1 Access and schema

This document describes the data models for Strategus modules and some instructions on how to access results in these models. We hold results on the OHDSI public database server shinydb that runs postgresql. You can install the postgresql JDBC drivers; this only needs to be done once.

It is recommend to specify the environmental variable DATABASECONNECT_JAR_FOLDER=<folder-of-your-choice> in .Renviron located in the user’s home directory. In the example below, however, we set the environmental variable manually in R to make this document more self-contained.

Sys.setenv(DATABASECONNECTOR_JAR_FOLDER = getwd())
DatabaseConnector::downloadJdbcDrivers(dbms = "postgresql")

and set-up connection details, in this case using keyring to hide usernames and passwords for security`

# OHDSI shinydb read-only credentials
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = keyring::key_get("sosTutorialServer"),
  user = keyring::key_get("sosTutorialUser"),
  password = keyring::key_get("sosTutorialPassword"))

Table 1.1 provides the schema names for SOS Challenge results.

Table 1.1: SOS Challenge study schema
SOS Challenge study schema
Fluoroquinolone and aortic aneurysms quinoloneaa
Intravitreal anti-VEGF and kidney failure antivegfkf

2 Data models

2.1 Characterization

2.1.1 Table analysis_ref

Field Type Key
database_id varchar(100) Y
run_id int Y
analysis_id int Y
analysis_name varchar N
domain_id varchar N
start_day int N
end_day int N
is_binary varchar(1) N
missing_means_zero varchar(1) N

2.1.2 Table cohort_counts

Field Type Key
run_id int Y
database_id varchar(100) Y
cohort_definition_id int N
row_count int N
person_count int N

2.1.3 Table cohort_details

Field Type Key
run_id int Y
database_id varchar(100) Y
cohort_definition_id int N
cohort_type varchar(10) N
target_cohort_id int N
outcome_cohort_id int N

2.1.4 Table covariate_ref

Field Type Key
database_id varchar(100) Y
run_id int Y
covariate_id bigint Y
covariate_name varchar N
analysis_id int N
concept_id bigint N

2.1.5 Table covariates

Field Type Key
database_id varchar(100) Y
run_id int Y
cohort_definition_id int Y
covariate_id bigint Y
sum_value int N
average_value float N

2.1.6 Table covariates_continuous

Field Type Key
database_id varchar(100) Y
run_id int Y
cohort_definition_id bigint Y
covariate_id int Y
count_value int N
min_value float N
max_value float N
average_value float N
standard_deviation float N
median_value float N
p_10_value float N
p_25_value float N
p_75_value float N
p_90_value float N

2.1.7 Table dechallenge_rechallenge

Field Type Key
database_id varchar(100) Y
dechallenge_stop_interval int Y
dechallenge_evaluation_window int Y
target_cohort_definition_id bigint Y
outcome_cohort_definition_id bigint Y
num_exposure_eras int N
num_persons_exposed int N
num_cases int N
dechallenge_attempt int N
dechallenge_fail int N
dechallenge_success int N
rechallenge_attempt int N
rechallenge_fail int N
rechallenge_success int N
pct_dechallenge_attempt float N
pct_dechallenge_success float N
pct_dechallenge_fail float N
pct_rechallenge_attempt float N
pct_rechallenge_success float N
pct_rechallenge_fail float N

2.1.8 Table rechallenge_fail_case_series

Field Type Key
database_id varchar(100) Y
dechallenge_stop_interval int N
dechallenge_evaluation_window int N
target_cohort_definition_id bigint Y
outcome_cohort_definition_id bigint Y
person_key int Y
subject_id bigint N
dechallenge_exposure_number int N
dechallenge_exposure_start_date_offset int N
dechallenge_exposure_end_date_offset int N
dechallenge_outcome_number int N
dechallenge_outcome_start_date_offset int N
rechallenge_exposure_number int N
rechallenge_exposure_start_date_offset int N
rechallenge_exposure_end_date_offset int N
rechallenge_outcome_number int N
rechallenge_outcome_start_date_offset int N

2.1.9 Table settings

Field Type Key
run_id int Y
database_id varchar(100) Y
covariate_setting_json varchar N
risk_window_start int N
risk_window_end int N
start_anchor varchar(15) N
end_anchor varchar(15) N

2.1.10 Table time_to_event

Field Type Key
database_id varchar(100) Y
target_cohort_definition_id bigint Y
outcome_cohort_definition_id bigint Y
outcome_type varchar(100) Y
target_outcome_type varchar(40) Y
time_to_event int N
num_events int N
time_scale varchar(20) N

