Visualization of Peeling Trajectories/Profiles
Description
Function for plotting the crossvalidated peeling trajectories/profiles of a PRSP
object.
Applies to the preselected covariates specified by user and
all other statistical quantities of interest at each iteration of the peeling sequence
(inner loop of our PRSP algorithm).
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
Arguments
object 
Object of class 
main 

toplot 

col.cov 

lty.cov 

lwd.cov 

col 

lty 

lwd 

cex 

add.legend 

text.legend 

nr 

nc 

device 
Graphic display device in {NULL, "PS", "PDF"}. Defaults to NULL (standard output screen). Currently implemented graphic display devices are "PS" (Postscript) or "PDF" (Portable Document Format). 
file 
File name for output graphic. Defaults to "Trajectory Plots". 
path 
Absolute path (without final (back)slash separator). Defaults to working directory path. 
horizontal 

width 

height 

... 
Generic arguments passed to other plotting functions. 
Details
The plot limits the display of trajectories to those only covariates that are used for peeling.
The plot includes box descriptive statistics (such as support), survival endpoint statistics (such as Maximum EventFree Time (MEFT), Minimum EventFree Probability (MEVP), LHR, LRT) and prediction performance (such as CER).
Value
Invisible. None. Displays the plot(s) on the specified device
.
Note
Enduser plotting function.
Author(s)
"JeanEudes Dazard, Ph.D." jxd101@case.edu
"Michael Choe, M.D." mjc206@case.edu
"Michael LeBlanc, Ph.D." mleblanc@fhcrc.org
"Alberto Santana, MBA." ahs4@case.edu
Maintainer: "JeanEudes Dazard, Ph.D." jxd101@case.edu
Acknowledgments: This project was partially funded by the National Institutes of Health NIH  National Cancer Institute (R01CA160593) to JE. Dazard and J.S. Rao.
References
Dazard JE., Choe M., LeBlanc M. and Rao J.S. (2015). "Crossvalidation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods." Statistical Analysis and Data Mining (in press).
Dazard JE., Choe M., LeBlanc M. and Rao J.S. (2014). "CrossValidation of Survival Bump Hunting by Recursive Peeling Methods." In JSM Proceedings, Survival Methods for Risk Estimation/Prediction Section. Boston, MA, USA. American Statistical Association IMS  JSM, p. 33663380.
Dazard JE., Choe M., LeBlanc M. and Rao J.S. (2015). "R package PRIMsrc: Bump Hunting by Patient Rule Induction Method for Survival, Regression and Classification." In JSM Proceedings, Statistical Programmers and Analysts Section. Seattle, WA, USA. American Statistical Association IMS  JSM, (in press).
Dazard JE. and J.S. Rao (2010). "Local Sparse Bump Hunting." J. Comp Graph. Statistics, 19(4):90092.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28  #===================================================
# Loading the library and its dependencies
#===================================================
library("PRIMsrc")
#=================================================================================
# Simulated dataset #1 (n=250, p=3)
# Non Replicated Combined CrossValidation (RCCV)
# Peeling criterion = LRT
# Optimization criterion = LRT
#=================================================================================
CVCOMB.synt1 < sbh(dataset = Synthetic.1,
cvtype = "combined", cvcriterion = "lrt",
B = 1, K = 5,
vs = TRUE, cpv = FALSE,
decimals = 2, probval = 0.5,
arg = "beta=0.05,
alpha=0.1,
minn=10,
L=NULL,
peelcriterion=\"lr\"",
parallel = FALSE, conf = NULL, seed = 123)
plot_boxtraj(object = CVCOMB.synt1,
main = paste("Crossvalidated peeling trajectories for model #1", sep=""),
toplot = CVCOMB.synt1$cvfit$cv.used,
device = NULL, file = "Trajectory Plots", path=getwd(),
horizontal = FALSE, width = 8.5, height = 11)
