Keep survival estimates only when the probability changes

Reduce the size of a survival result by removing time points at which the reported survival or cumulative-incidence probability is unchanged from the previous reported time. The first time point in every curve is always kept. Confidence limits for a retained time point are kept with its estimate.

Usage

filterSurvivalChanges(result)

Arguments

result

A summarised_result produced by CohortSurvival.

Value

A summarised_result with unchanged probabilities removed.

Details

Only survival_estimates rows are filtered. Event counts, summaries, attrition, settings, and other result types are returned unchanged. This makes the result suitable for plotSurvival(), while tables requesting an exact removed time point will not be able to display that time.

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]
result <- estimateSingleEventSurvival(
  cdm,
  targetCohortTable = "mgus_diagnosis",
  outcomeCohortTable = "death_cohort"
)
#> 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.
compactResult <- filterSurvivalChanges(result)
# }