonable_date->index_dates person_table_sets person_table_sets.sql person_table_sets->person_all_facts person_table_sets->index_dates person_table_sets->last_reasonable_date longest_observation_periods longest_observation_periods.sql longest_observation_periods->index_dates positive_words->lab_pos observation_period_lda_pin observation_period_lda_pin.sql observation_period_lda_pin->longest_observation_periods person_cohorts person_cohorts.sql person_cohorts->person_all_facts Charleson_scores_long_covid Charleson_scores_long_covid Charleson_scores_long_covid->person_all_facts Ll_all_patients_fact_table Ll_all_patients_fact_table Ll_all_patients_fact_table->person_all_facts person_cohort_epoch_definitions person_cohort_epoch_definitions.py person_cohort_epoch_definitions->person_cohorts person_epochs person_epochs.sql person_cohort_epoch_definitions->person_epochs person_epochs->condition_era_with_epochs person_lda_pin person_lda_pin.sql person_lda_pin->person_table_sets conditions_to_microvisits_lda_pin conditions_to_microvisits_lda_pin.sql conditions_to_microvisits_lda_pin->u07_ip_ed microvisit_to_macrovisit_lds_lda_pin microvisit_to_macrovisit_lds_lda_pin.sql microvisit_to_macrovisit_lds_lda_pin->u07_ip_ed index_dates_fix_yr10k->person_cohort_epoch_definitions charleson_scores_long_covid charleson_scores_long_covid.sql Fact_table_charlson_comorbidity_patient Fact_table_charlson_comorbidity_patient Fact_table_charlson_comorbidity_patient->charleson_scores_long_covid keep_sites keep_sites.sql keep_sites->manifest_lda_pin keep_sites->condition_era_lda_pin keep_sites->condition_occurrence_lda_pin keep_sites->observation_lda_pin keep_sites->measurement_lda_pin keep_sites->observation_period_lda_pin keep_sites->person_lda_pin keep_sites->conditions_to_microvisits_lda_pin keep_sites->microvisit_to_macrovisit_lds_lda_pin keep_sites->charleson_scores_long_covid ll_all_patients_fact_table ll_all_patients_fact_table.sql keep_sites->ll_all_patients_fact_table concept concept concept->concept_lda_pin concept_set_members concept_set_members concept_set_members->concept_set_members_lda_pin condition_era condition_era condition_era->condition_era_lda_pin condition_occurrence condition_occurrence condition_occurrence->condition_occurrence_lda_pin conditions_to_microvisits conditions_to_microvisits conditions_to_microvisits->conditions_to_microvisits_lda_pin Release_Version_Person Release_Version_Person Release_Version_Person->keep_sites all_patients_summary_facts_table_LDS all_patients_summary_facts_table_LDS all_patients_summary_facts_table_LDS->ll_all_patients_fact_table manifest manifest manifest->manifest_lda_pin measurement measurement measurement->measurement_lda_pin microvisit_to_macrovisit_lds microvisit_to_macrovisit_lds microvisit_to_macrovisit_lds->microvisit_to_macrovisit_lds_lda_pin observation observation observation->observation_lda_pin observation_period observation_period observation_period->observation_period_lda_pin person person person->person_lda_pin