Display the attrition of a survival result in a visual table

Usage

tableSurvivalAttrition(
  result,
  type = "gt",
  header = "variable_name",
  groupColumn = c("cdm_name", "target_cohort", "variable_level"),
  hide = c("estimate_name"),
  style = NULL,
  .options = list()
)

Arguments

result

A summarised_result object obtained either from estimateSingleEventSurvival() or estimateCompetingRiskSurvival().

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.

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.

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:

Pre-defined style: Use the name of a built-in style (e.g., "darwin"). See tableStyle() for available options.
YAML file path: Provide the path to an existing .yml file defining a new style.
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 visual table

Examples

# \donttest{
library(CohortSurvival)

cdm <- mockMGUS2cdm()

surv <- estimateSingleEventSurvival(
  cdm = 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.

tableSurvivalAttrition(surv)


  Reason id
      Reason
      
        Variable name
      
    
number_records
      number_subjects
      excluded_records
      excluded_subjects
    
mock; mgus_diagnosis_1; death_cohort
    
1
Initial qualifying events
1,384
1,384
0
0
2
No outcome event in washout period
1,384
1,384
0
0
3
Survival days for outcome less than 1
1,384
1,384
0
0
# }

Reason id	Reason	Variable name
Reason id	Reason	number_records	number_subjects	excluded_records	excluded_subjects
mock; mgus_diagnosis_1; death_cohort
1	Initial qualifying events	1,384	1,384	0	0
2	No outcome event in washout period	1,384	1,384	0	0
3	Survival days for outcome less than 1	1,384	1,384	0	0