Function for plotting the cross-validated tuning profiles of a PRSP object.
It uses the user's choice of statistics among the Log Hazard Ratio (LHR),
Log-Rank Test (LRT) or Concordance Error Rate (CER) as a function of the model tuning parameter,
that is, the optimal number of peeling steps of the peeling sequence (inner loop of our PRSP algorithm).
Object of class PRSP as generated by the main function sbh.
main
Charactervector. Main Title. Defaults to NULL.
xlab
Charactervector. X axis label. Defaults to "Peeling Steps".
ylab
Charactervector. Y axis label. Defaults to "Mean Profiles".
add.sd
Logical scalar. Shall the standard error bars be plotted? Defaults to TRUE.
add.legend
Logical scalar. Shall the legend be plotted? Defaults to TRUE.
add.profiles
Logical scalar. Shall the individual profiles (for all replicates) be plotted?
Defaults to TRUE.
pch
Integer scalar of symbol number for all the profiles. Defaults to 20.
col
Integer scalar of line color of the mean profile. Defaults to 1.
lty
Integer scalar of line type of the mean profile. Defaults to 1.
lwd
Integer scalar of line width of the mean profile. Defaults to 2.
cex
Integer scalar of symbol expansion for all the profiles. Defaults to 2.
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 "Profile Plot".
path
Absolute path (without final (back)slash separator). Defaults to working directory path.
horizontal
Logical scalar. Orientation of the printed image. Defaults to FALSE, that is potrait orientation.
width
Numeric scalar. Width of the graphics region in inches. Defaults to 8.5.
height
Numeric scalar. Height of the graphics region in inches. Defaults to 5.0.
...
Generic arguments passed to other plotting functions.
Details
Model tuning is done by applying the optimization criterion defined by the user's choice of specific statistic.
The goal is to find the optimal value of the number of steps by maximization of LHR or LRT, or minimization of CER.
Currently, this is done internally for visualization purposes, but it will ultimately offer the option to be done
interactively with the end-user as well for parameter choosing/model selection.
Value
Invisible. None. Displays the plot(s) on the specified device.
Acknowledgments: This project was partially funded by the National Institutes of Health
NIH - National Cancer Institute (R01-CA160593) to J-E. Dazard and J.S. Rao.
References
Dazard J-E., Choe M., LeBlanc M. and Rao J.S. (2015).
"Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods."
Statistical Analysis and Data Mining (in press).
Dazard J-E., Choe M., LeBlanc M. and Rao J.S. (2014).
"Cross-Validation 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. 3366-3380.
Dazard J-E., 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 J-E. and J.S. Rao (2010).
"Local Sparse Bump Hunting."
J. Comp Graph. Statistics, 19(4):900-92.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(PRIMsrc)
Loading required package: parallel
Loading required package: survival
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, round.POSIXt, trunc.POSIXt, units
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5
Loading required package: MASS
PRIMsrc 0.6.3
Type PRIMsrc.news() to see new features, changes, and bug fixes
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/PRIMsrc/plot_profile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_profile
> ### Title: Visualization for Model Selection/Validation
> ### Aliases: plot_profile
> ### Keywords: Exploratory Survival/Risk Analysis Survival/Risk Estimation &
> ### Prediction Non-Parametric Method Cross-Validation Bump Hunting
> ### Rule-Induction Method
>
> ### ** Examples
>
> #===================================================
> # Loading the library and its dependencies
> #===================================================
> library("PRIMsrc")
>
> #=================================================================================
> # Simulated dataset #1 (n=250, p=3)
> # Non Replicated Combined Cross-Validation (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)
Survival dataset provided.
Requested single 5-fold cross-validation without replications
Cross-validation technique: COMBINED
Cross-validation criterion: LRT
Variable pre-selection: TRUE
Computation of permutation p-values: FALSE
Peeling criterion: LRT
Parallelization: FALSE
Pre-selection of covariates and determination of directions of peeling...
Pre-selected covariates:
X1 X2 X3
1 2 3
Directions of peeling at each step of pre-selected covariates:
X1 X2 X3
1 -1 -1
Fitting and cross-validating the Survival Bump Hunting model using the PRSP algorithm ...
replicate : 1
seed : 123
Fold : 1
Fold : 2
Fold : 3
Fold : 4
Fold : 5
Success! 1 (replicated) cross-validation(s) has(ve) completed
Generating cross-validated optimal peeling lengths from all replicates ...
Generating cross-validated box memberships at each step ...
Generating cross-validated box rules for the pre-selected covariates at each step ...
Generating cross-validated modal trace values of covariate usage at each step ...
Covariates used for peeling at each step, based on covariate trace modal values:
X1 X2
1 2
Generating cross-validated box statistics at each step ...
Finished!
>
> plot_profile(object = CVCOMB.synt1,
+ main = "Cross-validated tuning profiles for model #1",
+ xlab = "Peeling Steps", ylab = "Mean Profiles",
+ pch=20, col="black", lty=1, lwd=2, cex=2,
+ add.sd = TRUE, add.legend = TRUE, add.profiles = TRUE,
+ device = NULL, file = "Profile Plot", path=getwd(),
+ horizontal = FALSE, width = 8.5, height = 5.0)
Device: 2
>
>
>
>
>
> dev.off()
null device
1
>