Description Usage Arguments Note Author(s) See Also Examples

This function creates a STEPP from the given point estimates and confidence intervals at desired percentiles.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
PlotSTEPP(data, outcome.var, outcome.class, trt = NULL, var,
covariate = NULL, strata = NULL, placebo.code = NULL,
active.code = NULL, quantile.type = 1, alpha = 0.05,
window.width = 0.25, min.pt = NULL, max.pt = NULL, by = 0.05,
yrange.lower = NULL, yrange.upper = NULL, xticks = NULL,
show.refline = TRUE, refline.color = "grey", show.refline.ac = TRUE,
refline.color.ac = "lightblue", estimate.color = "blue",
estimate.lty = 1, estimate.lwd = 2, surv.conf.type = "plain",
ties = "efron", ci.color = "black", ci.lty = 2, ci.lwd = 1,
ci.shade = TRUE,
plot.title = "STEPP: Subgroup Treatment Effect Pattern Plot",
sub.title = NULL, xlabel = "Biomarker Percentile", ylabel = NULL,
show.legend = TRUE, legend.loc = "topright",
legend.text = c("Point Estimate", paste((1 - alpha) * 100,
" percent Confidence Interval", sep = "")), legend.col = c(estimate.color,
ci.color), legend.lty = c(estimate.lty, ci.lty),
legend.lwd = c(estimate.lwd, ci.lwd), legend.bty = "n", bm.digits = 2,
actual.scale = FALSE, equal.in.LL = TRUE, equal.in.UL = FALSE,
pdf.name = NULL, pdf.param = list(width = 11, height = 8.5),
par.param = list(mar = c(4, 4, 3, 2)), csv.name = NULL)
``` |

`data` |
input data frame. Rows are patients and columns are variables (e.g. demographics variables, time to event variables, biomarker variables, treatment indicator, etc.). One patient per row. |

`outcome.var` |
outcome variable. In case of a 'survival', variable, it will be a vector of two variables: 1) time to event 2) censorship |

`outcome.class` |
outcome class of the 'outcome' variable. Can be either "continuous", "binary", or "survival". |

`trt` |
name of the treatment variable. |

`var` |
name of the biomarker variable. |

`covariate` |
vector specifying the covariate variables. This can be added to adjust for in the analysis for survival and continuous outcome variable classes. |

`strata` |
vector specifying the stratification variables. This can be added for the survival outcome variable class. |

`placebo.code` |
name of the control group within the treatment variable |

`active.code` |
name of the treatment/experimental group within the treatment variable |

`quantile.type` |
an integer between 1 and 9 selecting one of the nine quantile algorithms. See |

`alpha` |
confidence level (CI) for point estimate, i.e. 0.05 for 95 percent CI. Default is 0.05. |

`window.width` |
width of each window. Default is 0.25. |

`min.pt` |
minimum center.pt. Default is NULL. |

`max.pt` |
maximum center.pt. Default is NULL. |

`by` |
size of 'slide', i.e. speed of the window that moves along the x-axis. Default is 0.05. |

`yrange.lower` |
value of the lower y-axis. Default is NULL. |

`yrange.upper` |
value of the upper y-axis. Default is NULL. |

`xticks` |
x-tick marks. Default is NULL. |

`show.refline` |
if TRUE, the reference line will be displayed. Default is TRUE. |

`refline.color` |
color of the reference line. Default is "grey". |

`show.refline.ac` |
if TRUE, the reference line for effect in All Comers will be displayed. Default is TRUE. |

`refline.color.ac` |
color of the reference line for effect in All Comers. Default is "lightblue". |

`estimate.color` |
color of the estimate line. Default is "blue". |

`estimate.lty` |
type of the estimate line. Default is 1. |

`estimate.lwd` |
width of the estimate line. Default is 2. |

`surv.conf.type` |
confidence interval type. Default is "plain". see conf.type in survfit. |

`ties` |
Default is "efron". To match internal sas results, use "exact". See parameter "ties" in coxph. |

`ci.color` |
color of the CI lines. Default is "black". |

`ci.lty` |
type of the CI lines. Default is 2. |

`ci.lwd` |
width of the CI lines. Default is 1. |

`ci.shade` |
if TRUE, the area between the lower and upper CI lines will be shaded in gray. Default is TRUE. |

`plot.title` |
title of the plot. Default is "STEPP: Subgroup Treatment Effect Pattern Plot". |

`sub.title` |
subtitle of the plot, this will be displayed on the bottom of the plot. Default is NULL. |

`xlabel` |
x-axis label. Default is "Biomarker Percentile". |

`ylabel` |
y-axis label. Default is NULL. |

`show.legend` |
if TRUE, a legend will be displayed. Default is TRUE. |

`legend.loc` |
location of the legend to be displayed. Default is "topright". |

`legend.text` |
text to be displayed in the legend.
Default is |

`legend.col` |
colors of the legend. Default is |

`legend.lty` |
type of the legend lines. Default is |

`legend.lwd` |
width of the legend lines. Default is |

`legend.bty` |
type of box for the legend. Default is "n". |

`bm.digits` |
digits to be displayed/used for the lower and upper confidence level estimates. Default is 2. |

`actual.scale` |
if TRUE, it generates the figure using the actual scale instead of the scale in percentage. Default is FALSE. |

`equal.in.LL, equal.in.UL` |
if both are TRUE, window is defined using >= and <= (in legend: " |

`pdf.name` |
name of output pdf file. If it's NULL (default), the plots will be displayed but not saved as pdf. |

`pdf.param` |
a list of parameters that define pdf graphics device. See |

`par.param` |
a list of parameters that define graphcial parameters. See |

`csv.name` |
csv file name (includes numbers used in the graphs). If NULL (default), the function will return the result. |

Patient data without corresponding biomarker data are automatically removed. For survival data, censorship variable is 1 if an event happened, 0 if censored.

Alexey Pronin [email protected], Ning Leng [email protected], and previous team members (see DESCRIPTION)

SummaryTwoGroups

1 2 3 4 5 6 7 8 9 10 |

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