2.2 CohortDiagnostics

2.2.1 Table cohort

Field Type Key
cohort_id bigint Yes
cohort_name varchar No
sql varchar No

2.2.2 Table cohort_count

Field Type Key
cohort_id bigint Yes
cohort_entries float No
cohort_subjects float No
database_id varchar Yes

2.2.3 Table cohort_inc_result

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
mode_id bigint Yes
inclusion_rule_mask bigint Yes
person_count float No

2.2.4 Table cohort_inc_stats

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
rule_sequence bigint Yes
mode_id bigint Yes
person_count float No
gain_count float No
person_total float No

2.2.5 Table cohort_inclusion

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
rule_sequence bigint Yes
name varchar No
description varchar No

2.2.6 Table cohort_overlap

Field Type Key
either_subjects float No
both_subjects float No
t_only_subjects float No
c_only_subjects float No
t_before_c_subjects float No
c_before_t_subjects float No
same_day_subjects float No
t_in_c_subjects float No
c_in_t_subjects float No
target_cohort_id bigint Yes
comparator_cohort_id bigint Yes
database_id varchar Yes

2.2.7 Table cohort_relationships

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
comparator_cohort_id bigint Yes
start_day bigint Yes
end_day float Yes
subjects bigint No
sub_cs_before_ts bigint No
rec_cs_before_ts bigint No
sub_cs_on_ts bigint No
rec_cs_on_ts bigint No
sub_cs_after_ts bigint No
rec_cs_after_ts bigint No
sub_cs_before_te bigint No
rec_cs_before_te bigint No
sub_cs_on_te bigint No
rec_cs_on_te bigint No
sub_cs_after_te bigint No
rec_cs_after_te bigint No
sub_cs_window_t bigint No
rec_cs_window_t bigint No
sub_ce_window_t bigint No
rec_ce_window_t bigint No
sub_cs_window_ts bigint No
rec_cs_window_ts bigint No
sub_cs_window_te bigint No
rec_cs_window_te bigint No
sub_ce_window_ts bigint No
rec_ce_window_ts bigint No
sub_ce_window_te bigint No
rec_ce_window_te bigint No
sub_c_within_t bigint No
rec_c_within_t bigint No
c_days_before_ts bigint No
c_days_before_te bigint No
c_days_within_t_days bigint No
c_days_after_ts bigint No
c_days_after_te bigint No
t_days bigint No
c_days bigint No

2.2.8 Table cohort_summary_stats

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
mode_id bigint Yes
base_count float No
final_count float No

2.2.9 Table concept

Field Type Key
concept_id bigint Yes
concept_name varchar(255) No
domain_id varchar(20) No
vocabulary_id varchar(50) No
concept_class_id varchar(20) No
standard_concept varchar(1) No
concept_code varchar(255) No
valid_start_date Date No
valid_end_date Date No
invalid_reason varchar No

2.2.10 Table concept_ancestor

Field Type Key
ancestor_concept_id bigint Yes
descendant_concept_id bigint Yes
min_levels_of_separation int No
max_levels_of_separation int No

2.2.11 Table concept_relationship

Field Type Key
concept_id_1 bigint Yes
concept_id_2 bigint Yes
relationship_id varchar(20) Yes
valid_start_date Date No
valid_end_date Date No
invalid_reason varchar(1) No

2.2.12 Table concept_sets

Field Type Key
cohort_id bigint Yes
concept_set_id int Yes
concept_set_sql varchar No
concept_set_name varchar(255) No
concept_set_expression varchar No

2.2.13 Table concept_synonym

Field Type Key
concept_id bigint Yes
concept_synonym_name varchar Yes
language_concept_id bigint Yes

2.2.14 Table database

Field Type Key
database_id varchar Yes
database_name varchar No
description varchar No
is_meta_analysis varchar(1) No

2.2.15 Table domain

Field Type Key
domain_id varchar(20) Yes
domain_name varchar(255) No
domain_concept_id bigint No

2.2.16 Table incidence_rate

Field Type Key
cohort_count float No
person_years float No
gender varchar Yes
age_group varchar Yes
calendar_year varchar(4) Yes
incidence_rate float No
cohort_id bigint Yes
database_id varchar Yes

2.2.17 Table included_source_concept

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
concept_set_id int Yes
concept_id bigint Yes
concept_subjects float No
concept_count float No

