ggkmcif2Parameters: Additional parameters passed to ggkmcif2

In reportRmd: Tidy Presentation of Clinical Reporting

Additional parameters passed to ggkmcif2

Description

This section documents the additional parameters for ggkmcif2.

Usage

ggkmcif2Parameters(
  table.height = NULL,
  HR = FALSE,
  HR_pval = FALSE,
  conf.type = "log",
  main = NULL,
  stratalabs = NULL,
  strataname,
  stratalabs.table = NULL,
  strataname.table = strataname,
  median.text = FALSE,
  median.lines = FALSE,
  median.CI = FALSE,
  set.time.text = NULL,
  set.time.line = FALSE,
  set.time = 5,
  set.time.CI = FALSE,
  censor.marks = TRUE,
  censor.size = 3,
  censor.stroke = 1.5,
  fsize = 11,
  nsize = 3,
  lsize = 1,
  psize = 3.5,
  median.size = 3,
  median.pos = NULL,
  median.lsize = 1,
  set.size = 3,
  set.pos = NULL,
  set.lsize = 1,
  ylim = c(0, 1),
  linetype = NULL,
  xlim = NULL,
  legend.pos = NULL,
  pval.pos = NULL,
  event = c("col", "linetype"),
  flip.CIF = FALSE,
  cut = NULL,
  eventlabs = NULL,
  event.name = NULL,
  Numbers_at_risk_text = "Number at risk",
  HR.digits = 2,
  HR.pval.digits = 3,
  pval.digits = 3,
  median.digits = 3,
  set.time.digits = 3,
  print.n.missing = TRUE,
  returns = FALSE
)

Arguments

table.height	Relative height of risk table (0-1)
HR	boolean to specify if you want hazard ratios included in the plot
HR_pval	boolean to specify if you want HR p-values in the plot
conf.type	One of "none"(the default), "plain", "log" , "log-log" or "logit". Only enough of the string to uniquely identify it is necessary. The first option causes confidence intervals not to be generated. The second causes the standard intervals curve +- k *se(curve), where k is determined from conf.int. The log option calculates intervals based on the cumulative hazard or log(survival). The log-log option bases the intervals on the log hazard or log(-log(survival)), and the logit option on log(survival/(1-survival)).
main	String corresponding to main title. When NULL uses Kaplan-Meier Plot s, and "Cumulative Incidence Plot for CIF"
stratalabs	string corresponding to the labels of the covariate, when NULL will use the levels of the covariate
strataname	String of the covariate name default is nicename(cov)
stratalabs.table	String corresponding to the levels of the covariate for the number at risk table, when NULL will use the levels of the covariate. Can use a string of "-" when the labels are long
strataname.table	String of the covariate name for the number at risk table default is nicename(cov
median.text	boolean to specify if you want the median values added to the legend (or as added text if there are no covariates), for KM only
median.lines	boolean to specify if you want the median values added as lines to the plot, for KM only
median.CI	boolean to specify if you want the 95\ interval with the median text (Only for KM)
set.time.text	string for the text to add survival at a specified time (eg. year OS)
set.time.line	boolean to specify if you want the survival added as lines to the plot at a specified point
set.time	Numeric values of the specific time of interest, default is 5 (Multiple values can be entered)
set.time.CI	boolean to specify if you want the 95\ interval with the set time text
censor.marks	logical value. If TRUE, includes censor marks (only for KM curves)
censor.size	size of censor marks, default is 3
censor.stroke	stroke of censor marks, default is 1.5
fsize	font size
nsize	font size for numbers in the numbers at risk table
lsize	line size
psize	size of the pvalue
median.size	size of the median text (Only when there are no covariates)
median.pos	vector of length 2 corresponding to the median position (Only when there are no covariates)
median.lsize	line size of the median lines
set.size	size of the survival at a set time text (Only when there are no covariates)
set.pos	vector of length 2 corresponding to the survival at a set point position (Only when there are no covariates)
set.lsize	line size of the survival at set points
ylim	vector of length 2 corresponding to limits of y-axis. Default to NULL
linetype	vector of line types; default is solid for all lines
xlim	vector of length 2 corresponding to limits of x-axis. Default to NULL
legend.pos	Can be either a string corresponding to the legend position ("left","top", "right", "bottom", "none") or a vector of length 2 corresponding to the legend position (uses normalized units (ie the c(0.5,0.5) is the middle of the plot))
pval.pos	vector of length 2 corresponding to the p-value position
event	String specifying if the event should be mapped to the colour, or linetype when plotting both events to colour = "col", line type
flip.CIF	boolean to flip the CIF curve to start at 1
cut	numeric value indicating where to divide a continuous covariate (default is the median)
eventlabs	String corresponding to the event type names
event.name	String corresponding to the label of the event types
Numbers_at_risk_text	String for the label of the number at risk
HR.digits	Number of digits printed of the hazard ratio
HR.pval.digits	Number of digits printed of the hazard ratio pvalue
pval.digits	Number of digits printed of the Gray's/log rank pvalue
median.digits	Number of digits printed of the median pvalue
set.time.digits	Number of digits printed of the probability at a specified time
print.n.missing	Logical, should the number of missing be shown !Needs to be checked
returns	Logical, if TRUE a list contain the plot and at risk table is returned

reportRmd documentation built on April 4, 2025, 2:03 a.m.