Title: Estimate Survival from Common Data Model Cohorts
Version: 1.1.0
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
License: Apache License (≥ 2)
Encoding: UTF-8
RoxygenNote: 7.3.3
Imports: broom, CDMConnector (≥ 2.0.0), cli, clock, DBI, dplyr, glue, omopgenerics (≥ 1.1.0), PatientProfiles (≥ 1.3.1), purrr, rlang, survival (≥ 3.7.0), stats, stringr, tibble, tidyr
Suggests: testthat (≥ 3.0.0), CodelistGenerator, roxygen2, knitr, tictoc, rmarkdown, ggplot2, patchwork, cmprsk, duckdb, gt, flextable, scales, visOmopResults (≥ 1.4.0), extrafont
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
URL: https://darwin-eu-dev.github.io/CohortSurvival/
NeedsCompilation: no
Packaged: 2025-12-04 08:53:23 UTC; spet5356
Author: Kim López-Güell ORCID iD [aut, cre], Edward Burn ORCID iD [aut], Martí Català ORCID iD [aut], Xintong Li ORCID iD [aut], Danielle Newby ORCID iD [aut], Nuria Mercade-Besora ORCID iD [aut]
Maintainer: Kim López-Güell <kim.lopez@spc.ox.ac.uk>
Depends: R (≥ 4.1.0)
Repository: CRAN
Date/Publication: 2025-12-04 09:40:08 UTC

CohortSurvival: Estimate Survival from Common Data Model Cohorts

Description

logo

Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.

Author(s)

Maintainer: Kim López-Güell kim.lopez@spc.ox.ac.uk (ORCID)

Authors:

See Also

Useful links:

Add survival information to a cohort table

Description

Add survival information to a cohort table

Usage

addCohortSurvival(
  x,
  cdm,
  outcomeCohortTable,
  outcomeCohortId = 1,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  censorOnCohortExit = FALSE,
  censorOnDate = NULL,
  followUpDays = Inf,
  name = NULL
)

Arguments

x

cohort table to add survival information

cdm

CDM reference

outcomeCohortTable

The outcome cohort table of interest.

outcomeCohortId

ID of event cohorts to include. Only one outcome (and so one ID) can be considered. It can either be a cohort_definition_id value or a cohort_name.

outcomeDateVariable

Variable containing date of outcome event

outcomeWashout

Washout time in days for the outcome. If an individual has an outcome during the washout period, status and time will be set to NA

censorOnCohortExit

If TRUE, an individual's follow up will be censored at their cohort exit

censorOnDate

if not NULL, an individual's follow up will be censored at the given date

followUpDays

Number of days to follow up individuals (lower bound 1, upper bound Inf)

name

Name of the new table, if NULL a temporary table is returned.

Value

Two additional columns will be added to x. The "time" column will contain number of days to censoring. The "status" column will indicate whether the patient had the event (value: 1), or did not have the event (value: 0)

Examples



cdm <- mockMGUS2cdm()
cdm$mgus_diagnosis <- cdm$mgus_diagnosis |>
  addCohortSurvival(
    cdm = cdm,
    outcomeCohortTable = "death_cohort",
    outcomeCohortId = 1
  )

Convert survival result back to summarised result

Description

Internal function to convert a survival_result object back to a summarised_result format. This is the inverse operation of asSurvivalResult().

Usage

asSummarisedResult(result)

Arguments

result

A survival_result object.

Value

A summarised_result object.

A tidy implementation of the summarised_characteristics object.

Description

A tidy implementation of the summarised_characteristics object.

Usage

asSurvivalResult(result)

Arguments

result

A summarised_characteristics object.

Value

A tibble with a tidy version of the summarised_characteristics object.

Examples


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "death_cohort",
  outcomeCohortId = 1,
  eventGap = 7
) |>
asSurvivalResult()

Variables that can be used for faceting and colouring survival plots

Description

Variables that can be used for faceting and colouring survival plots

Usage

availableSurvivalGrouping(result, varying = FALSE)

Arguments

result

Survival results

varying

If FALSE (default), only variables with non-unique values will be returned, otherwise all available variables will be returned.

