SQL functions for cox proportional hazards. More...
Functions | |
float8 [] | array_avg_transition (float8[] state, float8[] x, boolean use_abs) |
float8 [] | array_avg_merge (float8[] left, float8[] right) |
float8 [] | array_avg_final (float8[] state) |
aggregate float8 [] | array_avg (float8[], boolean) |
void | coxph_train (varchar source_table, varchar output_table, varchar dependent_varname, varchar independent_varname, varchar right_censoring_status, varchar strata, varchar optimizer_params) |
Compute cox-regression coefficients and diagnostic statistics. More... | |
varchar | coxph_train () |
varchar | coxph_train (varchar message) |
void | coxph_train (varchar source_table, varchar output_table, varchar dependent_variable, varchar independent_variable, varchar right_censoring_status, varchar strata) |
Cox regression training function. More... | |
void | coxph_train (varchar source_table, varchar output_table, varchar dependent_variable, varchar independent_variable, varchar right_censoring_status) |
Cox regression training function. More... | |
void | coxph_train (varchar source_table, varchar output_table, varchar dependent_variable, varchar independent_variable) |
Cox regression training function. More... | |
void | coxph_predict (text model_table, text source_table, text id_col_name, text output_table, text pred_type, text reference) |
Predict the linear Predictor or the risk for the given data. More... | |
void | coxph_predict (text model_table, text source_table, text id_col_name, text output_table, text pred_type) |
void | coxph_predict (text model_table, text source_table, text id_col_name, text output_table) |
float8 | _coxph_predict_resp (float8[] coef, float8[] col_ind_var, float8[] mean_ind_var, text pred_type) |
float8 [] | _coxph_predict_terms (float8[] coef, float8[] col_ind_var, float8[] mean_ind_var) |
varchar | coxph_predict (varchar message) |
varchar | coxph_predict () |
float8 [] | _split_transition (float8[], float8, integer, integer) |
float8 [] | _split_merge (float8[], float8[]) |
float8 [] | _split_final (float8[]) |
aggregate float8 [] | _compute_splits (float8, integer, integer) |
integer | _compute_grpid (float8[] splits, float8 split_col, boolean reverse) |
integer | _compute_grpid (float8[] splits, float8 split_col) |
coxph_result | compute_coxph_result (float8[] coef, float8 l, float8[] d2l, integer niter, float8[] stds) |
coxph_step_result | coxph_improved_step_final (float8[] state) |
float8 [] | coxph_improved_step_transition (float8[] state, float8[] x, float8[] y, integer[] status, float8[] coef, float8[] max_coef) |
float8 [] | coxph_step_inner_final (float8[] state) |
float8 [] | coxph_step_outer_transition (float8[] state1, float8[] state2) |
coxph_step_result | coxph_improved_strata_step_final (float8[] state) |
aggregate float8 [] | coxph_improved_strata_step_outer (float8[] state) |
void | cox_zph (varchar coxph_model_table, varchar output_table) |
Test the proportional hazards assumption for a Cox regression model fit (coxph_train) More... | |
varchar | cox_zph () |
varchar | cox_zph (varchar message) |
float8 [] | __zph_transition (float8[] state, float8[] x, float8[] coef) |
float8 [] | __zph_merge (float8[] left_state, float8[] right_state) |
float8 [] | __zph_final (float8[] left_state) |
aggregate float8 [] | zph_agg (float8[] x, float8[] coef) |
float8 [] | __coxph_scale_resid (integer m, float8[] hessian, float8[] resid) |
float8 [] | __array_elem_corr_transition (float8[] state, float8[] x, float8 y) |
float8 [] | __array_elem_corr_merge (float8[] left_state, float8[] right_state) |
float8 [] | __array_elem_corr_final (float8[] state) |
aggregate float8 [] | array_elem_corr_agg (float8[] array_input, float8 common_elem) |
float8 [] | __coxph_resid_stat_transition (float8[] state, float8 w, float8[] residual, float8[] hessian, integer m) |
float8 [] | __coxph_resid_stat_merge (float8[] state1, float8[] state2) |
__cox_resid_stat_result | __coxph_resid_stat_final (float8[] state) |
aggregate float8 [] | __coxph_resid_stat_agg (float8 w, float8[] residual, float8[] hessian, integer m) |
void | cox_prop_hazards (varchar source_table, varchar out_table, varchar dependent_varname, varchar independent_varname, varchar status) |
Cox regression training function. More... | |
void | cox_prop_hazards (varchar source_table, varchar out_table, varchar dependent_variable, varchar independent_variable) |
Cox regression training function. More... | |
varchar | cox_prop_hazards (varchar usage_string) |
varchar | cox_prop_hazards () |
