From 18cc4339059edfa673ef33296c9298fd0c24f548 Mon Sep 17 00:00:00 2001 From: Martijn Schuemie Date: Mon, 16 Jan 2023 09:10:12 +0100 Subject: [PATCH 1/3] Update R_CMD_check_Hades.yaml Now also using checkout v2 in release step --- .github/workflows/R_CMD_check_Hades.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index 386f45b..fe6bcdf 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -114,7 +114,7 @@ jobs: steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 0 From d7258aef4f97ecf4702724d96146edbe206b6239 Mon Sep 17 00:00:00 2001 From: Anthony Sena Date: Mon, 13 Feb 2023 10:46:22 -0500 Subject: [PATCH 2/3] Update resultsDataModelSpecification.csv - fixes #8 --- .../resultsDataModelSpecification.csv | 188 +++++++++--------- 1 file changed, 94 insertions(+), 94 deletions(-) diff --git a/inst/settings/resultsDataModelSpecification.csv b/inst/settings/resultsDataModelSpecification.csv index 721940e..f960897 100644 --- a/inst/settings/resultsDataModelSpecification.csv +++ b/inst/settings/resultsDataModelSpecification.csv @@ -1,94 +1,94 @@ -table_name,column_name,data_type,is_required,primary_key,foreign key,empty_is_na,mincellcount,description -time_to_event,database_id,varchar(100),Y,Y,N,N,N,The database identifier -time_to_event,target_cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id for the target cohort -time_to_event,outcome_cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id for the outcome cohort -time_to_event,outcome_type,varchar(100),Y,Y,N,N,N,Is the outvome a first occurrence or repeat -time_to_event,target_outcome_type,varchar(40),Y,Y,N,N,N,When does the outcome occur relative to target -time_to_event,time_to_event,int,Y,N,N,N,N,The time (in days) from target index to outcome start -time_to_event,num_events,int,Y,N,N,N,N,Number of events that occur during the specified time to event -time_to_event,time_scale,varchar(20),Y,N,N,N,N,time scale for the number of events -rechallenge_fail_case_series,database_id,varchar(100),Y,Y,N,N,N,The database identifier -rechallenge_fail_case_series,dechallenge_stop_interval,int,Y,N,N,N,N,The time period that É -rechallenge_fail_case_series,dechallenge_evaluation_window,int,Y,N,N,N,N,The time period that É -rechallenge_fail_case_series,target_cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id for the target cohort -rechallenge_fail_case_series,outcome_cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id for the outcome cohort -rechallenge_fail_case_series,person_key,int,Y,Y,N,N,N,The dense rank for the patient (an identifier that is not the same as the database) -rechallenge_fail_case_series,subject_id,bigint,Y,N,N,N,N,The person identifier for the failed case series (optional) -rechallenge_fail_case_series,dechallenge_exposure_number,int,Y,N,N,N,N,The number of times a dechallenge has occurred -rechallenge_fail_case_series,dechallenge_exposure_start_date_offset,int,Y,N,N,N,N,The offset for the dechallenge start (number of days after index) -rechallenge_fail_case_series,dechallenge_exposure_end_date_offset,int,Y,N,N,N,N,The offset for the dechallenge end (number of days after index) -rechallenge_fail_case_series,dechallenge_outcome_number,int,Y,N,N,N,N,The number of times an outcome has occurred during the dechallenge -rechallenge_fail_case_series,dechallenge_outcome_start_date_offset,int,Y,N,N,N,N,The offset for the outcome start (number of days after index) -rechallenge_fail_case_series,rechallenge_exposure_number,int,Y,N,N,N,N,The number of times a rechallenge