Identify Characteristics of Patients in the OMOP Common Data Model

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Documentation for package ‘PatientProfiles’ version 1.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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addAge	Compute the age of the individuals at a certain date
addAgeQuery	Query to add the age of the individuals at a certain date
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
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	Function to disconnect from the mock
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", "binary", "date", or NA.