Table with survival summary

Table with survival summary

Usage

tableSurvival(
  x,
  times = NULL,
  timeScale = "days",
  header = c("estimate"),
  estimates = c("median_survival", "restricted_mean_survival"),
  type = "gt",
  groupColumn = NULL,
  hide = c("result_id", "estimate_type"),
  style = NULL,
  .options = list()
)

Arguments

x

Result from estimateSingleEventSurvival or estimateCompetingRiskSurvival

times

Times at which to report survival in the summary table

timeScale

Time unit to report survival in: days, months or years

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. Elements in header can be:

• Any of the columns returned by tableColumns(result) to create a header for these columns.

• Any other input to create an overall header.

estimates

Character vector specifying which estimates to include in the table. Options include: "median_survival", "restricted_mean_survival", "q0_survival", "q05_survival", "q25_survival", "q75_survival", "q95_survival", "q100_survival". By default it includes c("median_survival", "restricted_mean_survival").

type

Character string specifying the desired output table format. See tableType() for supported table types. If type = NULL, global options (set via setGlobalTableOptions()) will be used if available; otherwise, a default 'gt' table is created.

groupColumn

Columns to use as group labels, to see options use tableColumns(result). By default, the name of the new group will be the tidy* column names separated by ";". To specify a custom group name, use a named list such as: list("newGroupName" = c("variable_name", "variable_level")).

*tidy: The tidy format applied to column names replaces "_" with a space and converts to sentence case. Use rename to customise specific column names.

hide

Columns to drop from the output table. By default, result_id and estimate_type are always dropped.

style

Defines the visual formatting of the table. This argument can be provided in one of the following ways:

1. Pre-defined style: Use the name of a built-in style (e.g., "darwin"). See tableStyle() for available options.

2. YAML file path: Provide the path to an existing .yml file defining a new style.

3. List of custome R code: Supply a block of custom R code or a named list describing styles for each table section. This code must be specific to the selected table type. If style = NULL, the function will use global options (see setGlobalTableOptions()) or an existing _brand.yml file (if found); otherwise, the default style is applied. For more details, see the Styles vignette on the package website.

.options

A named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Value

A tibble containing a summary of observed survival in the required units

Examples

# \donttest{
cdm <- mockMGUS2cdm()
#> ■■■■■■■■■■■■■■■■■■■■■■■■■         80% | ETA:  1s
surv <- estimateSingleEventSurvival(cdm,
                                    targetCohortTable = "mgus_diagnosis",
                                    outcomeCohortTable = "death_cohort")
#> - 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` casted to character.
tableSurvival(surv, times = c(50,100,365))


  
CDM name
      
Target cohort
      
Outcome name
      

        
Estimate name
      
    
Number records
      
Number events
      
Median survival (95% CI)
      
Restricted mean survival (95% CI)
      
50 days survival estimate
      
100 days survival estimate
      
365 days survival estimate
    
mock
mgus_diagnosis
death_cohort
1,384
963
98.00 (92.00, 103.00)
133.00 (124.00, 141.00)
69.67 (67.28, 72.13)
48.50 (45.87, 51.29)
6.84 (3.36, 13.92)
# }