2.2.18 Table index_event_breakdown

Field Type Key
concept_id bigint Yes
concept_count float No
subject_count float No
cohort_id bigint Yes
database_id varchar Yes
domain_field varchar Yes
domain_table varchar Yes

2.2.19 Table metadata

Field Type Key
database_id varchar Yes
start_time varchar Yes
variable_field varchar Yes
value_field varchar No

2.2.20 Table orphan_concept

Field Type Key
cohort_id bigint Yes
concept_set_id int Yes
database_id varchar Yes
concept_id bigint Yes
concept_count float No
concept_subjects float No

2.2.21 Table relationship

Field Type Key
relationship_id varchar(20) Yes
relationship_name varchar(255) No
is_hierarchical varchar(1) No
defines_ancestry varchar(1) No
reverse_relationship_id varchar(20) Yes
relationship_concept_id bigint Yes

2.2.22 Table resolved_concepts

Field Type Key
cohort_id bigint Yes
concept_set_id int Yes
concept_id bigint Yes
database_id varchar Yes

2.2.23 Table subset_definition

Field Type Key
subset_definition_id bigint Yes
json varchar Yes

2.2.24 Table temporal_analysis_ref

Field Type Key
analysis_id int Yes
analysis_name varchar No
domain_id varchar(20) Yes
is_binary varchar(1) No
missing_means_zero varchar(1) No

2.2.25 Table temporal_covariate_ref

Field Type Key
covariate_id bigint Yes
covariate_name varchar No
analysis_id int No
concept_id bigint No

2.2.26 Table temporal_covariate_value

Field Type Key
cohort_id bigint Yes
covariate_id bigint Yes
sum_value float No
mean float No
sd float No
database_id varchar Yes

2.2.27 Table temporal_covariate_value_dist

Field Type Key
cohort_id bigint Yes
covariate_id bigint Yes
count_value float No
min_value float No
max_value float No
mean float No
sd float No
median_value float No
p_10_value float No
p_25_value float No
p_75_value float No
p_90_value float No
database_id varchar Yes

2.2.28 Table temporal_time_ref

Field Type Key
time_id int Yes
start_day float No
end_day float No

2.2.29 Table time_series

Field Type Key
cohort_id bigint Yes
database_id varchar Yes
period_begin Date Yes
period_end Date Yes
series_type varchar Yes
calendar_interval varchar Yes
records bigint No
subjects bigint No
person_days bigint No
person_days_in bigint No
records_start bigint No
subjects_start bigint No
subjects_start_in bigint No
records_end bigint No
subjects_end bigint No
subjects_end_in bigint No

2.2.30 Table visit_context

Field Type Key
cohort_id bigint Yes
visit_concept_id bigint Yes
visit_context varchar Yes
subjects float No
database_id varchar Yes

2.2.31 Table vocabulary

Field Type Key
vocabulary_id varchar(50) No
vocabulary_name varchar(255) No
vocabulary_reference varchar No
vocabulary_version varchar No
vocabulary_concept_id bigint No

2.3 CohortGenerator

2.3.1 Table cohort_censor_stats

Field Type Key
cohort_definition_id bigint Yes
lost_count bigint Yes

2.3.2 Table cohort_count

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
cohort_entries bigint Yes
cohort_subjects bigint Yes

2.3.3 Table cohort_count_neg_ctrl

Field Type Key
database_id varchar Yes
cohort_id bigint Yes
cohort_entries bigint Yes
cohort_subjects bigint Yes

2.3.4 Table cohort_definition

Field Type Key
cohort_definition_id bigint Yes
cohort_name varchar No
description varchar No
json text No
sql_command text No
subset_parent bigint No
is_subset int No
subset_definition_id bigint No

2.3.5 Table cohort_generation

Field Type Key
cohort_id bigint Yes
cohort_name varchar No
generation_status varchar No
start_time Timestamp No
end_time Timestamp No
database_id varchar Yes

2.3.6 Table cohort_inc_result

Field Type Key
database_id varchar Yes
cohort_definition_id bigint Yes
inclusion_rule_mask int Yes
person_count bigint Yes
mode_id int Yes

2.3.7 Table cohort_inc_stats

Field Type Key
database_id varchar Yes
cohort_definition_id bigint Yes
rule_sequence int Yes
person_count bigint Yes
gain_count bigint Yes
person_total bigint Yes
mode_id int Yes

2.3.8 Table cohort_inclusion

Field Type Key
cohort_definition_id bigint Yes
rule_sequence int Yes
name varchar Yes
description varchar No

