README

PatientProfiles contains functions for adding characteristics to OMOP CDM tables containing patient level data (e.g. condition occurrence, drug exposure, and so on) and OMOP CDM cohort tables. The characteristics that can be added include an individual´s sex, age, and days of prior observation Time varying characteristics, such as age, can be estimated relative to any date in the corresponding table. In addition, PatientProfiles also provides functionality for identifying intersections between a cohort table and OMOP CDM tables containing patient level data or other cohort tables.

Package installation

install.packages("PatientProfiles")

Citation

citation("PatientProfiles")
#> To cite package 'PatientProfiles' in publications use:
#> 
#>   Català M, Guo Y, Du M, Lopez-Guell K, Burn E, Mercade-Besora N
#>   (????). _PatientProfiles: Identify Characteristics of Patients in the
#>   OMOP Common Data Model_. R package version 1.4.3,
#>   <https://darwin-eu.github.io/PatientProfiles/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {PatientProfiles: Identify Characteristics of Patients in the OMOP Common Data Model},
#>     author = {Martí Català and Yuchen Guo and Mike Du and Kim Lopez-Guell and Edward Burn and Nuria Mercade-Besora},
#>     note = {R package version 1.4.3},
#>     url = {https://darwin-eu.github.io/PatientProfiles/},
#>   }

Example usage

Create a reference to data in the OMOP CDM format

The PatientProfiles package is designed to work with data in the OMOP CDM format, so our first step is to create a reference to the data using the CDMConnector package.

library(PatientProfiles)
library(dplyr)

library(RPostgres)
library(CDMConnector)

con <- dbConnect(
  drv = Postgres(),
  dbname = Sys.getenv("CDM5_POSTGRESQL_DBNAME"),
  host = Sys.getenv("CDM5_POSTGRESQL_HOST"),
  user = Sys.getenv("CDM5_POSTGRESQL_USER"),
  password = Sys.getenv("CDM5_POSTGRESQL_PASSWORD")
)

cdm <- cdmFromCon(
  con = con,
  cdmSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
  writeSchema = Sys.getenv("CDM5_POSTGRESQL_RESULT_SCHEMA")
)

To see how you would create a reference to your database please consult the CDMConnector package documentation. For this example though we’ll work with simulated data, and we’ll generate an example cdm reference like so:

cdm <- mockPatientProfiles(numberIndividuals = 1000, source = "duckdb")

Adding individuals´ characteristics

Adding characteristics to patient-level data

Say we wanted to get individuals´sex and age at condition start date for records in the condition occurrence table. We can use the addAge and addSex functions to do this:

cdm$condition_occurrence |>
  glimpse()
#> Rows: ??
#> Columns: 6
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ person_id                 <int> 814, 640, 731, 853, 505, 817, 270, 313, 138,…
#> $ condition_start_date      <date> 2008-02-05, 1920-08-28, 1970-04-23, 1915-04…
#> $ condition_end_date        <date> 2009-10-30, 1928-01-13, 1970-08-02, 1924-02…
#> $ condition_occurrence_id   <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1…
#> $ condition_concept_id      <int> 5, 6, 8, 2, 7, 9, 2, 4, 2, 1, 5, 4, 3, 6, 8,…
#> $ condition_type_concept_id <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…

cdm$condition_occurrence <- cdm$condition_occurrence |>
  addAge(indexDate = "condition_start_date") |>
  addSex()

cdm$condition_occurrence |>
  glimpse()
#> Rows: ??
#> Columns: 8
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ person_id                 <int> 138, 174, 207, 216, 239, 270, 276, 313, 317,…
#> $ condition_start_date      <date> 1939-09-09, 1912-06-21, 1926-12-14, 1928-05…
#> $ condition_end_date        <date> 1948-11-09, 1927-04-21, 1937-09-29, 1931-04…
#> $ condition_occurrence_id   <int> 9, 12, 23, 13, 32, 7, 20, 8, 24, 33, 14, 28,…
#> $ condition_concept_id      <int> 2, 4, 3, 3, 7, 2, 10, 4, 4, 2, 6, 9, 5, 8, 7…
#> $ condition_type_concept_id <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
#> $ age                       <int> 6, 4, 13, 8, 32, 18, 0, 25, 19, 34, 45, 38, …
#> $ sex                       <chr> "Female", "Male", "Female", "Male", "Male", …

