Package: RCASPAR 1.59.0

Douaa Mugahid

RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.

Authors:Douaa Mugahid, Lars Kaderali

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RCASPAR/json (API)

# Install 'RCASPAR' in R:

install.packages('RCASPAR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Bergamaschi - Gene expression data of 82 patients with 10 genes as covariates
survData - Survial data of 82 patients

On BioConductor:RCASPAR-1.59.0(bioc 3.24)RCASPAR-1.58.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

acgh geneexpression genetics proteomics visualization

3.30 score 3 scripts 357 downloads 17 exports 0 dependencies

Last updated from:60a3947144. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	143
linux-devel-x86_64	NOTE	204
source / vignettes	OK	181
linux-release-x86_64	NOTE	175
macos-release-arm64	NOTE	72
macos-oldrel-arm64	NOTE	101
windows-devel	NOTE	59
windows-release	NOTE	59
windows-oldrel	NOTE	65
wasm-release	OK	93

Exports:deriv_weight_estimator_BLH deriv_weight_estimator_BLH_noprior kmplt kmplt_svrl logrnk pltgamma pltprior simpson STpredictor_BLH STpredictor_xvBLH survivAURC survivROC trapezoid weight_estimator_BLH weight_estimator_BLH_noprior weights_BLH weights_xvBLH

Dependencies:

RCASPAR: Software for high-dimentional-data driven survival time prediction

Introduction | Arranging the input data for RCASPAR | Predicting patient survival times | Accessing the weights and baseline hazards returned | Plotting the KM curve of short and long survivors in the same plot | Plotting the receiver-operator curves at a particular time point | Generating a plot of the areas under all ROC curves and calculating the area under it | Comparing two populations according to their KM survival curves

Rendered fromRCASPAR.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Help page	Topics
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.	RCASPAR-package RCASPAR
Gene expression data of 82 patients with 10 genes as covariates	Bergamaschi
A function that gives the derivative of the objective function of the model for gradient-based optimization algorithms.	deriv_weight_estimator_BLH
A function that gives the derivative of the objective function of the model for gradient-based optimization algorithms without including the prior on the regression coefficients.	deriv_weight_estimator_BLH_noprior
Plot Kaplan Meier curve	kmplt
A function that plots the KM curves of $2-3$ patient sets in one graph.	kmplt_svrl
Performs Log Rank test on the long and short patient sets	logrnk
Plotting the gamma distribution of shape parameter	pltgamma
A function to visualize the shape of the prior on the weights with the chosen q and s parameters.	pltprior
A function that calculates the area under a curve based on the Simposon algorithm	simpson
Predicts the survival times of the validation set based on the regression coefficients and baseline hazards determined according to the Piecewise baseline hazard Cox regression model.	STpredictor_BLH
This function performs a cross validation on the full data set to help predict the survival times of the patients using the piecewise baseline hazard PH Cox model.	STpredictor_xvBLH
Survial data of 82 patients	survData
A function that calculates the area under a curve constructed from plotting the area under a ROC curve at the corresponding time point at which it was generated.	survivAURC
Generates the ROC curve at a given time point given the observed and predicted survival data in the presence of censored subjects.	survivROC
A function that calculates the area under a curve based on the Simposon algorithm	trapezoid
Returns the value of the objective function used for optimizing for the regression parameters and baseline hazards in the model.	weight_estimator_BLH
Returns the value of the objective function used for optimizing for the regression parameters and baseline hazards in the model, without including the prior on the regression coefficients.	weight_estimator_BLH_noprior
Optimization for the regression coefficients and baseline hazards that maximize the partial likelihood in our PW Cox PH regression model.	weights_BLH
A special version of STpredictor.BLH used within k-xv to predict the survival times of the kth validation group in the cross validation step.	weights_xvBLH

Package: RCASPAR 1.59.0

RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

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