Skip to contents

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: Cox_Relative_Risk(), RunCoxPlots()

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)
)
formula <- Cox(Starting_Age, Ending_Age, Cancer_Status) ~
  loglinear(a, b, c, 0) + plinear(d, 0) + multiplicative()
res <- CoxRun(formula, df, 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", paste(tempfile(),
    "run",
    sep = ""
  )), "studyid" = "UserID",
  "verbose" = FALSE
)
plot(res, df, plot_options)
#> list()