cdm$condition_occurrence |>
  filter(age >= 18 & age <= 65) |>
  filter(sex == "Male")
#> # Source:   SQL [?? x 8]
#> # Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#>   person_id condition_start_date condition_end_date condition_occurrence_id
#>       <int> <date>               <date>                               <int>
#> 1       239 1991-12-11           1996-11-27                              32
#> 2       404 1982-10-31           1984-12-04                              28
#> 3       682 1932-09-09           1937-08-15                              10
#> 4       814 2008-02-05           2009-10-30                               1
#> # ℹ 4 more variables: condition_concept_id <int>,
#> #   condition_type_concept_id <int>, age <int>, sex <chr>

Adding characteristics of a cohort

As with other tables in the OMOP CDM, we can work in a similar way with cohort tables. For example, say we have the below cohort table

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 2, 3, 1, 3, 3, 2, 2, 2, 2, 2, 3, 2, 1, 1, 2, 1…
#> $ subject_id           <int> 415, 780, 507, 560, 948, 940, 194, 643, 119, 298,…
#> $ cohort_start_date    <date> 1916-09-02, 1906-05-02, 1944-06-11, 1950-05-29, …
#> $ cohort_end_date      <date> 1937-04-16, 1928-07-12, 1948-03-30, 1961-06-14, …

We can add age, age groups, sex, and days of prior observation to a cohort like so

cdm$cohort1 <- cdm$cohort1 |>
  addAge(
    indexDate = "cohort_start_date",
    ageGroup = list(c(0, 18), c(19, 65), c(66, 100))
  ) |>
  addSex() |>
  addPriorObservation()

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 8
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 1, 1, 1, 2, 3, 2, 3, 3, 3, 3, 1, 1, 1, 2, 3, 2, 3…
#> $ subject_id           <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15…
#> $ cohort_start_date    <date> 1946-09-18, 1955-11-24, 1953-06-04, 1925-11-12, …
#> $ cohort_end_date      <date> 1974-02-24, 1960-02-26, 1955-11-09, 1930-06-10, …
#> $ age                  <int> 1, 33, 9, 6, 29, 10, 21, 23, 8, 18, 8, 5, 24, 7, …
#> $ age_group            <chr> "0 to 18", "19 to 65", "0 to 18", "0 to 18", "19 …
#> $ sex                  <chr> "Male", "Female", "Male", "Female", "Male", "Male…
#> $ prior_observation    <int> 625, 12380, 3442, 2507, 10630, 3733, 7745, 8553, …

We could use this information to subset the cohort. For example limiting to those with at least 365 days of prior observation available before their cohort start date like so

cdm$cohort1 |>
  filter(prior_observation >= 365)
#> # Source:   SQL [?? x 8]
#> # Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date   age
#>                   <int>      <int> <date>            <date>          <int>
#>  1                    1          1 1946-09-18        1974-02-24          1
#>  2                    1          2 1955-11-24        1960-02-26         33
#>  3                    1          3 1953-06-04        1955-11-09          9
#>  4                    2          4 1925-11-12        1930-06-10          6
#>  5                    3          5 1960-02-08        1960-10-07         29
#>  6                    2          6 1918-03-22        1922-05-22         10
#>  7                    3          7 1942-03-17        1944-07-08         21
#>  8                    3          8 1982-06-02        1990-11-15         23
#>  9                    3          9 1929-02-06        1936-07-28          8
#> 10                    3         10 1955-11-17        1958-12-22         18
#> # ℹ more rows
#> # ℹ 3 more variables: age_group <chr>, sex <chr>, prior_observation <int>

Cohort intersections

Detect the presence of another cohort in a certain window

We can use addCohortIntersectFlag to add a flag for the presence (or not) of a cohort in a certain window.