cox_prop_hazards_result | cox_prop_hazards_regr (varchar source, varchar indepColumn, varchar depColumn, varchar status, integer maxNumIterations=20, varchar optimizer="newton", float8 precision=0.0001) |
cox_prop_hazards_result | cox_prop_hazards_regr (varchar source, varchar indepColumn, varchar depColumn, varchar status) |
cox_prop_hazards_result | cox_prop_hazards_regr (varchar source, varchar indepColumn, varchar depColumn, varchar status, integer maxNumIterations) |
cox_prop_hazards_result | cox_prop_hazards_regr (varchar source, varchar indepColumn, varchar depColumn, varchar status, integer maxNumIterations, varchar optimizer) |
float8 [] | __array_element_min (float8[], float8[]) |
aggregate float8 [] | array_element_min (float8[]) |
float8 [] | __array_element_max (float8[], float8[]) |
aggregate float8 [] | array_element_max (float8[]) |
float8 [] __array_elem_corr_final | ( | float8 [] | state | ) |
float8 [] __array_elem_corr_merge | ( | float8 [] | left_state, |
float8 [] | right_state | ||
) |
float8 [] __array_elem_corr_transition | ( | float8 [] | state, |
float8 [] | x, | ||
float8 | y | ||
) |
float8 [] __array_element_max | ( | float8 | [], |
float8 | [] | ||
) |
float8 [] __array_element_min | ( | float8 | [], |
float8 | [] | ||
) |
aggregate float8 [] __coxph_resid_stat_agg | ( | float8 | w, |
float8 [] | residual, | ||
float8 [] | hessian, | ||
integer | m | ||
) |
__cox_resid_stat_result __coxph_resid_stat_final | ( | float8 [] | state | ) |
float8 [] __coxph_resid_stat_merge | ( | float8 [] | state1, |
float8 [] | state2 | ||
) |
float8 [] __coxph_resid_stat_transition | ( | float8 [] | state, |
float8 | w, | ||
float8 [] | residual, | ||
float8 [] | hessian, | ||
integer | m | ||
) |
float8 [] __coxph_scale_resid | ( | integer | m, |
float8 [] | hessian, | ||
float8 [] | resid | ||
) |
float8 [] __zph_final | ( | float8 [] | left_state | ) |
float8 [] __zph_merge | ( | float8 [] | left_state, |
float8 [] | right_state | ||
) |
float8 [] __zph_transition | ( | float8 [] | state, |
float8 [] | x, | ||
float8 [] | coef | ||
) |
integer _compute_grpid | ( | float8 [] | splits, |
float8 | split_col, | ||
boolean | reverse | ||
) |
integer _compute_grpid | ( | float8 [] | splits, |
float8 | split_col | ||
) |
aggregate float8 [] _compute_splits | ( | float8 | , |
integer | , | ||
integer | |||
) |
float8 _coxph_predict_resp | ( | float8 [] | coef, |
float8 [] | col_ind_var, | ||
float8 [] | mean_ind_var, | ||
text | pred_type | ||
) |
float8 [] _coxph_predict_terms | ( | float8 [] | coef, |
float8 [] | col_ind_var, | ||
float8 [] | mean_ind_var | ||
) |
float8 [] _split_final | ( | float8 | [] | ) |
float8 [] _split_merge | ( | float8 | [], |
float8 | [] | ||
) |
float8 [] _split_transition | ( | float8 | [], |
float8 | , | ||
integer | , | ||
integer | |||
) |
aggregate float8 [] array_avg | ( | float8 | [], |
boolean | |||
) |
float8 [] array_avg_final | ( | float8 [] | state | ) |
float8 [] array_avg_merge | ( | float8 [] | left, |
float8 [] | right | ||
) |
float8 [] array_avg_transition | ( | float8 [] | state, |
float8 [] | x, | ||
boolean | use_abs | ||
) |
aggregate float8 [] array_elem_corr_agg | ( | float8 [] | array_input, |
float8 | common_elem | ||
) |
aggregate float8 [] array_element_max | ( | float8 | [] | ) |
aggregate float8 [] array_element_min | ( | float8 | [] | ) |
coxph_result compute_coxph_result | ( | float8 [] | coef, |
float8 | l, | ||
float8 [] | d2l, | ||
integer | niter, | ||
float8 [] | stds | ||
) |
void cox_prop_hazards | ( | varchar | source_table, |
varchar | out_table, | ||
varchar | dependent_varname, | ||
varchar | independent_varname, | ||
varchar | status | ||
) |
void cox_prop_hazards | ( | varchar | source_table, |
varchar | out_table, | ||
varchar | dependent_variable, | ||
varchar | independent_variable | ||
) |
varchar cox_prop_hazards | ( | varchar | usage_string | ) |
varchar cox_prop_hazards | ( | ) |
cox_prop_hazards_result cox_prop_hazards_regr | ( | varchar | source, |
varchar | indepColumn, | ||
varchar | depColumn, | ||
varchar | status, | ||
integer | maxNumIterations = 20 , |
||
varchar | optimizer = "newton" , |
||
float8 | precision = 0.0001 |
||
) |
cox_prop_hazards_result cox_prop_hazards_regr | ( | varchar | source, |
varchar | indepColumn, | ||
varchar | depColumn, | ||
varchar | status | ||
) |
cox_prop_hazards_result cox_prop_hazards_regr | ( | varchar | source, |
varchar | indepColumn, | ||
varchar | depColumn, | ||
varchar | status, | ||
integer | maxNumIterations | ||
) |
