Package: PatientProfiles 1.5.0

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_1.5.0.tar.gz
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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:

9.80 score 2 stars 13 packages 428 scripts 1.5k downloads 54 exports 27 dependencies

Last updated from:e5f1c2d600. Checks:9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel-x86_64	OK	216
source / vignettes	OK	389
linux-release-x86_64	OK	269
macos-release-arm64	OK	140
macos-oldrel-arm64	OK	183
windows-devel	OK	281
windows-release	OK	215
windows-oldrel	OK	233
wasm-release	OK	140

Exports:addAge addAgeQuery addBirthday addBirthdayQuery addCategories addCdmName addCohortIntersectCount addCohortIntersectDate addCohortIntersectDays addCohortIntersectField addCohortIntersectFlag addCohortName addConceptIntersectCount addConceptIntersectDate addConceptIntersectDays addConceptIntersectField addConceptIntersectFlag addConceptName addDateOfBirth addDateOfBirthQuery addDeathDate addDeathDays addDeathFlag addDemographics addDemographicsQuery addFutureObservation addFutureObservationQuery addInObservation addInObservationQuery addObservationPeriodId addObservationPeriodIdQuery addPriorObservation addPriorObservationQuery addSex addSexQuery addTableIntersectCount addTableIntersectDate addTableIntersectDays addTableIntersectField addTableIntersectFlag availableEstimates benchmarkPatientProfiles endDateColumn filterCohortId filterInObservation mockDisconnect mockPatientProfiles settings sourceConceptIdColumn standardConceptIdColumn startDateColumn summariseResult suppress variableTypes

Dependencies:blob cli clock cpp11 DBI dbplyr dplyr generics glue lifecycle magrittr omopgenerics pillar pkgconfig purrr R6 rlang snakecase stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs withr

Adding cohort intersections

Introduction | Identifying cohort intersections | Options for identifying cohort intersection | Naming conventions for new variables

Rendered fromcohort-intersect.Rmdusingknitr::rmarkdown

Last update: 2025-10-02
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: 2025-10-02
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: 2025-10-02
Started: 2024-04-09

Summarise result

Introduction | Variables type | Estimates names | Summarise our first table

Rendered fromsummarise.Rmdusingknitr::rmarkdown

Last update: 2025-10-02
Started: 2024-04-09

Adding table intersections

Rendered fromtable-intersect.Rmdusingknitr::rmarkdown

Last update: 2025-10-02
Started: 2024-04-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute the age of the individuals at a certain date	addAge
Query to add the age of the individuals at a certain date	addAgeQuery
Add the birth day of an individual to a table	addBirthday
Add the birth day of an individual to a table	addBirthdayQuery
Categorize a numeric variable	addCategories
Add cdm name	addCdmName
It creates columns to indicate number of occurrences of intersection with a cohort	addCohortIntersectCount
Date of cohorts that are present in a certain window	addCohortIntersectDate
It creates columns to indicate the number of days between the current table and a target cohort	addCohortIntersectDays
It creates a column with the field of a desired intersection	addCohortIntersectField
It creates columns to indicate the presence of cohorts	addCohortIntersectFlag
Add cohort name for each cohort_definition_id	addCohortName
It creates column to indicate the count overlap information between a table and a concept	addConceptIntersectCount
It creates column to indicate the date overlap information between a table and a concept	addConceptIntersectDate
It creates column to indicate the days of difference from an index date to a concept	addConceptIntersectDays
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 concept	addConceptIntersectFlag
Add concept name for each concept_id	addConceptName
Add a column with the individual birth date	addDateOfBirth
Query to add a column with the individual birth date	addDateOfBirthQuery
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 date	addDemographics
Query to add demographic characteristics at a certain date	addDemographicsQuery
Compute the number of days till the end of the observation period at a certain date	addFutureObservation
Query to add the number of days till the end of the observation period at a certain date	addFutureObservationQuery
Indicate if a certain record is within the observation period	addInObservation
Query to add a new column to indicate if a certain record is within the observation period	addInObservationQuery
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 date	addPriorObservation
Query to add the number of days of prior observation in the current observation period at a certain date	addPriorObservationQuery
Compute the sex of the individuals	addSex
Query to add the sex of the individuals	addSexQuery
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 table.	addTableIntersectFlag
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 cdm	endDateColumn
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
Deprecated	mockDisconnect
It creates a mock database for testing PatientProfiles package	mockPatientProfiles
Get the name of the source concept_id column for a certain table in the cdm	sourceConceptIdColumn
Get the name of the standard concept_id column for a certain table in the cdm	standardConceptIdColumn
Get the name of the start date column for a certain table in the cdm	startDateColumn
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

Usage by other packages (reverse dependencies)