exposure has occurred -rechallenge_fail_case_series,rechallenge_exposure_start_date_offset,int,Y,N,N,N,N,The offset for the rechallenge start (number of days after index) -rechallenge_fail_case_series,rechallenge_exposure_end_date_offset,int,Y,N,N,N,N,The offset for the rechallenge end (number of days after index) -rechallenge_fail_case_series,rechallenge_outcome_number,int,Y,N,N,N,N,The number of times the outcome has occurred during the rechallenge -rechallenge_fail_case_series,rechallenge_outcome_start_date_offset,int,Y,N,N,N,N,The offset for the outcome start (number of days after index) -dechallenge_rechallenge,database_id,varchar(100),Y,Y,N,N,N,The database identifier -dechallenge_rechallenge,dechallenge_stop_interval,int,Y,Y,N,N,N,The dechallenge stop interval -dechallenge_rechallenge,dechallenge_evaluation_window,int,Y,Y,N,N,N,The dechallenge evaluation window -dechallenge_rechallenge,target_cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id for the target cohort -dechallenge_rechallenge,outcome_cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id for the outcome cohort -dechallenge_rechallenge,num_exposure_eras,int,Y,N,N,N,N,The number of exposure eras -dechallenge_rechallenge,num_persons_exposed,int,Y,N,N,N,N,The number of persons exposed -dechallenge_rechallenge,num_cases,int,Y,N,N,N,N,The number of cases -dechallenge_rechallenge,dechallenge_attempt,int,Y,N,N,N,N,The number of dechallenge attempts -dechallenge_rechallenge,dechallenge_fail,int,Y,N,N,N,N,The dechallenge fail count -dechallenge_rechallenge,dechallenge_success,int,Y,N,N,N,N,The dechallenge success count -dechallenge_rechallenge,rechallenge_attempt,int,Y,N,N,N,N,The rechallenge attempt count -dechallenge_rechallenge,rechallenge_fail,int,Y,N,N,N,N,The rechallenge fail count -dechallenge_rechallenge,rechallenge_success,int,Y,N,N,N,N,The rechallenge success count -dechallenge_rechallenge,pct_dechallenge_attempt,float,Y,N,N,N,N,The percentage of dechallenge attempts -dechallenge_rechallenge,pct_dechallenge_success,float,Y,N,N,N,N,The percentage of dechallenge success -dechallenge_rechallenge,pct_dechallenge_fail,float,Y,N,N,N,N,The percentage of dechallenge fails -dechallenge_rechallenge,pct_rechallenge_attempt,float,Y,N,N,N,N,The percentage of rechallenge attempts -dechallenge_rechallenge,pct_rechallenge_success,float,Y,N,N,N,N,The percentage of rechallenge success -dechallenge_rechallenge,pct_rechallenge_fail,float,Y,N,N,N,N,The percentage of rechallenge fails -analysis_ref,database_id,varchar(100),Y,Y,N,N,N,The database identifier -analysis_ref,run_id,int,Y,Y,N,N,N,The run identifier -analysis_ref,analysis_id,int,Y,Y,N,N,N,The analysis identifier -analysis_ref,analysis_name,varchar(MAX),Y,N,N,N,N,The analysis name -analysis_ref,domain_id,varchar(MAX),Y,N,N,N,N,The domain id -analysis_ref,start_day,int,Y,N,N,N,N,The start day -analysis_ref,end_day,int,Y,N,N,N,N,The end day -analysis_ref,is_binary,varchar(1),Y,N,N,N,N,Is this a binary analysis -analysis_ref,missing_means_zero,varchar(1),Y,N,N,N,N,Missing means zero -covariate_ref,database_id,varchar(100),Y,Y,N,N,N,The database identifier -covariate_ref,run_id,int,Y,Y,N,N,N,The run identifier -covariate_ref,covariate_id,bigint,Y,Y,N,N,N,The covariate identifier -covariate_ref,covariate_name,varchar(MAX),Y,N,N,N,N,The covariate name -covariate_ref,analysis_id,int,Y,N,N,N,N,The analysis identifier -covariate_ref,concept_id,bigint,Y,N,N,N,N,The concept identifier -covariates,database_id,varchar(100),Y,Y,N,N,N,The