ggkmcif2Parameters: Additional parameters passed to ggkmcif2

Description

Additional parameters passed to 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
)

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\ 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