summaryPSM: Extract information about fitted parametric survival models

In iain-t-bennett-roche/flexsurvPlus: Provides Functions to Perform Survival Analysis for Economic models

Extract information about fitted parametric survival models

Description

Extract information about fitted parametric survival models

Usage

summaryPSM(
  x,
  types = c("mean", "survival", "hazard", "cumhaz", "median", "rmst"),
  t = NULL,
  ci = FALSE,
  se = FALSE
)

Arguments

x	An object created by calling runPSM
types	A list of statistics to extract - see summary.flexsurvreg for details
t	The time points to be used - see summary.flexsurvreg for details
ci	Should a confidence interval be returned - see summary.flexsurvreg for details
se	Should a standard error be returned - see summary.flexsurvreg for details

Value

A data frame containing the following values

• Model - The Model as specified in runPSM model.type

• ModelF - an ordered factor of Model

• Dist - The distribution

• DistF - an ordered factor of Dist

• distr - as specified in runPSM distr

• Strata - Either Intervention or Reference

• StrataName - As specified by int_name and ref_name respectively in runPSM

• type - as defined by the types parameter see summary.flexsurvreg for details

• variable - "est", "lcl", "ucl", "se" respectively

• time - either NA or the time the statistic is evaluated at

• value - estimated value

Examples

require(dplyr)
require(ggplot2)

PFS_data <- sim_adtte(seed = 2020, rho = 0.6) %>%
filter(PARAMCD=="PFS") %>%
transmute(USUBJID,
            ARMCD,
            PFS_days = AVAL,
            PFS_event = 1- CNSR
)

psm_pfs <- runPSM(
  data = PFS_data,
  time_var = "PFS_days",
  event_var = "PFS_event",
  strata_var = "ARMCD",
  int_name = "A",
  ref_name = "B")

summaryPSM(psm_pfs, types = c("mean","rmst"), t = c(100,2000)) %>%
   filter(Dist == "Generalized Gamma", Strata == "Intervention")

summaryPSM(psm_pfs, types = "survival", t = seq(0,2000,100)) %>%
  ggplot(aes(x=time, y = value, color = StrataName, linetype = Model)) +
  geom_line()+
  facet_grid(~Dist)

summaryPSM(psm_pfs, types = "hazard", t = seq(0,5000,100)) %>%
  ggplot(aes(x=time, y = value, color = StrataName, linetype = Model)) +
  geom_line()+
  facet_grid(~Dist) +
  coord_cartesian(ylim = c(0,0.02))

summaryPSM(psm_pfs, types = "cumhaz", t = seq(0,5000,100)) %>%
  ggplot(aes(x=time, y = value, color = StrataName, linetype = Model)) +
  geom_line()+
  facet_grid(~Dist) +
  coord_cartesian(ylim = c(0,100))

iain-t-bennett-roche/flexsurvPlus documentation built on Aug. 1, 2022, 10:10 a.m.