# Result tables description ## Result of PheWAS analysis | Variable Name | Type | Description | | ----------------------- | ------- | ------------------------------------------------------------ | | `phecode` | String | Disease code (Phecode) used in PheWAS analysis | | `disease` | String | Disease name corresponding to the Phecode | | `system` | String | Phecode disease system corresponding to the Phecode (e.g., infectious diseases) | | `sex` | String | Sex-specificity of the disease (e.g., Both, Male, Female) | | `N_cases_exposed` | Integer | Number of individuals diagnosed with the disease in the exposed group | | `describe` | String | Descriptions of the model fitting state and removed covariates with reasons | | `exposed_group` | String | Incidence rate (unit: per 1,000 person-years) in the exposed group | | `unexposed_group` | String | Incidence rate (unit: per 1,000 person-years) in the unexposed group | | `phewas_coef` | Float | Estimated coefficient from the model | | `phewas_se` | Float | Standard error of the estimated coefficient | | `phewas_p` | Float | P-value indicating statistical significance of the coefficient | | `phewas_p_significance` | Boolean | Indicates whether the result is statistically significant based on adjusted p-value (True/False) | | `phewas_p_adjusted` | Float | Adjusted p-value accounting for multiple comparisons | ## Result of comorbidity strength estimation | Variable Name | Type | Description | | -------------------- | ------- | ------------------------------------------------------------ | | `phecode_d1` | Integer | Phecode for disease 1 in the disease pair | | `phecode_d2` | Integer | Phecode for disease 2 in the disease pair | | `name_disease_pair` | String | Name of the disease pair (format: "D1-D2") | | `N_exposed` | Integer | Total number of individuals in exposed group | | `n_total` | Integer | Number of exposed individuals included in the sub-cohort that meet the sex-specificity eligibility criteria for both diseases and after excluding those with history of either disease 1, disease 2, or related diseases | | `n_d1d2_diagnosis` | Integer | Number of individuals diagnosed with both diseases | | `n_d1_diagnosis` | Integer | Number of individuals diagnosed with disease 1 | | `n_d2_diagnosis` | Integer | Number of individuals diagnosed with disease 2 | | `n_d1d2_nontemporal` | Integer | Number of individuals diagnosed with both disease 1 and disease 2 but without defined temporal order (i.e., the time interval between the two diagnosis is smaller than or equal to `min_interval_days` or larger `max_interval_days`) | | `n_d1d2_temporal` | Integer | Number of individuals diagnosed with disease 1 followed by disease 2 in a defined temporal order (i.e., the time interval between the two diagnosis is larger than `min_interval_days` and smaller than or equal to`max_interval_days`) | | `n_d2d1_temporal` | Integer | Number of individuals diagnosed with disease 2 followed by disease 1 in a defined temporal order (i.e., the time interval between the two diagnosis is larger than `min_interval_days` and smaller than or equal to`max_interval_days`) | | `phi_coef` | Float | Phi coefficient (φ), Pearson’s correlations for two binary variables | | `phi_p` | Float | P-value for Phi coefficient significance | | `RR` | Float | Relative risk of observing both conditions in the same individual relative to expectation | | `RR_p` | Float | P-value for relative risk | | `phi_p_adjusted` | Float | Adjusted P-value for Phi coefficient (multiple comparisons) | | `RR_p_adjusted` | Float | Adjusted P-value for relative risk (multiple comparisons) | | `phi_p_significance` | Boolean | Whether the Phi is statistically significant based on adjusted p-value | | `RR_p_significance` | Boolean | Whether the RR is statistically significant based on adjusted p-value | | `disease_d1` | String | Name of disease 1 | | `system_d1` | String | Phecode disease system related to disease 1 | | `sex_d1` | String | Sex-specificity of disease 1 | | `disease_d2` | String | Name of disease 2 | | `system_d2` | String | Phecode disease system related to disease 2 | | `sex_d2` | String | Sex-specificity of disease 2 | ## Result of binomial test | Variable Name | Type | Description | | ------------------------- | ------- | ------------------------------------------------------------ | | `phecode_d1` | Float | Phecode for disease 1 in the temporal disease pair | | `phecode_d2` | Float | Phecode for disease 2 in the temporal disease pair | | `name_disease_pair` | String | Name of the temporal disease pair (e.g., D1->D2) | | `n_d1d2_nontemporal` | Float | Number of individuals diagnosed with both disease 1 and disease 2 but without defined temporal order (i.e., the time interval between the two diagnosis is smaller than or equal to `min_interval_days` or larger `max_interval_days`) | | `n_d1d2_temporal` | Float | Number of individuals diagnosed with disease 1 followed by disease 2 in a defined temporal order (i.e., the time interval between the two diagnosis is larger than `min_interval_days` and smaller than or equal to`max_interval_days`) | | `n_d2d1_temporal` | Float | Number of individuals diagnosed with disease 2 followed by disease 1 in a defined temporal order (i.e., the time interval between the two diagnosis is larger than `min_interval_days` and smaller than or equal to`max_interval_days`) | | `binomial_p` | Float | P-value from the binomial test for directionality | | `binomial_proportion` | Float | Proportion of successful outcomes in the binomial test | | `binomial_proportion_ci` | String | Confidence interval for the binomial proportion | | `disease_d1` | String | Name of disease 1 | | `system_d1` | String | Phecode disease system for disease 1 | | `sex_d1` | String | Sex-specificity of disease 1 | | `disease_d2` | String | Name of disease 2 | | `system_d2` | String | Phecode disease system for disease 2 | | `sex_d2` | String | Sex-specificity of disease 2 | | `binomial_p_significance` | Boolean | Indicates whether the result is statistically significant based on adjusted p-value | | `binomial_p_adjusted` | Float | Adjusted p-value for multiple comparisons | ## Result of comorbidity network analysis | Variable Name | Type | Description | | ------------------------------ | ------- | ------------------------------------------------------------ | | `phecode_d1` | Float | Phecode for disease 1 in the non-temporal disease pair | | `phecode_d2` | Float | Phecode for disease 2 in the non-temporal disease pair | | `name_disease_pair` | String | Name of the non-temporal disease pair (e.g., "D1-D2") | | `N_exposed` | Integer | Total number of individuals in exposed group | | `n_total` | Integer | Number of exposed individuals included in the sub-cohort that meet the sex-specificity eligibility criteria for both diseases and after excluding those with history of either disease 1, disease 2, or related diseases | | `n_exposed/n_cases` | String | Number of exposed individuals (individuals with diagnosis of D1) among cases (individuals with diagnosis of D2) | | `n_exposed/n_controls` | String | Number of exposed individuals (individuals with diagnosis of D1) among controls (individuals without diagnosis of D2) | | `comorbidity_network_method` | String | Method used for comorbidity network analysis | | `describe` | String | Description of the model fitting, removed covariates in the model, and reasons for removal of covariates in the model | | `co_vars_list` | String | List of covariates used in the model | | `co_vars_zvalues` | String | Z-values for each covariate in the model | | `comorbidity_beta` | Float | Estimated coefficient from the comorbidity model | | `comorbidity_se` | Float | Standard error of the estimated coefficient | | `comorbidity_p` | Float | P-value for the comorbidity coefficient | | `comorbidity_aic` | Float | Akaike information criterion for the model | | `disease_d1` | String | Name of the disease 1 | | `system_d1` | String | Phecode disease system for the disease 1 | | `sex_d1` | String | Sex-specificity of the disease 1 | | `disease_d2` | String | Name of the disease 2 | | `system_d2` | String | Phecode disease system for the disease 2 | | `sex_d2` | String | Sex-specificity of the disease 2 | | `comorbidity_p_significance` | Boolean | Whether the result is statistically significant based on adjusted p-value | | `comorbidity_p_adjusted` | Float | Adjusted p-value accounting for multiple comparisons | | **Columns for RPCN method** | | | | `alpha` | Float | Hyperparameter used for l1-norm (Weight multiplying the l1 penalty term) | | **Columns for PCN_PCA method** | | | | `pc_sum_variance_explained` | Float | The cumulative proportion of variance that is accounted for by a selected number of principal components in a Principal Component Analysis (sum of explained variance for principal components) | ## Result of disease trajectory analysis | Variable Name | Type | Description | | ------------------------------ | ------- | ------------------------------------------------------------ | | `phecode_d1` | Float | Phecode for disease 1 in the temporal disease pair | | `phecode_d2` | Float | Phecode for disease 2 in the temporal disease pair | | `name_disease_pair` | String | Name of the temporal disease pair (e.g., "D1 → D2") | | `N_exposed` | Integer | Total number of individuals in exposed group | | `n_total` | Integer | Number of exposed individuals included in the nested case-control dataset, where eligible cases (with diagnosis of D2) are all selected and matched with specified number of controls using incidence density sampling | | `n_exposed/n_cases` | String | Number of exposed individuals (individuals with diagnosis of D1) among cases (individuals with diagnosis of D2) | | `n_exposed/n_controls` | String | Number of exposed individuals (individuals with diagnosis of D1) among cases (individuals with diagnosis of D2) | | `trajectory_method` | String | Method used for disease trajectory analysis | | `describe` | String | Description of the model fitting, removed covariates in the model, and reasons for removal of covariates in the model | | `co_vars_list` | String | List of covariates included in the model | | `co_vars_zvalues` | String | Z-values for each covariate in the model | | `trajectory_beta` | Float | Estimated coefficient from the model | | `trajectory_se` | Float | Standard error of the estimated coefficient | | `trajectory_p` | Float | P-value for the coefficient | | `trajectory_aic` | Float | Akaike information criterion for the model | | `disease_d1` | String | Name of the disease 1 | | `system_d1` | String | Phecode disease system for the disease 1 | | `sex_d1` | String | Sex-specificity of the disease 1 | | `disease_d2` | String | Name of the disease 2 | | `system_d2` | String | Phecode disease system for the disease 2 | | `sex_d2` | String | Sex-specificity of the disease 2 | | `trajectory_p_significance` | Boolean | Whether the result is statistically significant based on adjusted p-value | | `trajectory_p_adjusted` | Float | Adjusted p-value accounting for multiple comparisons | | **Columns for RPCN method** | | | | `alpha` | Float | Hyperparameter used for l1-norm (weight multiplying the l1 penalty term) | | **Columns for PCN_PCA method** | | | | `pc_sum_variance_explained` | Float | The cumulative proportion of variance in a dataset that is accounted for by a selected number of principal components in a Principal Component Analysis (sum of explained variance for principal components) |