Man pages for syrona
Stratified Prevalence Comparison Across OMOP CDM Datasets
| add_pr_columns | Add prevalence ratio columns (log2 + natural + inference) to... |
| AGE_CLAMP_MAX | Age decade clamping: all ages >= this value merge into a... |
| apply_cohort_filter | Apply OHDSI cohort filtering to CDM table references. |
| apply_k_anonymity | Apply k-anonymity suppression to all extracted source tables. |
| ATC_CHAPTER_VOCAB | ATC vocabulary constants for chapter lookup. |
| build_forest_detail | Build a per-year forest plot for a single concept |
| build_forest_overview | Build an overview forest plot paired with the heatmap |
| build_forest_summary | Build a compact F/M/Both forest plot for a single concept |
| build_heatmap | Build an interactive heatmap of prevalence ratios |
| build_meta_row | Build a one-row tibble from run_meta output + aggregated... |
| build_point_diff | Build a dumbbell chart showing absolute prevalence values |
| build_pr_distribution | Build a PR distribution histogram from meta_summary data |
| build_pr_distribution_chapters | Build a faceted PR distribution - one small histogram per... |
| build_pyramid | Build an interactive population pyramid |
| CHAPTER_ROOTS | Anchor concept_ids for condition chapter assignment. |
| cohort_summary | Get summary statistics for a cohort. |
| compare_all | Run the full comparison pipeline for two datasets across... |
| compare_domain | Run the full comparison pipeline for one domain. |
| compare_meta_agegroups | Meta-analysis across years: one row per concept_id x sex x... |
| compare_meta_by_sex | Meta-analysis across age groups: one row per concept_id x... |
| compare_meta_summary | Meta-analysis across sexes: one row per concept_id (sex =... |
| compare_yearly | Compare two datasets at the per-year stratum level. |
| CONDITION_RELATIONSHIPS | SNOMED relationship types to extract as condition attributes. |
| create_caresite_cohort | Create an OHDSI cohort from a care site. |
| create_cohort_table | Create an OHDSI-standard cohort table. |
| delete_cohort | Delete a cohort from the cohort table. |
| dot-build_caresite_sql | Build the SELECT SQL for care-site cohort generation. |
| DRUG_RELATIONSHIPS | Drug attribute relationships (empty - RxNorm relationships... |
| extract_all | Run the full source data extraction pipeline. |
| extract_condition_attributes | Extract condition SNOMED attributes. |
| extract_condition_chapters | Extract condition chapter and sub-chapter assignments. |
| extract_condition_info | Extract condition concept metadata. |
| extract_condition_prevalence | Extract condition prevalence (ACHILLES-404 numerator + 116... |
| extract_death_counts | Extract death counts by year x sex x age group (ACHILLES-504... |
| extract_demographics | Extract demographics (birth year x sex). |
| extract_denominators | Extract the ACHILLES-116 denominator: persons observed per... |
| extract_drug_chapters | Extract drug chapter assignments (ATC 1st level). |
| extract_drug_info | Extract drug (ingredient) concept metadata. |
| extract_drug_prevalence | Extract drug prevalence at the Ingredient level. |
| extract_procedure_attributes | Extract procedure SNOMED attributes. |
| extract_procedure_chapters | Extract procedure chapter and sub-chapter assignments. |
| extract_procedure_info | Extract procedure concept metadata. |
| extract_procedure_prevalence | Extract procedure prevalence. |
| format_fold | Format a log2 prevalence ratio as a fold difference string |
| format_pval | Format p-values in Nature style |
| GENDER_LABELS | Gender concept_id to label mapping. |
| insert_cohort | Insert a cohort from a local data frame. |
| K_ANONYMITY | k-anonymity threshold. Any stratum cell with fewer patients... |
| list_care_sites | List care sites with patient counts. |
| list_comparisons | List available comparisons. |
| list_datasets | List all available datasets. |
| load_comparison | Load a previously saved comparison from CSV. |
| load_dataset | Load a previously saved dataset from CSV. |
| load_syrona_theme | Load all Syrona design tokens into the calling environment |
| PROCEDURE_CHAPTER_ROOTS | Anchor concept_ids for procedure chapter assignment. |
| PROCEDURE_RELATIONSHIPS | SNOMED relationship types to extract as procedure attributes. |
| run_app | Run the Syrona dashboard |
| run_meta | Run meta-analysis on a vector of log2 prevalence ratios. |
| save_comparison | Save comparison tables to CSV. |
| save_dataset | Save extracted tables to CSV. |
| SOURCES_DIR | Base directory for extracted source data. |
| suppress_domain | Apply k-anonymity suppression to a single domain's tables. |
| syrona_connect | Connect to a DuckDB OMOP CDM. |
| syrona_connect_pg | Connect to a PostgreSQL OMOP CDM. |
| syrona_disconnect | Disconnect from an OMOP CDM database. |
| syrona-package | syrona: Stratified prevalence comparison across OMOP CDM... |
| truncate_name | Truncate a concept name to a maximum number of characters |
| weight_color | Map population weight (%) to a hex color on a log-scale... |