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 1, 2, 3, 1, 2, 2, 3, 2, 2, 2
#> $ subject_id           <int> 1, 2, 10, 9, 3, 7, 6, 8, 4, 5
#> $ cohort_start_date    <date> 1992-07-20, 1979-03-29, 1987-04-30, 1982-04-23, 1…
#> $ cohort_end_date      <date> 2000-07-17, 1984-08-07, 1987-05-10, 1985-05-08, 1…

cdm$cohort1 <- cdm$cohort1 |>
  addCohortIntersectFlag(
    targetCohortTable = "cohort2",
    window = c(-Inf, -1)
  )

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 7
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 1, 2, 3, 1, 2, 2, 2, 2, 2
#> $ subject_id           <int> 10, 9, 3, 6, 1, 2, 7, 8, 4, 5
#> $ cohort_start_date    <date> 1987-04-30, 1982-04-23, 1962-01-26, 2012-07-24, 1…
#> $ cohort_end_date      <date> 1987-05-10, 1985-05-08, 1962-11-06, 2014-06-17, 2…
#> $ cohort_2_minf_to_m1  <dbl> 0, 1, 0, 1, 0, 0, 0, 0, 0, 0
#> $ cohort_1_minf_to_m1  <dbl> 1, 0, 1, 0, 0, 0, 0, 0, 0, 0
#> $ cohort_3_minf_to_m1  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0

Count appearances of a certain cohort in a certain window

If we wanted the number of appearances, we could instead use the addCohortIntersectCount function

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 2, 1, 3, 2, 1, 1, 1, 2, 2, 1
#> $ subject_id           <int> 2, 3, 6, 8, 4, 7, 5, 1, 9, 10
#> $ cohort_start_date    <date> 1938-06-21, 1993-11-29, 1977-10-21, 1968-11-30, 1…
#> $ cohort_end_date      <date> 1948-04-26, 1994-01-01, 1985-11-25, 1972-09-03, 1…

cdm$cohort1 <- cdm$cohort1 |>
  addCohortIntersectCount(
    targetCohortTable = "cohort2",
    targetCohortId = 1,
    window = list("short_term" = c(1, 30), "mid_term" = c(31, 180))
  )

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 6
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 1, 1, 1, 2, 3, 2, 1, 2, 2, 1
#> $ subject_id           <int> 3, 4, 7, 2, 6, 8, 5, 1, 9, 10
#> $ cohort_start_date    <date> 1993-11-29, 1989-12-28, 1952-08-05, 1938-06-21, 1…
#> $ cohort_end_date      <date> 1994-01-01, 1995-07-31, 1953-05-23, 1948-04-26, 1…
#> $ cohort_1_mid_term    <dbl> 1, 1, 1, 0, 0, 0, 0, 0, 0, 0
#> $ cohort_1_short_term  <dbl> 1, 1, 1, 0, 0, 0, 0, 0, 0, 0

Add a column with the first/last event in a certain window

Say we wanted the date at which an individual was in another cohort then we can use the addCohortIntersectDate function. As there might be multiple records for the other cohort, we can also choose the first or the last appearance in that cohort.

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 2, 2, 2, 2, 1, 3, 1, 3, 1, 1
#> $ subject_id           <int> 4, 5, 7, 6, 9, 8, 3, 2, 1, 10
#> $ cohort_start_date    <date> 1938-11-11, 1922-07-20, 1950-02-23, 1985-12-16, 1…
#> $ cohort_end_date      <date> 1943-08-29, 1927-03-23, 1953-08-20, 1989-03-20, 1…

cdm$cohort1 <- cdm$cohort1 |>
  addCohortIntersectDate(
    targetCohortTable = "cohort2",
    targetCohortId = 1,
    order = "first",
    window = c(-Inf, Inf)
  )

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 5
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 3, 1, 2, 2, 2, 2, 1, 1, 1
#> $ subject_id           <int> 8, 2, 10, 4, 5, 7, 6, 9, 3, 1
#> $ cohort_start_date    <date> 1954-12-03, 1963-02-19, 1945-03-20, 1938-11-11, 1…
#> $ cohort_end_date      <date> 1969-08-13, 1963-02-20, 1945-09-11, 1943-08-29, 1…
#> $ cohort_1_minf_to_inf <date> 1929-07-25, 1914-10-14, 1942-12-05, NA, NA, NA, …

