Package: PatientProfiles 1.2.0

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]

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PatientProfiles.pdf |PatientProfiles.html✨
PatientProfiles/json (API)
NEWS

# Install 'PatientProfiles' in R:

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

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

On CRAN:

47 exports 6 stars 3.62 score 45 dependencies 8 dependents 155 scripts 974 downloads

Last updated 4 days agofrom:98a6d1e318. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 13 2024
R-4.5-win	OK	Sep 13 2024
R-4.5-linux	OK	Sep 13 2024
R-4.4-win	OK	Sep 13 2024
R-4.4-mac	OK	Sep 13 2024
R-4.3-win	OK	Sep 13 2024
R-4.3-mac	OK	Sep 13 2024

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

Dependencies:backports bit bit64 blob CDMConnector checkmate cli clipr cpp11 crayon DBI dbplyr diffobj dplyr fansi fs generics glue hms jsonlite lifecycle magrittr omopgenerics pillar pkgconfig prettyunits progress purrr R6 readr rematch2 rlang snakecase stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs visOmopResults vroom waldo withr

Adding cohort intersections

Rendered fromcohort-intersect.Rmdusingknitr::rmarkdownon Sep 13 2024.

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

Adding concept intersections

Rendered fromconcept-intersect.Rmdusingknitr::rmarkdownon Sep 13 2024.

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

Adding patient demographics

Rendered fromdemographics.rmdusingknitr::rmarkdownon Sep 13 2024.

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

Summarise result

Rendered fromsummarise.Rmdusingknitr::rmarkdownon Sep 13 2024.

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

Adding table intersections

Rendered fromtable-intersect.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2024-07-28
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
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 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 creates column to indicate the flag overlap information between a table and a concept	addConceptIntersectFlag
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
Get the name of the end date column for a certain table in the cdm	endDateColumn
Function to disconnect from the mock	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", "binary", "date", or NA.	variableTypes

Usage by other packages (reverse dependencies)