2.3.9 Table cohort_summary_stats

Field Type Key
database_id varchar Yes
cohort_definition_id bigint Yes
base_count bigint Yes
final_count bigint Yes
mode_id int Yes

2.4 CohortIncidence

2.4.1 Table incidence_summary

Field Type Key
ref_id int no
database_id varchar(255) no
source_name varchar(255) no
target_cohort_definition_id bigint no
target_name varchar(255) no
tar_id bigint no
tar_start_with varchar(10) no
tar_start_offset bigint no
tar_end_with varchar(10) no
tar_end_offset bigint no
subgroup_id bigint no
subgroup_name varchar(255) no
outcome_id bigint no
outcome_cohort_definition_id bigint no
outcome_name varchar(255) no
clean_window bigint no
age_id int no
age_group_name varchar(255) no
gender_id int no
gender_name varchar(255) no
start_year int no
persons_at_risk_pe bigint no
persons_at_risk bigint no
person_days_pe bigint no
person_days bigint no
person_outcomes_pe bigint no
person_outcomes bigint no
outcomes_pe bigint no
outcomes bigint no
incidence_proportion_p100p float no
incidence_rate_p100py float no

2.5 CohortMethod

2.5.1 Table cm_analysis

Field Type Key
analysis_id int Yes
description varchar No
definition varchar No

2.5.2 Table cm_attrition

Field Type Key
sequence_number int Yes
description varchar No
subjects int No
exposure_id int Yes
target_id int Yes
comparator_id int Yes
analysis_id int Yes
outcome_id int Yes
database_id varchar Yes

2.5.3 Table cm_covariate

Field Type Key
covariate_id bigint Yes
covariate_name varchar No
analysis_id int Yes
covariate_analysis_id int No
database_id varchar Yes

2.5.4 Table cm_covariate_analysis

Field Type Key
covariate_analysis_id int Yes
covariate_analysis_name varchar No
analysis_id int Yes

2.5.5 Table cm_covariate_balance

Field Type Key
database_id varchar Yes
target_id int Yes
comparator_id int Yes
outcome_id int Yes
analysis_id int Yes
covariate_id bigint Yes
target_mean_before float No
comparator_mean_before float No
std_diff_before float No
target_mean_after float No
comparator_mean_after float No
std_diff_after float No

2.5.6 Table cm_diagnostics_summary

Field Type Key
analysis_id int Yes
target_id int Yes
comparator_id int Yes
outcome_id int Yes
database_id varchar Yes
max_sdm float No
shared_max_sdm float No
equipoise float No
mdrr float No
attrition_fraction float No
ease float No
balance_diagnostic varchar(20) No
shared_balance_diagnostic varchar(20) No
equipoise_diagnostic varchar(20) No
mdrr_diagnostic varchar(20) No
attrition_diagnostic varchar(20) No
ease_diagnostic varchar(20) No
unblind int No

2.5.7 Table cm_follow_up_dist

Field Type Key
target_id int Yes
comparator_id int Yes
outcome_id int Yes
analysis_id int Yes
target_min_days float No
target_p_10_days float No
target_p_25_days float No
target_median_days float No
target_p_75_days float No
target_p_90_days float No
target_max_days float No
comparator_min_days float No
comparator_p_10_days float No
comparator_p_25_days float No
comparator_median_days float No
comparator_p_75_days float No
comparator_p_90_days float No
comparator_max_days float No
target_min_date Date No
target_max_date Date No
comparator_min_date Date No
comparator_max_date Date No
database_id varchar Yes

2.5.8 Table cm_interaction_result

Field Type Key
analysis_id int No
target_id int No
comparator_id int No
outcome_id int No
interaction_covariate_id int No
rr float No
ci_95_lb float No
ci_95_ub float No
p float No
target_subjects int No
comparator_subjects int No
target_days int No
comparator_days int No
target_outcomes int No
comparator_outcomes int No
log_rr float No
se_log_rr float No
calibrated_rr float No
calibrated_ci_95_lb float No
calibrated_ci_95_ub float No
calibrated_p float No
calibrated_log_rr float No
calibrated_se_log_rr float No
database_id varchar No

2.5.9 Table cm_kaplan_meier_dist

Field Type Key
time_day int Yes
target_survival float No
target_survival_lb float No
target_survival_ub float No
comparator_survival float No
comparator_survival_lb float No
comparator_survival_ub float No
target_at_risk int No
comparator_at_risk int No
target_id int Yes
comparator_id int Yes
outcome_id int Yes
analysis_id int Yes
database_id varchar Yes

