Skip to contents

Plot method for a haz1ts object.

Source: R/plot.haz1tsLMM.R
plot.haz1tsLMM.Rd

plot.haz1tsLMM() is a plot method for objects of class haz1tsLMM.

Usage

# S3 method for class 'haz1tsLMM'
plot(
  x,
  which_plot = c("hazard", "covariates"),
  plot_grid = NULL,
  plot_options = list(),
  ...
)

Arguments

x

The output of the function fit1ts.

which_plot

The type of plot required. Can be one of "hazard" (default) or "covariates".

plot_grid

(optional) A named vector containing the parameters to build a new grid of intervals over s for plotting the estimated hazard on a finer grid. This must be of the form: plot_grid = c(smin, smax, ds), where smin, smax are the minimum and maximum values desired for the intervals over s, and ds is the distance between intervals over s. If not specified, the plotting is done using the same B-splines basis as for the estimation. The function will check if the parameters for the grid provided by the user are compatible with those originally used to construct the B-splines for estimating the model. If not, the grid will be adjusted accordingly and a warning will be returned.

plot_options

A list with all possible options for any of the plots:

  • loghazard A Boolean. Default is FALSE. If FALSE the function returns a plot of the hazard curve, if TRUE the function returns a plot of the log-hazard curve.

  • log10hazard A Boolean. Default is FALSE. If TRUE it returns a plot of the log10-hazard curve.

  • col The color of the curve plotted. Default is "black".

  • add_CI A Boolean. If TRUE (default) the confidence bands will be added.

  • col_CI The color for the confidence bands. The default is the same color of the curve, with a 50% transparency level.

  • main The title of the plot.

  • xlab The label of the time axis (plotted on the x axis).

  • ylab The label of the y-axis (hazard, log-hazard or log10-hazard).

  • xlim A vector with two elements defining the limits of the time scale on the x axis.

  • ylim A vector with two elements defining the limits of function plotted on the y axis (hazard, log-hazard or log10-hazard).

  • xmin The minimum value on the x-axis.

  • ymin The minimum value on the y-axis.

  • cex_main The magnification to be used for the main title, default is 1.2 .

  • cex_lab The magnification to be used for the axis labels, default is 1 .

  • HR A Boolean. If TRUE the HRs with their CIs will be plotted. Default is FALSE (plot the beta with their CIs).

  • symmetric_CI A Boolean. Default is TRUE. If a plot of the HRs is required (HR == TRUE), then plot symmetrical Confidence Intervals, based on the SEs for the HRs calculated by delta method. If FALSE, then CIs are obtained by exponentiating the CIs for the betas.

  • confidence The level of confidence for the CIs. Default is .95 (alpha = 0.05).

  • col_beta The color for the plot of the covariates' effects.

  • pch The symbol for plotting the point estimates.

...

Further arguments to plot.

Value

A plot of the type required.

Details

The function obtainSmoothTrend from the R-package LMMsolver is used here. We refer the interested readers to https://biometris.github.io/LMMsolver/ for more details on LMMsolver and its usage.

Examples

## preparing data - no covariates
dt1ts <- prepare_data(data = reccolon2ts,
                      s_in = "entrys",
                      s_out = "timesr",
                      events = "status",
                      ds = 180)

## fitting the model with fit1ts() - default options

mod1 <- fit1ts(dt1ts,
optim_method = "LMMsolver")
plot(mod1)