Package index • PatientProfiles

Add individual patient characteristics

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

Add multiple individual patient characteristics

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

addDemographics(): Compute demographic characteristics at a certain date

Add death information

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 a value from a cohort intersection

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

addCohortIntersectFlag(): It creates columns to indicate the presence of cohorts

Add a value from a concept intersection

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 value from an omop standard table intersection

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.

Query functions

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

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

Summarise patient characteristics

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.

Suppress counts of a summarised_result object

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

reexports suppress settings: Objects exported from other packages

Create a mock database with OMOP CDM format data

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

mockDisconnect(): Deprecated

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

Other functions

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", "binary", "date", 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