Summarise the observation period table getting some overall statistics in a summarised_result object.

Usage

summariseObservationPeriod(
  cdm,
  estimates = c("mean", "sd", "min", "q05", "q25", "median", "q75", "q95", "max",
    "density"),
  missingData = TRUE,
  quality = TRUE,
  byOrdinal = TRUE,
  ageGroup = NULL,
  sex = FALSE,
  dateRange = NULL,
  observationPeriod = lifecycle::deprecated()
)

Arguments

cdm

A cdm_reference object.

estimates

Estimates to summarise the variables of interest ( records per person, duration in days and days to next observation period).

missingData

Logical. If TRUE, includes a summary of missing data for relevant fields.

quality

Logical. If TRUE, performs basic data quality checks, including:

Number of subjects not included in person table
Number of records with end date before start date
Number of records with start date before the person's birth date

byOrdinal

Boolean variable. Whether to stratify by the ordinal observation period (e.g., 1st, 2nd, etc.) (TRUE) or simply analyze overall data (FALSE)

ageGroup

A list of age groups to stratify results by.

sex

Boolean variable. Whether to stratify by sex (TRUE) or not (FALSE).

dateRange

A vector of two dates defining the desired study period. Only the start_date column of the OMOP table is checked to ensure it falls within this range. If dateRange is NULL, no restriction is applied.

observationPeriod

deprecated.

Value

A summarised_result object with the summarised data.

Examples

# \donttest{
library(OmopSketch)
library(dplyr, warn.conflicts = FALSE)

cdm <- mockOmopSketch(numberIndividuals = 100)

result <- summariseObservationPeriod(cdm = cdm)
#> Warning: These columns contain missing values, which are not permitted:
#> "period_type_concept_id"

result |>
  glimpse()
#> Rows: 3,126
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "mockOmopSketch", "mockOmopSketch", "mockOmopSketch",…
#> $ group_name       <chr> "observation_period_ordinal", "observation_period_ord…
#> $ group_level      <chr> "all", "all", "all", "all", "all", "all", "all", "all…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "Records per person", "Records per person", "Records …
#> $ variable_level   <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
#> $ estimate_name    <chr> "mean", "sd", "min", "q05", "q25", "median", "q75", "…
#> $ estimate_type    <chr> "numeric", "numeric", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "1", "0", "1", "1", "1", "1", "1", "1", "1", "3297.8"…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

PatientProfiles::mockDisconnect(cdm)
# }