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 3, 3, 3, 3, 1, 3, 2, 1, 1
#> $ subject_id           <int> 5, 8, 6, 1, 7, 9, 3, 2, 10, 4
#> $ cohort_start_date    <date> 1948-10-29, 1929-07-30, 1938-03-07, 1947-04-25, 1…
#> $ cohort_end_date      <date> 1952-10-15, 1930-09-16, 1940-04-22, 1948-03-22, 2…

cdm$cohort1 <- cdm$cohort1 |>
  addCohortIntersectDate(
    targetCohortTable = "cohort2",
    targetCohortId = 1,
    order = "last",
    window = c(-Inf, Inf)
  )

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 5
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 3, 1, 3, 3, 3, 3, 2, 1, 1
#> $ subject_id           <int> 6, 1, 9, 5, 8, 7, 3, 2, 10, 4
#> $ cohort_start_date    <date> 1938-03-07, 1947-04-25, 1958-12-30, 1948-10-29, 1…
#> $ cohort_end_date      <date> 1940-04-22, 1948-03-22, 1975-01-06, 1952-10-15, 1…
#> $ cohort_1_minf_to_inf <date> 1923-06-06, 1922-10-10, 1969-03-25, NA, NA, NA, …

Add the number of days instead of the date

Instead of returning a date, we could return the days to the intersection by using addCohortIntersectDays

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 3, 2, 1, 1, 2, 1, 1, 3, 3
#> $ subject_id           <int> 9, 4, 1, 3, 8, 10, 7, 2, 6, 5
#> $ cohort_start_date    <date> 1922-11-01, 1933-04-23, 1961-09-09, 1932-10-19, 1…
#> $ cohort_end_date      <date> 1926-01-29, 1971-01-01, 1963-08-29, 1938-11-18, 1…

cdm$cohort1 <- cdm$cohort1 |>
  addCohortIntersectDays(
    targetCohortTable = "cohort2",
    targetCohortId = 1,
    order = "last",
    window = c(-Inf, Inf)
  )

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 5
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 3, 2, 1, 3, 3, 1, 2, 1, 1, 3
#> $ subject_id           <int> 4, 1, 8, 5, 9, 3, 10, 7, 2, 6
#> $ cohort_start_date    <date> 1933-04-23, 1961-09-09, 1955-07-31, 1931-08-05, 1…
#> $ cohort_end_date      <date> 1971-01-01, 1963-08-29, 1967-08-18, 1933-06-05, 1…
#> $ cohort_1_minf_to_inf <dbl> 15815, -202, -3652, 4575, NA, NA, NA, NA, NA, NA

Combine multiple cohort intersects

If we want to combine multiple cohort intersects we can concatenate the operations using the pipe operator:

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 1, 1, 2, 2, 2, 2, 2, 1, 2, 3
#> $ subject_id           <int> 10, 3, 1, 8, 5, 6, 7, 2, 9, 4
#> $ cohort_start_date    <date> 1942-04-12, 2013-06-07, 2004-09-20, 1937-05-23, 1…
#> $ cohort_end_date      <date> 1942-10-19, 2017-02-20, 2005-11-04, 1957-12-10, 1…

cdm$cohort1 <- cdm$cohort1 |>
  addCohortIntersectDate(
    targetCohortTable = "cohort2",
    targetCohortId = 1,
    order = "last",
    window = c(-Inf, Inf)
  ) |>
  addCohortIntersectCount(
    targetCohortTable = "cohort2",
    targetCohortId = 1,
    window = c(-Inf, Inf)
  )

cdm$cohort1 |>
  glimpse()
#> Rows: ??
#> Columns: 5
#> Database: DuckDB 1.4.0 [root@Darwin 24.6.0:R 4.4.1/:memory:]
#> $ cohort_definition_id <int> 1, 2, 1, 1, 2, 2, 2, 2, 2, 3
#> $ subject_id           <int> 10, 5, 2, 3, 1, 8, 6, 7, 9, 4
#> $ cohort_start_date    <date> 1942-04-12, 1923-07-21, 1947-06-02, 2013-06-07, 2…
#> $ cohort_end_date      <date> 1942-10-19, 1924-04-07, 1954-10-29, 2017-02-20, 2…
#> $ cohort_1_minf_to_inf <dbl> 1, 1, 1, 0, 0, 0, 0, 0, 0, 0

PatientProfiles

Package overview