plot.survfit            package:survival            R Documentation

_P_l_o_t _M_e_t_h_o_d _f_o_r '_s_u_r_v_f_i_t'

_D_e_s_c_r_i_p_t_i_o_n:

     A plot of survival curves is produced, one curve for each strata. 
     The 'log=T' option does extra work to avoid log(0), and to try to
     create a  pleasing result.  If there are zeros, they are plotted
     by default at  0.8 times the smallest non-zero value on the
     curve(s).

_U_s_a_g_e:

     ## S3 method for class 'survfit':
     plot(x, conf.int=, mark.time=TRUE, 
      mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, yscale=1,  
      firstx=0, firsty=1, xmax, ymin=0, fun, 
      xlab="", ylab="", xaxs="S", ...)

_A_r_g_u_m_e_n_t_s:

       x: an object of class 'survfit', usually returned by the
          'survfit' function.  

conf.int: determines whether confidence intervals will be plotted.  The
          default is to  do so if there is only 1 curve, i.e., no
          strata.  

mark.time: controls the labeling of the curves.  If set to 'FALSE', no
          labeling is done.  If 'TRUE', then curves are marked at each
          censoring time which is not also a death time.  If
          'mark.time' is a  numeric vector, then curves are marked at
          the specified time points.  

    mark: vector of mark parameters, which will be used to label the
          curves.  The 'lines' help file contains examples of the
          possible marks.  The vector is reused cyclically if it is
          shorter than the number of curves.  

     col: a vector of integers specifying colors for each curve.  The
          default value is 1.  

     lty: a vector of integers specifying line types for each curve. 
          The default value is 1.  

     lwd: a vector of numeric values for line widths. The default value
          is 1.  

     cex: a numeric value specifying the size of the marks.  This is
          not treated as a vector; all marks have the same size. 

     log: a logical value, if TRUE the y axis wll be on a log scale. 
          Alternately, one of the standard character strings "x", "y",
          or "xy" can be given to specific logarithmic horizontal
          and/or vertical axes. 

  yscale: a numeric value used to multiply the labels on the y axis.  A
          value of 100, for instance, would be used to give a percent
          scale.  Only the labels are  changed, not the actual plot
          coordinates, so that adding a curve with 
          "'lines(surv.exp(...))'", say,   will perform as it did
          without the 'yscale' argument.  

  xscale: a numeric value used like 'yscale' for labels on the x axis. 
           A value of 365.25 will give labels in years instead of the
          original days.   

firstx, firsty: the starting point for the survival curves.  If either
          of these is set to  'NA' the plot will start at the first
          time point of the curve.  By default, the plot program obeys
          tradition by having the plot start at (0,0).

          If 'start.time' argument is used in 'survfit', 'firstx' is
          set to that value. 

    xmax: the maximum horizontal plot coordinate.  This can be used to
          shrink the range of a plot.  It shortens the curve before
          plotting it, so that unlike using the 'xlim' graphical
          parameter, warning messages about out of bounds points are
          not generated. 

    ymin: lower boundary for y values.  Survival curves are most often
          drawn in the  range of 0-1, even if none of the curves
          approach zero.  The parameter is ignored if the 'fun'
          argument is present, or if it has been set to 'NA'.  

     fun: an arbitrary function defining a transformation of the
          survival curve.  For example 'fun=log' is an alternative way
          to draw a log-survival curve  (but with the axis labeled with
          log(S) values),  and 'fun=sqrt' would generate a curve on
          square root scale.  Four often used transformations can be
          specified with a character  argument instead: '"log"' is the
          same as using the 'log=T' option,  '"event"' plots cumulative
          events (f(y) = 1-y),   '"cumhaz"' plots the cumulative hazard
          function (f(y) = -log(y)), and  '"cloglog"' creates a
          complimentary log-log survival plot (f(y) =  log(-log(y))
          along with log scale for the x-axis).   

    xlab: label given to the x-axis.  

    ylab: label given to the y-axis.  

    xaxs: either '"S"' for a survival curve or a standard x axis style
          as listed in 'par'. Survival curves are usually displayed
          with the curve touching the y-axis, but not touching the
          bounding box of the plot on the other 3 sides. Type '"S"'
          accomplishes this by manipulating the plot range and then
          using the '"i"' style internally. 

     ...: for future methods

_V_a_l_u_e:

     a list with components 'x' and 'y', containing the coordinates of
     the last point  on each of the curves (but not the confidence
     limits).    This may be useful for labeling.

_B_u_g_s:

     Survival curve objects created from a 'coxph' model does not
     include the censoring times. Therefore, specifying 'mark.time=T'
     does not work. If you want to mark censoring times on the curve(s)
     resulting    from a 'coxph' fit, provide a vector of times as the
     'mark.time' argument   in the call to 'plot.survfit' or
     'lines.survfit'.

_S_e_e _A_l_s_o:

     'par',   'survfit',   'lines.survfit'.

_E_x_a_m_p_l_e_s:

     leukemia.surv <- survfit(Surv(time, status) ~ x, data = aml) 
     plot(leukemia.surv, lty = 2:3) 
     legend(100, .9, c("Maintenance", "No Maintenance"), lty = 2:3) 
     title("Kaplan-Meier Curves\nfor AML Maintenance Study") 
     lsurv2 <- survfit(Surv(time, status) ~ x, aml, type='fleming') 
     plot(lsurv2, lty=2:3, fun="cumhaz", 
             xlab="Months", ylab="Cumulative Hazard") 

