R: Identify Characteristics of Patients in the OMOP Common Data Model

# Identify Characteristics of Patients in the OMOP Common Data Model

## Documentation for package ‘PatientProfiles’ version 1.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

addAge | Compute the age of the individuals at a certain date
addAgeQuery | Query to add the age of the individuals at a certain date
addBirthday | Add the birth day of an individual to a table
addBirthdayQuery | Add the birth day of an individual to a table
addCategories | Categorize a numeric variable
addCdmName | Add cdm name
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
addCohortName | Add cohort name for each cohort_definition_id
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
addConceptName | Add concept name for each concept_id
addDateOfBirth | Add a column with the individual birth date
addDateOfBirthQuery | Query to add a column with the individual birth date
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.
addDemographics | Compute demographic characteristics at a certain date
addDemographicsQuery | Query to add demographic characteristics at a certain date
addFutureObservation | Compute the number of days till the end of the observation period at a certain date
addFutureObservationQuery | Query to add 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
addInObservationQuery | Query to add a new column to indicate if a certain record is within the observation period
addObservationPeriodId | Add the ordinal number of the observation period associated that a given date is in.
addObservationPeriodIdQuery | Add the ordinal number of the observation period associated that a given date is in. Result is not computed, only query is added.
addPriorObservation | Compute the number of days of prior observation in the current observation period at a certain date
addPriorObservationQuery | Query to add the number of days of prior observation in the current observation period at a certain date
addSex | Compute the sex of the individuals
addSexQuery | Query to add the sex of the individuals
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.
availableEstimates | Show the available estimates that can be used for the different variable_type supported.
benchmarkPatientProfiles | Benchmark intersections and demographics functions for a certain source (cdm).
endDateColumn | Get the name of the end date column for a certain table in the cdm
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.
mockDisconnect | Deprecated
mockPatientProfiles | It creates a mock database for testing PatientProfiles package
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
startDateColumn | Get the name of the start date column for a certain table in the cdm
summariseResult | Summarise variables using a set of estimate functions. The output will be a formatted summarised_result object.
variableTypes | Classify the variables between 5 types: "numeric", "categorical", "logical", "date", "integer", or NA.