Convert survival summarised results to a survival-specific format

Convert the long omopgenerics::summarised_result returned by estimateSingleEventSurvival() or estimateCompetingRiskSurvival() into a wider survival_result object that is easier to inspect manually. The main object contains time-specific estimates when available. Event counts, summary statistics, and attrition are stored as attributes named "events", "summary", and "attrition".

Usage

asSurvivalResult(result)

Arguments

result

A summarised_result object.

Value

A survival_result object.

Details

The plotting and table functions in CohortSurvival accept both formats. The original summarised_result is usually preferable for exporting, binding with other omopgenerics results, and reporting through visOmopResults.

Examples

# \donttest{
cdm <- mockMGUS2cdm()
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpvdDdf9/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> Creating a new cdm
#> Uploading table person (1384 rows) - [1/7]
#> Uploading table observation_period (1384 rows) - [2/7]
#> Uploading table visit_occurrence (1 rows) - [3/7]
#> Uploading table death_cohort (963 rows) - [4/7]
#> Uploading table mgus_diagnosis (1384 rows) - [5/7]
#> Uploading table progression (115 rows) - [6/7]
#> Uploading table progression_type (230 rows) - [7/7]
surv <- estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "death_cohort",
  outcomeCohortId = 1,
  eventGap = 7
) |>
asSurvivalResult()
#> ℹ `outcomeWashout` was not provided and defaults to "Inf".
#> ℹ People with any outcome before target cohort entry will be excluded from the
#>   analysis.
#> ℹ Getting survival for target cohort 'mgus_diagnosis' and outcome cohort
#>   'death_cohort'
#> Getting overall estimates
#> `eventgap`, `outcome_washout`, `censor_on_cohort_exit`, `follow_up_days`, and
#> `minimum_survival_days` cast to character.
#> Warning: eventgap column will be added to the survival result object to include all
#> relevant information
# }