D3_PERSONS

contains the cleaned version of PERSONS, where birth date and death date are reconstituted as dates

D3_events_DEATH

D3_output_spells_category

contains the spells exited from CreateSpells, i.e., all the continuous spells of observation period of each person, stratified per op_meaning op_meaning is by default the same for all observation periods, and is set in 05_subpopulations_restricting_meanings for those data sources where the analysis is conducted on subpopulations having different sets of data banks

conceptsetdataset

these are multiple datasets, one per each conceptset, which is a value in the list c(conceptsets_exact_matching, conceptsets_children_matching), set in 07_algorithms. Each conceptset dataset is named after the conceptset. Each conceptset is associated to a list of codes. The dataset is obtained by retrieving records from the CDM bearing a code that match one of the codes in the codelist. The matching can be exact (for the conceptsets in conceptsets_exact_matching) or per ascendant (for conceptsets in conceptsets_children_matching) . Records are retrieved from the EVENTS table, but also from other tables which may bear a record, such as PROCEDURES or VACCINES

itemsetdataset

promptsetdataset

D3_clean_vaccines

This dataset contains all the records of a COVID vaccine, including their imputation and modifications and exclusion criteria. Exclusion criteria must be applied before using the variable in the next steps

D3_vaccines_curated

This dataset contains only the records of a COVID vaccine that enter the study

D5_Flowchart_criteria_for_doses

Flowchart of the exlusion of covid vaccines records

D3_clean_all_vaccines

This dataset contains the records of all the curated doses of all vaccines in the instance listed in Table 4 of the SAP, including the curated covid vaccines. It is obtained from the original conceptsets datastes by replicating each vaccination record as many times as the indicators that it is used for, see the first example in the tab Example: a record with Vacco Id DIP-HIB-PER-POL-TET is replicated 3 times, once per the indicator DPT, once per the indicator HiB, and once for the indicator Pol. Then, each record is labelled with various exclusion citeria, most importantly, records with dats 30 daya apart form a previous record as marked as 'duplicates'. In the next step, all the record labelled as 'removed row' will be removed

D3_all_vaccines_curated

This dataset contains the records of all the curated doses of all roots of indicators in the instance listed in Table 7 of the SAP. Doses of covid vaccines are included. It is obtained by D3_clean_all_vaccines by excluding records that are duplicates or of bad quality, and after appending the curated covid vaccines

D5_Flowchart_criteria_for_all_vaccines

D3_clean_spells

D3_selection_criteria_from_PERSONS_to_source_population

D4_source_population

contains the cohort of persons in the data source where the, study cohorts will be nested

Flowchart_exclusion_criteria

D3_cohort_ImmDis

Metadata Data Model Parameters Example Example HT Example_EN Example HT sensitivity {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D3_cohort_{ImmDis}","Persons in the source population that have at least a code of {ImmDis} during study period, with selection crieria and date of entrance and start of followup in the cohort of each group of prompts"

Flowchart_exclusion_criteria_ImmDis

D3_components_flare_TD_ImmDis

D3_flares_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D3_flares_{ImmDis}","Persons that enter the follow up in the cohort of {ImmDis}, with all their flares happened after entrance in the cohort (including before starting followup)","persons that are in the cohort of {ImmDis} with entering_follow_up_{ImmDis} == 1"

D3_events_SECCOMP_complex

D3_TD_condition

D3_followup_periods_in_cohort_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D3_followup_periods_in_cohort_{ImmDis}","Persons that are in the cohort of {ImmDis}, with all periods of follow-up","persons that are in the cohort of {ImmDis} with entering_follow_up_{ImmDis} == 1","D3_cohort_{ImmDis} where entering_follow_up_{ImmDis} == 1"

D3_pregnancy_while_in_followup_periods_in_cohort_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D3_pregnancy_while_in_followup_periods_in_cohort_{ImmDis}","Pregnancies that overlap period(s) while the oerson is in follow-up in the cohort of {ImmDis}","D3_pregnancy_final","D3_pregnancy_final","as many as the distinct periods of follow up that overlap the pregnancy","= 0"