2.5.10 Table cm_likelihood_profile

Field Type Key
log_rr float Yes
log_likelihood float No
target_id int Yes
comparator_id int Yes
outcome_id int Yes
analysis_id int Yes
database_id varchar Yes

2.5.11 Table cm_preference_score_dist

Field Type Key
analysis_id int Yes
target_id int Yes
comparator_id int Yes
database_id varchar Yes
preference_score float Yes
target_density float No
comparator_density float No

2.5.12 Table cm_propensity_model

Field Type Key
target_id int Yes
comparator_id int Yes
analysis_id int Yes
database_id varchar Yes
covariate_id bigint Yes
coefficient float No

2.5.13 Table cm_result

Field Type Key
analysis_id int Yes
target_id int Yes
comparator_id int Yes
outcome_id int Yes
rr float No
ci_95_lb float No
ci_95_ub float No
p float No
target_subjects int No
comparator_subjects int No
target_days int No
comparator_days int No
target_outcomes int No
comparator_outcomes int No
log_rr float No
se_log_rr float No
llr float No
calibrated_rr float No
calibrated_ci_95_lb float No
calibrated_ci_95_ub float No
calibrated_p float No
calibrated_log_rr float No
calibrated_se_log_rr float No
database_id varchar Yes

2.5.14 Table cm_shared_covariate_balance

Field Type Key
database_id varchar Yes
target_id int Yes
comparator_id int Yes
analysis_id int Yes
covariate_id bigint Yes
target_mean_before float No
comparator_mean_before float No
std_diff_before float No
target_mean_after float No
comparator_mean_after float No
std_diff_after float No

2.5.15 Table cm_target_comparator_outcome

Field Type Key
outcome_id int Yes
outcome_of_interest int No
true_effect_size float No
target_id int Yes
comparator_id int Yes

2.6 PatientLevelPrediction

2.6.1 Table attrition

Field Type Key
performance_id int No
outcome_id int No
description varchar No
target_count int No
unique_people int No
outcomes int No

2.6.2 Table calibration_summary

Field Type Key
performance_id int No
evaluation varchar No
prediction_threshold float No
person_count_at_risk int No
person_count_with_outcome int No
average_predicted_probability float No
st_dev_predicted_probability float No
min_predicted_probability float No
p_25_predicted_probability float No
median_predicted_probability float No
p_75_predicted_probability float No
max_predicted_probability float No
observed_incidence float No

2.6.3 Table cohort_definition

Field Type Key
cohort_definition_id bigint No
cohort_name varchar No
description text No
json text No
sql_command text No

2.6.4 Table cohorts

Field Type Key
cohort_id int Yes
cohort_definition_id bigint No
cohort_name varchar No

2.6.5 Table covariate_settings

Field Type Key
covariate_setting_id int Yes
covariate_settings_json text No

2.6.6 Table covariate_summary

Field Type Key
performance_id int No
covariate_id bigint No
covariate_name varchar No
concept_id float No
covariate_value float No
covariate_count int No
covariate_mean float No
covariate_st_dev float No
with_no_outcome_covariate_count int No
with_no_outcome_covariate_mean float No
with_no_outcome_covariate_st_dev float No
with_outcome_covariate_count int No
with_outcome_covariate_mean float No
with_outcome_covariate_st_dev float No
standardized_mean_diff float No

2.6.7 Table database_details

Field Type Key
database_id int Yes
database_meta_data_id varchar No

2.6.8 Table database_meta_data

Field Type Key
database_id varchar Yes
cdm_source_name varchar No
cdm_source_abbreviation varchar No
cdm_holder varchar No
source_description text No
source_documentation_reference varchar No
cdm_etl_reference varchar No
source_release_date varchar No
cdm_release_date varchar No
cdm_version varchar No
vocabulary_version varchar No
max_obs_period_end_date varchar No

2.6.9 Table demographic_summary

Field Type Key
performance_id int No
evaluation varchar No
age_group varchar No
gen_group varchar No
person_count_at_risk int No
person_count_with_outcome int No
average_predicted_probability float No
st_dev_predicted_probability float No
min_predicted_probability float No
p_25_predicted_probability float No
p_50_predicted_probability float No
p_75_predicted_probability float No
max_predicted_probability float No

2.6.10 Table diagnostic_designs

Field Type Key
diagnostic_id int Yes
probast_id varchar No
value varchar No

2.6.11 Table diagnostic_outcomes

Field Type Key
diagnostic_id int No
xvalue int No
outcome_percent float No
aggregation varchar No
probast_id varchar No
input_type varchar No

