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Performs Cox Proportional Hazard model plots

Source: R/BasicRun.R
plot.coxres.Rd

plot.coxres uses user provided data, time/event columns, vectors specifying the model, and options to choose and save plots

Usage

# S3 method for class 'coxres'
plot(x, df, plot_options, a_n = c(), ...)

Arguments

x

result object from a regression, class coxres

df

a data.table containing the columns of interest

plot_options

list of parameters controlling the plot options, see RunCoxPlots() for different options

a_n

list of initial parameter values, used to determine the number of parameters. May be either a list of vectors or a single vector.

...

can include the named entries for the plot_options parameter

Value

saves the plots in the current directory and returns the data used for plots

See also

Other Plotting Wrapper Functions: plotMartingale.coxres(), plotRisk.coxres(), plotSchoenfeld.coxres(), plotSurvival.coxres()

Examples

library(data.table)
## basic example code reproduced from the starting-description vignette
df <- data.table::data.table(
  UserID = c(112, 114, 213, 214, 115, 116, 117),
  Starting_Age = c(18, 20, 18, 19, 21, 20, 18),
  Ending_Age = c(30, 45, 57, 47, 36, 60, 55),
  Cancer_Status = c(0, 0, 1, 0, 1, 0, 0),
  a = c(0, 1, 1, 0, 1, 0, 1),
  b = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
  c = c(10, 11, 10, 11, 12, 9, 11),
  d = c(0, 0, 0, 1, 1, 1, 1)
)
control <- list(
  ncores = 1, lr = 0.75, maxiters = c(1, 1),
  halfmax = 1
)
formula <- Cox(Starting_Age, Ending_Age, Cancer_Status) ~
  loglinear(a, b, c, 0) + plinear(d, 0) + multiplicative()
res <- CoxRun(formula, df,
  control = control,
  a_n = list(c(1.1, -0.1, 0.2, 0.5), c(1.6, -0.12, 0.3, 0.4))
)
plot_options <- list(
  type = c("surv", paste0(
    tempfile(),
    "run"
  )), studyid = "UserID",
  verbose = FALSE
)
res_plot <- plot(res, df, plot_options)