database identifier -covariates,run_id,int,Y,Y,N,N,N,The run identifier -covariates,cohort_definition_id,int,Y,Y,N,N,N,The cohort definition id -covariates,covariate_id,bigint,Y,Y,N,N,N,The covaraite id -covariates,sum_value,int,Y,N,N,N,N,The sum value -covariates,average_value,float,Y,N,N,N,N,The average value -covariates_continuous,database_id,varchar(100),Y,Y,N,N,N,The database identifier -covariates_continuous,run_id,int,Y,Y,N,N,N,The run identifier -covariates_continuous,cohort_definition_id,bigint,Y,Y,N,N,N,The cohort definition id -covariates_continuous,covariate_id,int,Y,Y,N,N,N,The covariate identifier -covariates_continuous,count_value,int,Y,N,N,N,N,The count value -covariates_continuous,min_value,float,Y,N,N,N,N,The min value -covariates_continuous,max_value,float,Y,N,N,N,N,The max value -covariates_continuous,average_value,float,Y,N,N,N,N,The average value -covariates_continuous,standard_deviation,float,Y,N,N,N,N,The standard devidation -covariates_continuous,median_value,float,Y,N,N,N,N,The median value -covariates_continuous,p_10_value,float,Y,N,N,N,N,The 10th percentile -covariates_continuous,p_25_value,float,Y,N,N,N,N,The 25th percentile -covariates_continuous,p_75_value,float,Y,N,N,N,N,The 75th percentile -covariates_continuous,p_90_value,float,Y,N,N,N,N,The 90th percentile -settings,run_id,int,Y,Y,N,N,N,The run identifier -settings,database_id,varchar(100),Y,Y,N,N,N,The database identifier -settings,covariate_setting_json,varchar(max),Y,N,N,N,N,The covariate settings JSON -settings,risk_window_start,int,Y,N,N,N,N,The risk window start -settings,risk_window_end,int,Y,N,N,N,N,The risk window end -settings,start_anchor,varchar(15),Y,N,N,N,N,The start anchor -settings,end_anchor,varchar(15),Y,N,N,N,N,The end anchor -cohort_details,run_id,int,Y,Y,N,N,N,The run identifier -cohort_details,database_id,varchar(100),Y,Y,N,N,N,The database identifier -cohort_details,cohort_definition_id,int,Y,N,N,N,N,The study cohort id -cohort_details,cohort_type,varchar(10),Y,N,N,N,N,The cohort type -cohort_details,target_cohort_id,int,Y,N,N,N,N,The target cohort id -cohort_details,outcome_cohort_id,int,Y,N,N,N,N,The outcome cohort id +table_name,column_name,data_type,is_required,primary_key,empty_is_na,min_cell_count,description +time_to_event,database_id,varchar(100),Y,Y,N,N,The database identifier +time_to_event,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort +time_to_event,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort +time_to_event,outcome_type,varchar(100),Y,Y,N,N,Is the outvome a first occurrence or repeat +time_to_event,target_outcome_type,varchar(40),Y,Y,N,N,When does the outcome occur relative to target +time_to_event,time_to_event,int,Y,N,N,N,The time (in days) from target index to outcome start +time_to_event,num_events,int,Y,N,N,N,Number of events that occur during the specified time to event +time_to_event,time_scale,varchar(20),Y,N,N,N,time scale for the number of events +rechallenge_fail_case_series,database_id,varchar(100),Y,Y,N,N,The database identifier +rechallenge_fail_case_series,dechallenge_stop_interval,int,Y,N,N,N,The time period that É +rechallenge_fail_case_series,dechallenge_evaluation_window,int,Y,N,N,N,The time period that É +rechallenge_fail_case_series,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort +rechallenge_fail_case_series,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort +rechallenge_fail_case_series,person_key,int,Y,Y,N,N,The dense rank for the patient (an identifier that