2.6.12 Table diagnostic_participants

Field Type Key
diagnostic_id int No
design varchar No
metric varchar No
value float No
probast_id varchar No

2.6.13 Table diagnostic_predictors

Field Type Key
diagnostic_id int No
days_to_event int No
outcome_at_time int No
observed_at_start_of_day bigint No
input_type varchar No

2.6.14 Table diagnostic_summary

Field Type Key
diagnostic_id int No
probast_id varchar No
result_value varchar No

2.6.15 Table diagnostics

Field Type Key
diagnostic_id int Yes
model_design_id int No
database_id int No
execution_date_time varchar No

2.6.16 Table evaluation_statistics

Field Type Key
performance_id int No
evaluation varchar No
metric varchar No
value float No

2.6.17 Table feature_engineering_settings

Field Type Key
feature_engineering_setting_id int Yes
feature_engineering_settings_json text No

2.6.18 Table model_designs

Field Type Key
model_design_id int Yes
target_id int No
outcome_id int No
tar_id int No
plp_data_setting_id int No
population_setting_id int No
model_setting_id int No
covariate_setting_id int No
sample_setting_id int No
split_setting_id int No
feature_engineering_setting_id int No
tidy_covariates_setting_id int No

2.6.19 Table model_settings

Field Type Key
model_setting_id int Yes
model_type varchar No
model_settings_json varchar No

2.6.20 Table models

Field Type Key
model_id int Yes
analysis_id varchar No
model_design_id int No
database_id int No
model_type varchar No
plp_model_file text No
train_details text No
preprocessing text No
execution_date_time varchar No
training_time varchar No
intercept float No

2.6.21 Table performances

Field Type Key
performance_id int Yes
model_design_id int No
development_database_id int No
validation_database_id int No
target_id int No
outcome_id int No
tar_id int No
plp_data_setting_id int No
population_setting_id int No
model_development int No
execution_date_time varchar No
plp_version varchar No

2.6.22 Table plp_data_settings

Field Type Key
plp_data_setting_id int Yes
plp_data_settings_json text No

2.6.23 Table population_settings

Field Type Key
population_setting_id int Yes
population_settings_json text No

2.6.24 Table prediction_distribution

Field Type Key
performance_id int No
evaluation varchar No
class_label int No
person_count int No
average_predicted_probability float No
st_dev_predicted_probability float No
min_predicted_probability float No
p_05_predicted_probability float No
p_25_predicted_probability float No
median_predicted_probability float No
p_75_predicted_probability float No
p_95_predicted_probability float No
max_predicted_probability float No

2.6.25 Table recalibrations

Field Type Key
recalibration_id int Yes
original_model_id int No
recalibrated_model_id int No
recalibration_type varchar No
recalibration_json varchar No

2.6.26 Table sample_settings

Field Type Key
sample_setting_id int Yes
sample_settings_json text No

2.6.27 Table split_settings

Field Type Key
split_setting_id int Yes
split_settings_json text No

2.6.28 Table tars

Field Type Key
tar_id int Yes
tar_start_day int No
tar_start_anchor varchar No
tar_end_day int No
tar_end_anchor varchar No

2.6.29 Table threshold_summary

Field Type Key
performance_id int No
evaluation varchar No
prediction_threshold float No
preference_threshold float No
positive_count int No
negative_count int No
true_count int No
false_count int No
true_positive_count int No
true_negative_count int No
false_positive_count int No
false_negative_count int No
f_1_score float No
accuracy float No
sensitivity float No
false_negative_rate float No
false_positive_rate float No
specificity float No
positive_predictive_value float No
false_discovery_rate float No
negative_predictive_value float No
false_omission_rate float No
positive_likelihood_ratio float No
negative_likelihood_ratio float No
diagnostic_odds_ratio float No

2.6.30 Table tidy_covariates_settings

Field Type Key
tidy_covariates_setting_id int Yes
tidy_covariates_settings_json text No

2.7 Fields with minimum values

Some fields contain patient counts or fractions that are easily converted to patient counts. To prevent identifiability, these fields are subject to a minimum value. When the value falls below this minimum, it is replaced with the negative value of the minimum. For example, if the minimum subject count is 5, and the actual count is 2, the value stored in the data model will be -5, which could be represented as ‘<5’ to the user. Note that the value 0 is permissible, as it identifies no persons.