Package: PatientProfiles 1.6.1

Martí Català

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

Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.

Authors:Martí Català [aut, cre], Yuchen Guo [aut], Mike Du [aut], Kim Lopez-Guell [aut], Edward Burn [aut], Nuria Mercade-Besora [aut], Xintong Li [ctb], Xihang Chen [ctb]

PatientProfiles_1.6.1.tar.gz
PatientProfiles_1.6.1.zip(r-4.7-any)PatientProfiles_1.6.1.zip(r-4.6-any)PatientProfiles_1.6.1.zip(r-4.5-any)
PatientProfiles_1.6.1.tgz(r-4.6-any)PatientProfiles_1.6.1.tgz(r-4.5-any)
PatientProfiles_1.6.1.tar.gz(r-4.7-any)PatientProfiles_1.6.1.tar.gz(r-4.6-any)
PatientProfiles_1.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PatientProfiles/json (API)

# Install 'PatientProfiles' in R:
install.packages('PatientProfiles', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/patientprofiles/issues

Pkgdown/docs site:https://darwin-eu.github.io

On CRAN:

Conda:

9.81 score 2 stars 14 packages 356 scripts 1.5k downloads 58 exports 27 dependencies

Last updated from:c7049da0b1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK293
source / vignettesOK451
linux-releaseOK266
macos-releaseOK219
macos-oldrelOK204
windows-develOK226
windows-releaseOK216
windows-oldrelOK216
wasm-releaseOK159

Exports:addAgeaddAgeQueryaddBirthdayaddBirthdayQueryaddCategoriesaddCdmNameaddCohortEventDateaddCohortEventDaysaddCohortIntersectCountaddCohortIntersectDateaddCohortIntersectDaysaddCohortIntersectFieldaddCohortIntersectFlagaddCohortNameaddConceptEventDateaddConceptEventDaysaddConceptIntersectCountaddConceptIntersectDateaddConceptIntersectDaysaddConceptIntersectFieldaddConceptIntersectFlagaddConceptNameaddDateOfBirthaddDateOfBirthQueryaddDeathDateaddDeathDaysaddDeathFlagaddDemographicsaddDemographicsQueryaddFutureObservationaddFutureObservationQueryaddInObservationaddInObservationQueryaddObservationPeriodIdaddObservationPeriodIdQueryaddPriorObservationaddPriorObservationQueryaddSexaddSexQueryaddTableIntersectCountaddTableIntersectDateaddTableIntersectDaysaddTableIntersectFieldaddTableIntersectFlagavailableEstimatesbenchmarkPatientProfilesendDateColumnfilterCohortIdfilterInObservationmockDisconnectmockPatientProfilessettingssourceConceptIdColumnstandardConceptIdColumnstartDateColumnsummariseResultsuppressvariableTypes

Dependencies:blobcliclockcpp11DBIdbplyrdplyrgenericsgluelifecyclemagrittromopgenericspillarpkgconfigpurrrR6rlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrswithr

Adding cohort intersections
Introduction | Identifying cohort intersections | Options for identifying cohort intersection | Naming conventions for new variables
Rendered fromcohort-intersect.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2024-04-09

Adding concept intersections
Introduction | Adding variables from concept sets | Adding multiple concept based variables | Cohort-based versus concept-based intersections
Rendered fromconcept-intersect.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2024-04-09

Adding patient demographics
Introduction | Adding characteristics to OMOP CDM tables | Adding characteristics to a cohort tables | Getting multiple characteristics at once
Rendered fromdemographics.rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2024-04-09

Adding first or last events
Introduction | Finding a cohort event | Finding a concept event | First, last, and censoring | Events occurring on the same date | Multiple windows and column names
Rendered fromevent.rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2026-08-05

Summarise result
Introduction | Variables type | Estimates names | Summarise our first table
Rendered fromsummarise.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2024-04-09

Adding table intersections
Rendered fromtable-intersect.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2024-04-09