Examples


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(cdm,
                                    targetCohortTable = "mgus_diagnosis",
                                    outcomeCohortTable = "death_cohort")
availableSurvivalGrouping(surv)

Estimate survival for a given event and competing risk of interest using cohorts in the OMOP Common Data Model

Description

Estimate survival for a given event and competing risk of interest using cohorts in the OMOP Common Data Model

Usage

estimateCompetingRiskSurvival(
  cdm,
  targetCohortTable,
  outcomeCohortTable,
  competingOutcomeCohortTable,
  targetCohortId = NULL,
  outcomeCohortId = NULL,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  competingOutcomeCohortId = NULL,
  competingOutcomeDateVariable = "cohort_start_date",
  competingOutcomeWashout = Inf,
  censorOnCohortExit = FALSE,
  censorOnDate = NULL,
  followUpDays = Inf,
  strata = NULL,
  eventGap = 30,
  estimateGap = 1,
  restrictedMeanFollowUp = NULL,
  minimumSurvivalDays = 1
)

Arguments

cdm

CDM reference

targetCohortTable

The target cohort table of interest.

outcomeCohortTable

The outcome cohort table of interest.

competingOutcomeCohortTable

The competing outcome cohort table of interest.

targetCohortId

Target cohorts to include. It can either be a cohort_definition_id value or a cohort_name. Multiple ids are allowed.

outcomeCohortId

Outcome cohorts to include. It can either be a cohort_definition_id value or a cohort_name. Multiple ids are allowed.

outcomeDateVariable

Variable containing date of outcome event

outcomeWashout

Washout time in days for the outcome

competingOutcomeCohortId

Competing outcome cohorts to include. It can either be a cohort_definition_id value or a cohort_name. Multiple ids are allowed.

competingOutcomeDateVariable

Variable containing date of competing outcome event

competingOutcomeWashout

Washout time in days for the competing outcome

censorOnCohortExit

If TRUE, an individual's follow up will be censored at their cohort exit

censorOnDate

if not NULL, an individual's follow up will be censored at the given date

followUpDays

Number of days to follow up individuals (lower bound 1, upper bound Inf)

strata

strata

eventGap

Days between time points for which to report survival events, which are grouped into the specified intervals.

estimateGap

Days between time points for which to report survival estimates. First day will be day zero with risk estimates provided for times up to the end of follow-up, with a gap in days equivalent to eventGap.

restrictedMeanFollowUp

number of days of follow-up to take into account when calculating restricted mean for all cohorts

minimumSurvivalDays

Minimum number of days required for the main cohort to have survived

Value

tibble with survival information for desired cohort, including: time, people at risk, survival probability, cumulative incidence, 95 CIs, strata and outcome. A tibble with the number of events is outputted as an attribute of the output

Examples


cdm <- mockMGUS2cdm()
surv <- estimateCompetingRiskSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "progression",
  outcomeCohortId = 1,
  competingOutcomeCohortTable = "death_cohort",
  competingOutcomeCohortId = 1,
  eventGap = 7
)

Estimate survival for a given event of interest using cohorts in the OMOP Common Data Model

Description

Estimate survival for a given event of interest using cohorts in the OMOP Common Data Model

Usage

estimateSingleEventSurvival(
  cdm,
  targetCohortTable,
  outcomeCohortTable,
  targetCohortId = NULL,
  outcomeCohortId = NULL,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  censorOnCohortExit = FALSE,
  censorOnDate = NULL,
  followUpDays = Inf,
  strata = NULL,
  eventGap = 30,
  estimateGap = 1,
  restrictedMeanFollowUp = NULL,
  minimumSurvivalDays = 1
)

Arguments

cdm

CDM reference

targetCohortTable

targetCohortTable

outcomeCohortTable

The outcome cohort table of interest.

targetCohortId

Target cohorts to include. It can either be a cohort_definition_id value or a cohort_name. Multiple ids are allowed.

outcomeCohortId

Outcome cohorts to include. It can either be a cohort_definition_id value or a cohort_name. Multiple ids are allowed.

outcomeDateVariable

Variable containing date of outcome event

outcomeWashout

Washout time in days for the outcome

censorOnCohortExit

If TRUE, an individual's follow up will be censored at their cohort exit

censorOnDate

if not NULL, an individual's follow up will be censored at the given date

followUpDays

Number of days to follow up individuals (lower bound 1, upper bound Inf)

strata

strata

eventGap

Days between time points for which to report survival events, which are grouped into the specified intervals.

estimateGap

Days between time points for which to report survival estimates. First day will be day zero with risk estimates provided for times up to the end of follow-up, with a gap in days equivalent to eventGap.

restrictedMeanFollowUp

number of days of follow-up to take into account when calculating restricted mean for all cohorts

minimumSurvivalDays

Minimum number of days required for the main cohort to have survived

Value

tibble with survival information for desired cohort, including: time, people at risk, survival probability, cumulative incidence, 95 CIs, strata and outcome. A tibble with the number of events is outputted as an attribute of the output

Examples


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "death_cohort",
  outcomeCohortId = 1,
  eventGap = 7
)

Create mock CDM reference with survival::mgus2 dataset

Description

Create mock CDM reference with survival::mgus2 dataset

Usage

mockMGUS2cdm()

Value

CDM reference containing data from the survival::mgus2 dataset

Examples

 
cdm <- mockMGUS2cdm()
cdm$person

Additional arguments for the function tableSurvival()

Description

It provides a list of allowed inputs for .option argument in tableSurvival and their given default value.

