Package: PatientProfiles 1.2.3

Marti Catala

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:Marti Catala [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_1.2.3.tar.gz
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PatientProfiles.pdf |PatientProfiles.html✨
PatientProfiles/json (API)
NEWS

# 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 site:https://darwin-eu.github.io

On CRAN:

9.71 score 1 stars 10 packages 225 scripts 1.2k downloads 46 exports 40 dependencies

Last updated 2 months agofrom:ea69eac70c. Checks:5 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winNOTEFeb 17 2025
R-4.5-macNOTEFeb 17 2025
R-4.5-linuxNOTEFeb 17 2025
R-4.4-winOKFeb 17 2025
R-4.4-macOKFeb 17 2025
R-4.3-winOKFeb 17 2025
R-4.3-macOKFeb 17 2025

Exports:addAgeaddAgeQueryaddCategoriesaddCdmNameaddCohortIntersectCountaddCohortIntersectDateaddCohortIntersectDaysaddCohortIntersectFlagaddCohortNameaddConceptIntersectCountaddConceptIntersectDateaddConceptIntersectDaysaddConceptIntersectFlagaddDateOfBirthaddDateOfBirthQueryaddDeathDateaddDeathDaysaddDeathFlagaddDemographicsaddDemographicsQueryaddFutureObservationaddFutureObservationQueryaddInObservationaddInObservationQueryaddObservationPeriodIdaddObservationPeriodIdQueryaddPriorObservationaddPriorObservationQueryaddSexaddSexQueryaddTableIntersectCountaddTableIntersectDateaddTableIntersectDaysaddTableIntersectFieldaddTableIntersectFlagavailableEstimatesendDateColumnmockDisconnectmockPatientProfilessettingssourceConceptIdColumnstandardConceptIdColumnstartDateColumnsummariseResultsuppressvariableTypes

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprcpp11crayonDBIdbplyrdplyrfansigenericsgluehmsjsonlitelifecyclemagrittromopgenericspillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Adding cohort intersections

Rendered fromcohort-intersect.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-12-19
Started: 2024-04-09

Adding concept intersections

Rendered fromconcept-intersect.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-12-19
Started: 2024-04-09

Adding patient demographics

Rendered fromdemographics.rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-12-19
Started: 2024-04-09

Summarise result

Rendered fromsummarise.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-07-28
Started: 2024-04-09

Adding table intersections

Rendered fromtable-intersect.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-12-19
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
Categorize a numeric variableaddCategories
Add cdm nameaddCdmName
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 columns to indicate the presence of cohortsaddCohortIntersectFlag
Add cohort name for each cohort_definition_idaddCohortName
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 creates column to indicate the flag overlap information between a table and a conceptaddConceptIntersectFlag
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 table.addTableIntersectFlag
Show the available estimates that can be used for the different variable_type supported.availableEstimates
Get the name of the end date column for a certain table in the cdmendDateColumn
Function to disconnect from the mockmockDisconnect
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", "binary", "date", or NA.variableTypes