valorate.plot.sampling.densities: PLOT CO-OCCURRENCE DENSITIES FORMING A LOG-RANK DISTRIBUTION
In valorate: Velocity and Accuracy of the LOg-RAnk TEst

Description Usage Arguments Details Value Author(s) References See Also Examples

Plots the densities of each co-occurrence that shapes the final log-rank distribution for a n1 group size.

valorate.plot.sampling.densities(vro, n1, 
  type, log, xlim, ylim, ncol, main, 
  rug, add, w.sum, sampling, 
  weighted,legends.cex, weights.cex,
  weights.pos, w.sum.lwd=3,
  y.limit=1e-13,
  ...)

valorate.plot.sampling.densities.figure(vro, n1, type, log, 
  xlim, ylim, main, rug, rug.size, 
  sub, w.sum, sampling, ncol, 
  y.limit=1e-13, ...)

`vro`	the valorate object.
`n1`	the size of the 'mutated' or interested survival group. It can be also the numerical/logical 'x' vector as in valorate.survdiff in which case n1 and vstat are estimated.
`type`	typical plot parameter: "p"=points, "l"=lines (default), "o"=overlap.
`log`	typical plot parameter : specify which axis are shown in logarithm base 10.
`xlim`	typical plot parameter.
`ylim`	typical plot parameter.
`ncol`	number of columns for legends.
`main`	typical plot parameter. The default is an expression depending on the parameters.
`rug`	if FALSE removes the drawing of rugs.
`add`	if FALSE assumes plots are added to existing one. Not valid for all functions.
`w.sum`	if FALSE removes the drawing of the weighted sum distribution (the final log-rank distibution).
`sampling`	if TRUE includes the drawing of a crude-histogram version of the overall distribution (the final log-rank distibution).
`weighted`	if TRUE the densities of each co-occurrence is weighted to its overall contribution (proportion of combinations). Nice! to explain the overall distribution.
`legends.cex`	the character expansion for legends.
`weights.cex`	the character expansion for legends of the weights
`weights.pos`	the position of the weights "middle"=above each curve, "left", or "right".
`w.sum.lwd`	the line width of the weighted sum line.
`...`	parameters forwarded to plot.
`rug.size`	determine the size of rugs made in valorate.plot.sampling.densities.figure
`sub`	specifies the character to include in each plot.
`y.limit`	specifies the lowest density value. The default is 1e-13. This is useful for log="y".

Plots the densities of each co-occurrence that shapes the final log-rank distribution for a n1 group size. valorate.plot.sampling.densities plots all co-occurrences in the same figure whereas valorate.plot.sampling.densities.figure plots all in separated figures.

Nothing.

Victor Trevino vtrevino@itesm.mx

Trevino et al. 2016 http://bioinformatica.mty.itesm.mx/valorateR

new.valorate. valorate.survdiff.

## Create a random population of 100 subjects 
## having 20 events
subjects <- numeric(100)
subjects[sample(100,20)] <- 1
vo <- new.valorate(rank=subjects, sampling.size=100000, verbose=TRUE)

## Not run: valorate.plot.sampling.densities(vo, 5)
## Not run: valorate.plot.sampling.densities(vo, 10)
## Not run: valorate.plot.sampling.densities(vo, 20, weighted=TRUE)

## Not run: valorate.plot.sampling.densities.figure(vo, 5)