Usage

optionsTableSurvival()

Value

The default .options named list.

Examples

{
optionsTableSurvival()
}

Plot survival results

Description

Plot survival results

Usage

plotSurvival(
  result,
  ribbon = TRUE,
  facet = NULL,
  colour = NULL,
  cumulativeFailure = FALSE,
  riskTable = FALSE,
  riskInterval = 30,
  logLog = FALSE,
  timeScale = "days",
  style = NULL
)

Arguments

result

Survival results

ribbon

If TRUE, the plot will join points using a ribbon

facet

Variables to use for facets

colour

Variables to use for colours

cumulativeFailure

whether to plot the cumulative failure probability instead of the survival probability

riskTable

Whether to print risk table below the plot

riskInterval

Interval of time to print risk table below the plot

logLog

If TRUE, the survival probabilities are transformed using the log-log formula

timeScale

The scale of time in the x-axis. Can be "days", "months", or "years"

style

A character string defining the visual theme to apply to the plot. You can set this to NULL to apply the standard ggplot2 default style, or provide a name for one of the package's pre-defined styles. Refer to the plotStyle() function for all available style pre-defined themes. For further customization, you can always modify the returned ggplot object directly.

Value

A plot of survival probabilities over time

Examples


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(cdm,
                                    targetCohortTable = "mgus_diagnosis",
                                    outcomeCohortTable = "death_cohort")
plotSurvival(surv)

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

omopgenerics

attrition, bind, cohortCodelist, cohortCount, exportSummarisedResult, importSummarisedResult, settings, suppress

Table with survival events

Description

Table with survival events

Usage

riskTable(
  x,
  eventGap = NULL,
  header = c("estimate"),
  type = "gt",
  groupColumn = NULL,
  hide = c("result_id", "estimate_type"),
  style = NULL,
  .options = list()
)

Arguments

x

Result from estimateSingleEventSurvival or estimateCompetingRiskSurvival.

eventGap

Event gap defining the times at which to report the risk table information. Must be one of the eventGap inputs used for the estimation function. If NULL, all available are reported.

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.

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 the risk table information (n_risk, n_events, n_censor) for all times within the event gap specified.

Examples


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(cdm,
                                    targetCohortTable = "mgus_diagnosis",
                                    outcomeCohortTable = "death_cohort")
riskTable(surv)

Helper for consistent documentation of tables.

Description

Helper for consistent documentation of tables.

Arguments

result

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

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.

hide

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

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.

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.

columnOrder

Character vector establishing the position of the columns in the formatted table. Columns in either header, groupColumn, or hide will be ignored.

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.

Table with survival summary

Description

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


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(cdm,
                                    targetCohortTable = "mgus_diagnosis",
                                    outcomeCohortTable = "death_cohort")
tableSurvival(surv, times = c(50,100,365))

Display the attrition of a survival result in a visual table

Description

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:

  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 visual table

Examples


library(CohortSurvival)

cdm <- mockMGUS2cdm()

surv <- estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  outcomeCohortTable = "death_cohort"
)

tableSurvivalAttrition(surv)

Table with survival events

Description

Table with survival events

Usage

tableSurvivalEvents(
  x,
  eventGap = NULL,
  header = c("estimate"),
  type = "gt",
  groupColumn = NULL,
  hide = c("result_id", "estimate_type"),
  style = NULL,
  .options = list()
)

Arguments

x

Result from estimateSingleEventSurvival or estimateCompetingRiskSurvival.

eventGap

Event gap defining the times at which to report the risk table information. Must be one of the eventGap inputs used for the estimation function. If NULL, all available are reported.

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.

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 the risk table information (n_risk, n_events, n_censor) for all times within the event gap specified.

Examples


cdm <- mockMGUS2cdm()
surv <- estimateSingleEventSurvival(cdm,
                                    targetCohortTable = "mgus_diagnosis",
                                    outcomeCohortTable = "death_cohort")
tableSurvivalEvents(surv)