D3_TD_pregnancy_during_followup_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D3_TD_pregnancy_during_followup_{ImmDis}","Time-dependent dataset stating when a person in follow-up in the cohort of {ImmDis} is pregnant. Unlike inD3_pregnancy_while_in_followup_periods_in_cohort_{ImmDis}, in this dataset there is no memory of which oregnancy is involved, this dataset is only meant to label person-time in followup as pregnant or non-pregnant"

D3_followup_periods_in_cohort_with_pregnancy_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D3_followup_periods_in_cohort_with_pregnancy_{ImmDis}","Persons that are in the cohort of {ImmDis}, with all periods of follow-up","persons that are in the cohort of {ImmDis} with entering_follow_up_{ImmDis} == 1","D3_cohort_{ImmDis} where entering_follow_up_{ImmDis} == 1"

D4_persontime_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D4_persontime_{ImmDis}","Persontime in the follow up of {ImmDis}, with 1st, 2nd, and 3rd flares, per strata of gender and age. Use CountPersonTime on D3_followup_periods_in_cohort_{ImmDis} and D3_flares_{ImmDis}, with birth date from D3_PERSONS to create the strata oif ageband"

D4_persontime_Cube_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D4_persontime_Cube_{ImmDis}","Persontime in the follow up of {ImmDis}, with flares, per strata of gender and age, incuding hyerarcical partial sums (all genders, all agebands).","hyerarchies of strata of age and gender"

D4_population_Cube_ImmDis

D4_analytical_dataset_KM_ImmDis

Metadata Data Model Parameters Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D4_analytical_dataset_KM_{ImmDis}","Persons that are in the cohort of {ImmDis}, with first periods of follow-up and flare (if any): this is the analytical dataset that enters the calculation of cumulative incidence at 180 days and at 365 days.

D4_components_flare_ImmDis

D5_Table_1_Attrition_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_1_Attrition_{ImmDis}","Attrition table for the cohort of the disease {ImmDis}","datasource",null,"1","1","datasource","datasource","{ImmDis}",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"8253986f1e8616adaf4e8a4c519c1895"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["ds","n_1_","n_2_","p_2_","n_3_","p_3","n_4_","p_4_","n_5_","p_5_","n_6_","p_6_","n_7_","p_7_","n_8_","p_8_","n_9_","p_9_","n_10_","p_10_"],"Description":["data source name, as stored in CDM_SOURCE, plus possible specification of subpopulation","Total persons in the data instance"

D5_Table_2_Cohort_characteristics_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_2_Cohort_characteristics_{ImmDis}",null,"datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"983b2cf27b366b5a9fd886af35b9999b"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["ds","n_1_","n_2_","p_2_","n_3_","p_3","n_4_","p_4_","pc_5_","pc_6_","pc_7_","n_8_","p_8_","n_9_","p_9_","n_10_","p_10_","n_11_","p_11_","py_12"],"Description":["data source name, as stored in CDM_SOURCE, plus possible specification of subpopulation","Total cohort population","Female (n/%)","n_2 as a % of the total cohort population"

D5_Table_3_Covariates_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_3_Covariates_{ImmDis}",null,"datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"891c19ae080f9dd66c307005d001f738"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["ds","n_1_","n_{Cov_{ImmDis}_{j}}_","p_{Cov_{ImmDis}_{j}}_",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Description":["data source name, as stored in CDM_SOURCE, plus possible specification of subpopulation","Total cohort population","Female (n/%)","n_{Cov{ImmDis}{j}}_ as a % of the total cohort population"

D5_Table_4_IR_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_4_IR_{ImmDis}","IR of flares (first, second, third)","datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"5bfa67a8f6a04d94a6f395a2e39be2fb"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["ds","n_1_","n_2_","py_0_","n3_","py_1_","m_1_0_","ir_1_","ll_1_","ul_1_","npr_1_","pypr_1_","mpr_1_","irpr_1_","llpr_1","ulpr_1","n_1_2_","m_2_0_","ir_2_","ll_2_"],"Description":["data source name, as stored in CDM_SOURCE, plus possible specification of subpopulation","Total cohort population","Number of persons who started the follow-up 90 days after the inclusion to the cohort"