Readme and manuals

Help Manual

Help pageTopics
Compute the age of the individuals at a certain dateaddAge
Query to add the age of the individuals at a certain dateaddAgeQuery
Add the birth day of an individual to a tableaddBirthday
Add the birth day of an individual to a tableaddBirthdayQuery
Categorize a numeric variableaddCategories
Add cdm nameaddCdmName
Add the first or last cohort event and its dateaddCohortEventDate
Add the first or last cohort event and its relative daysaddCohortEventDays
It creates columns to indicate number of occurrences of intersection with a cohortaddCohortIntersectCount
Date of cohorts that are present in a certain windowaddCohortIntersectDate
It creates columns to indicate the number of days between the current table and a target cohortaddCohortIntersectDays
It creates a column with the field of a desired intersectionaddCohortIntersectField
It creates columns to indicate the presence of cohortsaddCohortIntersectFlag
Add cohort name for each cohort_definition_idaddCohortName
Add the first or last concept event and its dateaddConceptEventDate
Add the first or last concept event and its relative daysaddConceptEventDays
It creates column to indicate the count overlap information between a table and a conceptaddConceptIntersectCount
It creates column to indicate the date overlap information between a table and a conceptaddConceptIntersectDate
It creates column to indicate the days of difference from an index date to a conceptaddConceptIntersectDays
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.addConceptIntersectField
It creates column to indicate the flag overlap information between a table and a conceptaddConceptIntersectFlag
Add concept name for each concept_idaddConceptName
Add a column with the individual birth dateaddDateOfBirth
Query to add a column with the individual birth dateaddDateOfBirthQuery
Add date of death for individuals. Only death within the same observation period than 'indexDate' will be observed.addDeathDate
Add days to death for individuals. Only death within the same observation period than 'indexDate' will be observed.addDeathDays
Add flag for death for individuals. Only death within the same observation period than 'indexDate' will be observed.addDeathFlag
Compute demographic characteristics at a certain dateaddDemographics
Query to add demographic characteristics at a certain dateaddDemographicsQuery
Compute the number of days till the end of the observation period at a certain dateaddFutureObservation
Query to add the number of days till the end of the observation period at a certain dateaddFutureObservationQuery
Indicate if a certain record is within the observation periodaddInObservation
Query to add a new column to indicate if a certain record is within the observation periodaddInObservationQuery
Add the ordinal number of the observation period associated that a given date is in.addObservationPeriodId
Add the ordinal number of the observation period associated that a given date is in. Result is not computed, only query is added.addObservationPeriodIdQuery
Compute the number of days of prior observation in the current observation period at a certain dateaddPriorObservation
Query to add the number of days of prior observation in the current observation period at a certain dateaddPriorObservationQuery
Compute the sex of the individualsaddSex
Query to add the sex of the individualsaddSexQuery
Compute number of intersect with an omop table.addTableIntersectCount
Compute date of intersect with an omop table.addTableIntersectDate
Compute time to intersect with an omop table.addTableIntersectDays
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.addTableIntersectField
Compute a flag intersect with an omop tableaddTableIntersectFlag
Show the available estimates that can be used for the different variable_type supported.availableEstimates
Benchmark intersections and demographics functions for a certain source (cdm).benchmarkPatientProfiles
Get the name of the end date column for a certain table in the cdmendDateColumn
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.filterCohortId
Filter the rows of a 'cdm_table' to the ones in observation that 'indexDate' is in observation.filterInObservation
DeprecatedmockDisconnect
It creates a mock database for testing PatientProfiles packagemockPatientProfiles
Get the name of the source concept_id column for a certain table in the cdmsourceConceptIdColumn
Get the name of the standard concept_id column for a certain table in the cdmstandardConceptIdColumn
Get the name of the start date column for a certain table in the cdmstartDateColumn
Summarise variables using a set of estimate functions. The output will be a formatted summarised_result object.summariseResult
Classify the variables between 5 types: "numeric", "categorical", "logical", "date", "integer", or NA.variableTypes