Package 'OmopConstructor'

Create achilles tables

Description

Create achilles tables

Usage

buildAchillesTables(cdm, achillesId = NULL)

Arguments

cdm	A cdm_reference object
achillesId	A vector of achilles ids. You can also use "minimal", "default" or "all" to point to a subset of analyses. Or also "person", "observation period", ... to run the analyses refering to a certain category.

Value

The cdm_reference object with the achilles tables populated.

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Build the drug_era table

Description

Build the drug_era table

Usage

buildDrugEra(cdm, collapseDays = 30L)

Arguments

cdm	A cdm_reference object.
collapseDays	Number of days that two exposures can be separated to be collapsed in a single era.

Value

The lazy drug_era table.

Examples

library(omock)
library(OmopConstructor)
library(dplyr, warn.conflicts = TRUE)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")

cdm$drug_era <- buildDrugEra(cdm = cdm)
cdm$drug_era |>
  glimpse()

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Build observation_period table from data recorded in the cdm_reference

Description

Build observation_period table from data recorded in the cdm_reference

Usage

buildObservationPeriod(
  cdm,
  collapseDays = Inf,
  persistenceDays = Inf,
  dateRange = as.Date(c("1900-01-01", NA)),
  censorAge = 120L,
  recordsFrom = c("drug_exposure", "visit_occurrence"),
  periodTypeConceptId = 32817L
)

Arguments

cdm	A cdm_reference object.
collapseDays	Distance between records to be collapsed.
persistenceDays	Number of days added at the end of an observation period as persistence window.
dateRange	Range of dates to be considered. By default '1900-01-01' is used as start date, whereas for censor date the first available of source_release_date, cdm_release_date, and Sys.Date() will be used.
censorAge	Age to censor individuals if they reach a certain age. The last day in observation of the individual will be the day prior to their birthday.
recordsFrom	Tables to retrieve observation records from.
periodTypeConceptId	Choose the observation_period_type_concept_id that best represents how the period was determined. Accepted Concepts.

Value

The cdm_reference object with a new observation_period.

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Collapse records of a cdm_table into episodes.

Description

Collapse records of a cdm_table into episodes.

Usage

collapseRecords(
  x,
  startDate,
  endDate,
  by,
  gap = 0L,
  toSummarise = character(),
  name = NULL
)

Arguments

x	A cdm_table object.
startDate	Column in x that points to the start date of the record.
endDate	Column in x that point to the end date of the record.
by	Columns in x that aggregate the records.
gap	Integer; distance allowed between two consecutive records to be collapsed.
toSummarise	Columns in x that we want to be keep, the different columns will be added up.
name	Name of the new cdm_table created.

Value

The x cdm_table with the records collapsed.

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