D5_Table_5_IR_ImmDis_stratum

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_5_IR_{ImmDis}_{stratum}","IR of flares (first, second, third), in varioud strata of the population","datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"f5cabd740c8202e15d1de76dc13569da"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["ds","n_1_","n_2_","py_0_","n3_","py_1_","m_1_0_","ir_1_","ll_1_","ul_1_","npr_1_","pypr_1_","mpr_1_","irpr_1_","llpr_1","ulpr_1","n_1_2_","m_2_0_","ir_2_","ll_2_"],"Description":["data source name, as stored in CDM_SOURCE, plus possible specification of subpopulation"

D5_Table_6_Impact_of_component_flare_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_9_Impact_of_component_flare_{ds}_{ImmDis}","Impact on the cumulative incidence of first flare of {ImmDis} of combining the building blocks in the algorithm","Algorithm entering the analysis",null,"1","1","Algorithm","Algorithm","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"e83ff358bcde09060b9e55c54aea5ca8"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["Algorithms","N","Total in the component (left-hand OR right-hand)"

D5_Table_7_cumulative_incidence_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_7_cumulative_incidence_{ImmDis}","cumulative indicence of flares of {ImmDis}, at 6 and at 12 months","datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"b4ce4d8432553c94bfac4e177f83af72"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["period","ageband","gender","ci_","ll_","ul_",null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Description":["period when the cumulative incidence is calculated","ageband","gender","cumulative incidence","lower limit of confidence interval 95%"

D5_data_KM_figure_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_data_KM_figure_{ImmDis}","daily survival probability of {ImmDis} until 365 days","datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"2fb1eed52a0aa733d8320ea78fbe40d0"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["day","surv",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Description":["day of followup from 1 to 365","probability of survival",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Format":["integer","double",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Vocabulary":["1-365",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Description / Notes":[null,"3 digit",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Parameters":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"Source tables and variables"

D5_Table_8_Impact_of_ablation_cohort_ImmDis

Metadata Data Model Parameters Augmented shell table Example {"x":{"tag":{"name":"Reactable","attribs":{"data":{"metadata_name":["Name of the dataset","Content of the dataset","Unit of observation","Dataset where the list of UoOs is fully listed and with 1 record per UoO","How many observations per UoO","NxUoO","Variables capturing the UoO","Primary key","Parameters",null,null,null,null,null,null,null,null,null,null,null],"metadata_content":["D5_Table_8_Impact_of_ablation_cohort_{ImmDis}","Impact of using selected prompts on number of participants persons and delay of entrance in the cohort of {ImmDis}","datasource",null,"1","1","datasource","datasource","ImmDis",null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"metadata_name","name":"metadata_name","type":"character"},{"id":"metadata_content","name":"metadata_content","type":"character"}],"sortable":false,"searchable":true,"pagination":false,"highlight":true,"bordered":true,"striped":true,"style":{"maxWidth":1800},"height":"600px","dataKey":"62d24e57211dd3bdfde8690627e31745"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]} {"x":{"tag":{"name":"Reactable","attribs":{"data":{"Varname":["ds","n_1","n_1_{group_of_prompts}","p_1_{group_of_prompts}","n_2","n_2_{group_of_prompts}","n_3","n_3_{group_of_prompts}","n_4","n_4_{group_of_prompts}","n_4_main_not_{group_of_prompts}","p_4_main_not_{group_of_prompts}","n_4_both_{group_of_prompts}","p_4_both_{group_of_prompts}","median_time_to_entry_main","p25_time_to_entry_main","p75_time_to_entry_main","median_time_to_entry_{group_of_prompts}","p25_time_to_entry_{group_of_prompts}","p75_time_to_entry_{group_of_prompts}"],"Description":["data source name, as stored in CDM_SOURCE, plus possible specification of subpopulation"

D6_Table_1_Attrition_ImmDis

D6_Table_2_Cohort_characteristics_ImmDis

D6_Table_3_Covariates_ImmDis

D6_Table_4_IR_ImmDis

D6_Table_7_cumulative_incidence_ImmDis

D6_Table_8_Impact_of_ablation_cohort_ImmDis

Figure_ablation_ImmDis

Section_10.X_ImmDis