Identify Characteristics of Patients in the OMOP Common Data Model

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Documentation for package ‘PatientProfiles’ version 0.8.0

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

Help Pages

addAge	Compute the age of the individuals at a certain date
addCategories	Categorize a numeric variable
addCdmName	Add cdm name
addCohortIntersect	Compute the intersect with a target cohort, you can compute the number of occurrences, a flag of presence, a certain date and/or the time difference
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
addConceptIntersect	It creates columns to indicate overlap information between a table 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
addConceptIntersectFlag	It creates column to indicate the flag overlap information between a table and a concept
addDateOfBirth	Add a column with the individual birth date
addDeathDate	Add date of death for individuals. Only death within the same observation period than 'indeDate' will be observed.
addDeathDays	Add days to death for individuals. Only death within the same observation period than 'indeDate' will be observed.
addDeathFlag	Add flag for death for individuals. Only death within the same observation period than 'indeDate' will be observed.
addDemographics	Compute demographic characteristics 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
addIntersect	It creates columns to indicate overlap information between two tables
addLargeScaleCharacteristics	This function is used to add columns with the large scale characteristics of a cohort table.
addPriorObservation	Compute the number of days of prior observation in the current observation period at a certain date
addSex	Compute the sex of the individuals
addTableIntersect	Compute the intersect with an omop table, you can compute the number of occurrences, a flag of presence, a certain date, the time difference and/or obtain a certain column.
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.
assertNameStyle	Assert whether a nameStyle contains the needed information.
availableEstimates	Show the available estimates that can be used for the different variable_type supported.
availableFunctions	Show the available functions for the 4 classifications of data that are supported (numeric, date, binary and categorical)
endDateColumn	Get the name of the end date column for a certain table in the cdm
formatCharacteristics	Format a summarised_characteristics object into a visual table.
gtCharacteristics	Create a gt table from a summarisedCharacteristics object.
gtResult	Create a gt table from a summary object.
mockPatientProfiles	It creates a mock database for testing PatientProfiles package
optionsTableCharacteristics	Additional arguments for the function tableCharacteristics.
optionsTableCohortOverlap	Additional arguments for the function tableCohortOverlap.
optionsTableCohortTiming	Additional arguments for the function tableCohortTiming.
plotCharacteristics	Create a ggplot from the output of summariseCharacteristics. 'r lifecycle::badge("deprecated")'
plotCohortIntersect	Plot summariseCohortIntersect output.
plotCohortOverlap	Plot the result of summariseCohortOverlap.
plotCohortTiming	Plot summariseCohortTiming results.
plotDemographics	Plot summariseDemographics output.
plotLargeScaleCharacteristics	create a ggplot from the output of summariseLargeScaleCharacteristics.
plotTableIntersect	Plot summariseTableIntersect output.
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
summariseCharacteristics	Summarise characteristics of individuals
summariseCohortCounts	Summarise counts for each different cohort. You can add a list of stratifications.
summariseCohortIntersect	Summarise cohort intersection information
summariseCohortOverlap	Summarise cohort overlap
summariseCohortTiming	Summarise cohort timing
summariseConceptIntersect	Summarise concept intersect with a cohort_table
summariseDemographics	Summarise demographics of individuals
summariseLargeScaleCharacteristics	This function is used to summarise the large scale characteristics of a cohort table
summariseResult	Summarise variables using a set of estimate functions. The output will be a formatted summarised_result object.
summariseTableIntersect	Summarise table intersection information
tableCharacteristics	Format a summarised_characteristics object into a visual table.
tableCohortIntersect	Format a summariseCohortIntersect result into a visual table.
tableCohortOverlap	Format a summariseOverlapCohort result into a visual table.
tableCohortTiming	Format a summariseCohortTiming result into a visual table.
tableDemographics	Format a summariseDemographics result into a visual table.
tableLargeScaleCharacteristics	Format a summarised_large_scale_characteristics object into a visual table.
tableTableIntersect	Format a summariseTableIntersect result into a visual table.
variableTypes	Classify the variables between 5 types: "numeric", "categorical", "binary", "date", or NA.