is not the same as the database) +rechallenge_fail_case_series,subject_id,bigint,Y,N,N,N,The person identifier for the failed case series (optional) +rechallenge_fail_case_series,dechallenge_exposure_number,int,Y,N,N,N,The number of times a dechallenge has occurred +rechallenge_fail_case_series,dechallenge_exposure_start_date_offset,int,Y,N,N,N,The offset for the dechallenge start (number of days after index) +rechallenge_fail_case_series,dechallenge_exposure_end_date_offset,int,Y,N,N,N,The offset for the dechallenge end (number of days after index) +rechallenge_fail_case_series,dechallenge_outcome_number,int,Y,N,N,N,The number of times an outcome has occurred during the dechallenge +rechallenge_fail_case_series,dechallenge_outcome_start_date_offset,int,Y,N,N,N,The offset for the outcome start (number of days after index) +rechallenge_fail_case_series,rechallenge_exposure_number,int,Y,N,N,N,The number of times a rechallenge exposure has occurred +rechallenge_fail_case_series,rechallenge_exposure_start_date_offset,int,Y,N,N,N,The offset for the rechallenge start (number of days after index) +rechallenge_fail_case_series,rechallenge_exposure_end_date_offset,int,Y,N,N,N,The offset for the rechallenge end (number of days after index) +rechallenge_fail_case_series,rechallenge_outcome_number,int,Y,N,N,N,The number of times the outcome has occurred during the rechallenge +rechallenge_fail_case_series,rechallenge_outcome_start_date_offset,int,Y,N,N,N,The offset for the outcome start (number of days after index) +dechallenge_rechallenge,database_id,varchar(100),Y,Y,N,N,The database identifier +dechallenge_rechallenge,dechallenge_stop_interval,int,Y,Y,N,N,The dechallenge stop interval +dechallenge_rechallenge,dechallenge_evaluation_window,int,Y,Y,N,N,The dechallenge evaluation window +dechallenge_rechallenge,target_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the target cohort +dechallenge_rechallenge,outcome_cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id for the outcome cohort +dechallenge_rechallenge,num_exposure_eras,int,Y,N,N,N,The number of exposure eras +dechallenge_rechallenge,num_persons_exposed,int,Y,N,N,N,The number of persons exposed +dechallenge_rechallenge,num_cases,int,Y,N,N,N,The number of cases +dechallenge_rechallenge,dechallenge_attempt,int,Y,N,N,N,The number of dechallenge attempts +dechallenge_rechallenge,dechallenge_fail,int,Y,N,N,N,The dechallenge fail count +dechallenge_rechallenge,dechallenge_success,int,Y,N,N,N,The dechallenge success count +dechallenge_rechallenge,rechallenge_attempt,int,Y,N,N,N,The rechallenge attempt count +dechallenge_rechallenge,rechallenge_fail,int,Y,N,N,N,The rechallenge fail count +dechallenge_rechallenge,rechallenge_success,int,Y,N,N,N,The rechallenge success count +dechallenge_rechallenge,pct_dechallenge_attempt,float,Y,N,N,N,The percentage of dechallenge attempts +dechallenge_rechallenge,pct_dechallenge_success,float,Y,N,N,N,The percentage of dechallenge success +dechallenge_rechallenge,pct_dechallenge_fail,float,Y,N,N,N,The percentage of dechallenge fails +dechallenge_rechallenge,pct_rechallenge_attempt,float,Y,N,N,N,The percentage of rechallenge attempts +dechallenge_rechallenge,pct_rechallenge_success,float,Y,N,N,N,The percentage of rechallenge success +dechallenge_rechallenge,pct_rechallenge_fail,float,Y,N,N,N,The percentage of rechallenge fails +analysis_ref,database_id,varchar(100),Y,Y,N,N,The database identifier +analysis_ref,run_id,int,Y,Y,N,N,The run identifier +analysis_ref,analysis_id,int,Y,Y,N,N,The analysis identifier +analysis_ref,analysis_name,varchar,Y,N,N,N,The analysis name +analysis_ref,domain_id,varchar,Y,N,N,N,The domain id +analysis_ref,start_day,int,Y,N,N,N,The start day +analysis_ref,end_day,int,Y,N,N,N,The end day +analysis_ref,is_binary,varchar(1),Y,N,N,N,Is this a binary analysis +analysis_ref,missing_means_zero,varchar(1),Y,N,N,N,Missing means zero +covariate_ref,database_id,varchar(100),Y,Y,N,N,The database identifier +covariate_ref,run_id,int,Y,Y,N,N,The run identifier +covariate_ref,covariate_id,bigint,Y,Y,N,N,The covariate identifier +covariate_ref,covariate_name,varchar,Y,N,N,N,The covariate name +covariate_ref,analysis_id,int,Y,N,N,N,The analysis identifier +covariate_ref,concept_id,bigint,Y,N,N,N,The concept identifier +covariates,database_id,varchar(100),Y,Y,N,N,The database identifier +covariates,run_id,int,Y,Y,N,N,The run identifier +covariates,cohort_definition_id,int,Y,Y,N,N,The cohort definition id +covariates,covariate_id,bigint,Y,Y,N,N,The covaraite id +covariates,sum_value,int,Y,N,N,N,The sum value +covariates,average_value,float,Y,N,N,N,The average value +covariates_continuous,database_id,varchar(100),Y,Y,N,N,The database identifier +covariates_continuous,run_id,int,Y,Y,N,N,The run identifier +covariates_continuous,cohort_definition_id,bigint,Y,Y,N,N,The cohort definition id +covariates_continuous,covariate_id,int,Y,Y,N,N,The covariate identifier +covariates_continuous,count_value,int,Y,N,N,N,The count value +covariates_continuous,min_value,float,Y,N,N,N,The min value +covariates_continuous,max_value,float,Y,N,N,N,The max value +covariates_continuous,average_value,float,Y,N,N,N,The average value +covariates_continuous,standard_deviation,float,Y,N,N,N,The standard devidation +covariates_continuous,median_value,float,Y,N,N,N,The median value +covariates_continuous,p_10_value,float,Y,N,N,N,The 10th percentile +covariates_continuous,p_25_value,float,Y,N,N,N,The 25th percentile +covariates_continuous,p_75_value,float,Y,N,N,N,The 75th percentile +covariates_continuous,p_90_value,float,Y,N,N,N,The 90th percentile +settings,run_id,int,Y,Y,N,N,The run identifier +settings,database_id,varchar(100),Y,Y,N,N,The database identifier +settings,covariate_setting_json,varchar,Y,N,N,N,The covariate settings JSON +settings,risk_window_start,int,Y,N,N,N,The risk window start +settings,risk_window_end,int,Y,N,N,N,The risk window end +settings,start_anchor,varchar(15),Y,N,N,N,The start anchor +settings,end_anchor,varchar(15),Y,N,N,N,The end anchor +cohort_details,run_id,int,Y,Y,N,N,The run identifier +cohort_details,database_id,varchar(100),Y,Y,N,N,The database identifier +cohort_details,cohort_definition_id,int,Y,N,N,N,The study cohort id +cohort_details,cohort_type,varchar(10),Y,N,N,N,The cohort type +cohort_details,target_cohort_id,int,Y,N,N,N,The target cohort id +cohort_details,outcome_cohort_id,int,Y,N,N,N,The outcome cohort id From da3f3d35562abea03c7e0a59aff2670855c0cba0 Mon Sep 17 00:00:00 2001 From: jreps Date: Mon, 13 Feb 2023 16:18:25 -0500 Subject: [PATCH 3/3] Update DESCRIPTION --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a971d29..6e7ab62 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Characterization Type: Package Title: Characterizations of Cohorts -Version: 0.0.5 -Date: 2023-01-12 +Version: 0.0.6 +Date: 2023-02-13 Authors@R: c( person("Jenna", "Reps", , "reps@ohdsi.org", role = c("aut", "cre")), person("Patrick", "Ryan", , "ryan@ohdsi.org", role = c("aut"))