Package index • bigPLScox

All functions

Xmicro.censure_compl_imp: Imputed Microsat features

align_big_plscox(): Align a GD fit to a PLS fit (optional refit)

bigPLScox-package bigPLScox: bigPLScox-package

bigSurvSGD.na.omit(): Fit Survival Models with Stochastic Gradient Descent

big_pls_cox(): Partial Least Squares Components for Cox Models with Big Matrices

big_pls_cox_fast(): Partial Least Squares Components for Cox Models (fast backend)

big_pls_cox_gd(): Gradient based PLS Cox for big matrices

big_pls_cox_transform(): Transform new data to PLS–Cox scores

`%*%`(<big.matrix>,<big.matrix>) `%*%`(<matrix>,<big.matrix>) `%*%`(<big.matrix>,<matrix>) Arith(<big.matrix>,<big.matrix>) Arith(<big.matrix>,<matrix>) Arith(<matrix>,<big.matrix>) Arith(<numeric>,<big.matrix>) Arith(<big.matrix>,<numeric>): Matrix and arithmetic operations for big.matrix objects

bigscale(): Construct Scaled Design Matrices for Big Survival Models

component_information() select_ncomp(): Information criteria for component selection

computeDR(): Compute deviance residuals

coxDKgplsDR(): Fitting a Direct Kernel group PLS model on the (Deviance) Residuals

coxDKsgplsDR(): Fitting a Direct Kernel group sparse PLS model on the (Deviance) Residuals

coxDKspls_sgplsDR(): Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals

cox_deviance_residuals() cox_deviance_details() cox_deviance_residuals_big() cox_partial_deviance_big() benchmark_deviance_residuals(): Cox deviance residuals via C++ backends

coxgpls(): Fitting a Cox-Model on group PLSR components

coxgplsDR(): Fitting a Cox-Model on group PLSR components using the (Deviance) Residuals

coxsgpls(): Fitting a Cox-Model on group sparse PLSR components

coxsgplsDR(): Fitting a Cox-Model on group sparse PLSR components using the (Deviance) Residuals

coxspls_sgpls(): Fitting a Cox-Model on sparse PLSR components

coxspls_sgplsDR(): Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals

cv.big_pls_cox() cv.big_pls_cox_gd(): Cross-validation for big-memory PLS-Cox models

cv.coxDKgplsDR(): Cross-validating a Direct Kernel group PLS model fitted on the (Deviance) Residuals

cv.coxDKsgplsDR(): Cross-validating a Direct Kernel group sparse PLS model fitted on the (Deviance) Residuals

cv.coxDKspls_sgplsDR(): Cross-validating a Direct Kernel sparse PLS model fitted on the (Deviance) Residuals

cv.coxgpls(): Cross-validating a Cox-Model fitted on group PLSR components

cv.coxgplsDR(): Cross-validating a Cox-Model fitted on group PLSR components using (Deviance) Residuals

cv.coxsgpls(): Cross-validating a Cox-Model fitted on sparse group PLSR components

cv.coxsgplsDR(): Cross-validating a Cox-Model fitted on sparse group PLSR components using (Deviance) Residuals

cv.coxspls_sgpls(): Cross-validating a Cox-Model fitted on sparse PLSR components

cv.coxspls_sgplsDR(): Cross-validating a Cox-Model fitted on sparse PLSR components components using (Deviance) Residuals

dCox_sim: Simulated survival dataset for Cox models

dataCox(): Cox Proportional Hazards Model Data Generation From Weibull Distribution

gd_diagnostics(): Extract Diagnostics from a big_pls_cox_gd Model

micro.censure: Microsat features and survival times

partialbigSurvSGDv0(): Incremental Survival Model Fitting with Pre-Scaled Data

plot(<big_pls_cox>): Plot method for big_pls_cox objects

plot(<big_pls_cox_gd>): Plot method for big_pls_cox_gd objects

predict(<big_pls_cox>): Predict method for big-memory PLS-Cox models

predict(<big_pls_cox_fast>): Predictions for fast big PLS–Cox fits

predict(<big_pls_cox_gd>): Predict method for big_pls_cox_gd

predict(<coxgpls>) predict(<coxgplsDR>) predict(<coxsgpls>) predict(<coxsgplsDR>) predict(<coxspls_sgpls>) predict(<coxDKgplsDR>) predict(<coxDKsgplsDR>) predict(<coxDKspls_sgplsDR>): Predict survival summaries from legacy Cox-PLS fits

predict(<gPLS>) predict(<pls.cox>) predict(<sPLS>) predict(<sgPLS>): Predict responses and latent scores from PLS fits

print(<big_pls_cox>): Print method for big_pls_cox objects

print(<big_pls_cox_gd>): Print method for big_pls_cox_gd objects

print(<summary.big_pls_cox_fast>): Print method for summary.big_pls_cox_fast objects

sim_data: Simulated dataset

summary(<big_pls_cox>): Summary for big_pls_cox objects

summary(<big_pls_cox_fast>): Summary for big_pls_cox objects

summary(<big_pls_cox_gd>): Summary for big_pls_cox_gd objects