cox_prop_hazards_result cox_prop_hazards_regr | ( | varchar | source, |
varchar | indepColumn, | ||
varchar | depColumn, | ||
varchar | status, | ||
integer | maxNumIterations, | ||
varchar | optimizer | ||
) |
void cox_zph | ( | varchar | coxph_model_table, |
varchar | output_table | ||
) |
coxph_model_table | Name of the table that contains the Cox Proportional Hazards model |
output_table | Name of the output table to contain the statistics to test the proportional hazards assumption |
rho FLOAT8[]
- Array of correlation coefficient between survival time and the scaled Schoenfeld residualschi_square FLOAT8[]
- Chi-square test statistic for thep_value FLOAT8[]
- Two-side p-value for the chi-square test varchar cox_zph | ( | ) |
varchar cox_zph | ( | varchar | message | ) |
coxph_step_result coxph_improved_step_final | ( | float8 [] | state | ) |
float8 [] coxph_improved_step_transition | ( | float8 [] | state, |
float8 [] | x, | ||
float8 [] | y, | ||
integer [] | status, | ||
float8 [] | coef, | ||
float8 [] | max_coef | ||
) |
coxph_step_result coxph_improved_strata_step_final | ( | float8 [] | state | ) |
aggregate float8 [] coxph_improved_strata_step_outer | ( | float8 [] | state | ) |
void coxph_predict | ( | text | model_table, |
text | source_table, | ||
text | id_col_name, | ||
text | output_table, | ||
text | pred_type, | ||
text | reference | ||
) |
model_table | Name of the table containing the cox model. |
source_table | Name of the table containing the prediction data. |
output_table | Name of the table to store the prediction results into. |
pred_type | Type of prediction. Can be one of 'linear_predictors', 'risk' or 'terms'. |
reference | Reference level to use for centering predictions. Can be one of 'overall' or 'strata'. |
void coxph_predict | ( | text | model_table, |
text | source_table, | ||
text | id_col_name, | ||
text | output_table, | ||
text | pred_type | ||
) |
void coxph_predict | ( | text | model_table, |
text | source_table, | ||
text | id_col_name, | ||
text | output_table | ||
) |
varchar coxph_predict | ( | varchar | message | ) |
varchar coxph_predict | ( | ) |
float8 [] coxph_step_inner_final | ( | float8 [] | state | ) |
float8 [] coxph_step_outer_transition | ( | float8 [] | state1, |
float8 [] | state2 | ||
) |
void coxph_train | ( | varchar | source_table, |
varchar | output_table, | ||
varchar | dependent_varname, | ||
varchar | independent_varname, | ||
varchar | right_censoring_status, | ||
varchar | strata, | ||
varchar | optimizer_params | ||
) |
To include an intercept in the model, set one coordinate in the independentVariables
array to 1.
source_table | Name of the source relation containing the training data |
output_table | Name of the output relation to contain the coxph_train model |
independent_varname | Name of the independent column |
dependent_varname | Name of the dependent column measuring time of death |
right_censoring_status | Name of the column that determines right censoring support |
strata | Comma-separated list of column names on which to stratify the data |
optimizer_params | Comma-separated list of parameters for the optimizer function |
coef FLOAT8[]
- Array of coefficients, \( \boldsymbol \beta \)log_likelihood FLOAT8
- Log-likelihood \(l(\boldsymbol \beta)\)std_err FLOAT8[]
- Array of standard errors, \( \mathit{se}(c_1), \dots, \mathit{se}(c_k) \)z_stats FLOAT8[]
- Array of Wald z-statistics, \( \boldsymbol z \)p_values FLOAT8[]
- Array of Wald p-values, \( \boldsymbol p \)hessian FLOAT8[]
- Hessian Matrixnum_iterations INTEGER
- The number of iterations before the algorithm terminatedSELECT coxph_train( 'source_table', 'output_table', 'dependent_varname', 'independent_varname' 'right_censoring_status', 'strata' );
SELECT coef from output_table
See Cox-Proportional Hazards Regression for more details.
varchar coxph_train | ( | ) |
varchar coxph_train | ( | varchar | message | ) |
void coxph_train | ( | varchar | source_table, |
varchar | output_table, | ||
varchar | dependent_variable, | ||
varchar | independent_variable, | ||
varchar | right_censoring_status, | ||
varchar | strata | ||
) |
void coxph_train | ( | varchar | source_table, |
varchar | output_table, | ||
varchar | dependent_variable, | ||
varchar | independent_variable, | ||
varchar | right_censoring_status | ||
) |
void coxph_train | ( | varchar | source_table, |
varchar | output_table, | ||
varchar | dependent_variable, | ||
varchar | independent_variable | ||
) |
aggregate float8 [] zph_agg | ( | float8 [] | x, |
float8 [] | coef | ||
) |