Package index • PatientProfiles

Add patient characteristics to a table in the OMOP Common Data Model

addAge(): Compute the age of the individuals at a certain date
addSex(): Compute the sex of the individuals
addDateOfBirth(): Add a column with the individual birth date
addPriorObservation(): Compute the number of days of prior observation in the current observation period at a certain date
addFutureObservation(): Compute the number of days till the end of the observation period at a certain date
addInObservation(): Indicate if a certain record is within the observation period
addBirthday() experimental: Add the birth day of an individual to a table

Add a set of patient characteristics to a table in the OMOP Common Data Model

Add patient death information to a table in the OMOP Common Data Model

addDeathDate(): Add date of death for individuals. Only death within the same observation period than indexDate will be observed.
addDeathDays(): Add days to death for individuals. Only death within the same observation period than indexDate will be observed.
addDeathFlag(): Add flag for death for individuals. Only death within the same observation period than indexDate will be observed.

Add the first or last cohort or concept event in a window, together with its date or days relative to an index date.

addCohortEventDate(): Add the first or last cohort event and its date
addCohortEventDays(): Add the first or last cohort event and its relative days
addConceptEventDate(): Add the first or last concept event and its date
addConceptEventDays(): Add the first or last concept event and its relative days

Add a variable indicating the intersection between a table in the OMOP Common Data Model and a cohort table.

addCohortIntersectCount(): It creates columns to indicate number of occurrences of intersection with a cohort
addCohortIntersectDate(): Date of cohorts that are present in a certain window
addCohortIntersectDays(): It creates columns to indicate the number of days between the current table and a target cohort
addCohortIntersectField(): It creates a column with the field of a desired intersection
addCohortIntersectFlag(): It creates columns to indicate the presence of cohorts

Add a variable indicating the intersection between a table in the OMOP Common Data Model and a concept.

addConceptIntersectCount(): It creates column to indicate the count overlap information between a table and a concept
addConceptIntersectDate(): It creates column to indicate the date overlap information between a table and a concept
addConceptIntersectDays(): It creates column to indicate the days of difference from an index date to a concept
addConceptIntersectField(): It adds a custom column (field) from the intersection with a certain table subsetted by concept id. In general it is used to add the first value of a certain measurement.
addConceptIntersectFlag(): It creates column to indicate the flag overlap information between a table and a concept

Add a variable indicating the intersection between a table in the OMOP Common Data Model and a standard omop table.

addTableIntersectCount(): Compute number of intersect with an omop table.
addTableIntersectDate(): Compute date of intersect with an omop table.
addTableIntersectDays(): Compute time to intersect with an omop table.
addTableIntersectField(): Intersecting the cohort with columns of an OMOP table of user's choice. It will add an extra column to the cohort, indicating the intersected entries with the target columns in a window of the user's choice.
addTableIntersectFlag(): Compute a flag intersect with an omop table

These functions add the same information than their analogous add* function but, the result is not computed into a table.

addAgeQuery(): Query to add the age of the individuals at a certain date
addBirthdayQuery() experimental: Add the birth day of an individual to a table
addDateOfBirthQuery(): Query to add a column with the individual birth date
addDemographicsQuery(): Query to add demographic characteristics at a certain date
addFutureObservationQuery(): Query to add the number of days till the end of the observation period at a certain date
addInObservationQuery(): Query to add a new column to indicate if a certain record is within the observation period
addObservationPeriodIdQuery(): Add the ordinal number of the observation period associated that a given date is in. Result is not computed, only query is added.
addPriorObservationQuery(): Query to add the number of days of prior observation in the current observation period at a certain date
addSexQuery(): Query to add the sex of the individuals

Function that allow the user to summarise patient characteristics (characteristics must be added priot the use of the function)

summariseResult(): Summarise variables using a set of estimate functions. The output will be a formatted summarised_result object.

Function that allow the user to suppress counts and estimates for a certain minCellCount

Function that allow the user to create new OMOP CDM mock data

mockDisconnect(): Deprecated
mockPatientProfiles(): It creates a mock database for testing PatientProfiles package

Helper functions

benchmarkPatientProfiles(): Benchmark intersections and demographics functions for a certain source (cdm).
addCohortName(): Add cohort name for each cohort_definition_id
addConceptName(): Add concept name for each concept_id
addCdmName(): Add cdm name
addCategories(): Categorize a numeric variable
addObservationPeriodId(): Add the ordinal number of the observation period associated that a given date is in.
filterCohortId(): Filter a cohort according to cohort_definition_id column, the result is not computed into a table. only a query is added. Used usually as internal functions of other packages.
filterInObservation(): Filter the rows of a cdm_table to the ones in observation that indexDate is in observation.
variableTypes(): Classify the variables between 5 types: "numeric", "categorical", "logical", "date", "integer", or NA.
availableEstimates(): Show the available estimates that can be used for the different variable_type supported.
startDateColumn(): Get the name of the start date column for a certain table in the cdm
endDateColumn(): Get the name of the end date column for a certain table in the cdm
sourceConceptIdColumn(): Get the name of the source concept_id column for a certain table in the cdm
standardConceptIdColumn(): Get the name of the standard concept_id column for a certain table in the cdm