# Partial Least Squares for Cox Models with Big Matrices

## Documentation for package ‘bigPLScox’ version 0.8.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

bigPLScox-package | bigPLScox-package
%*%-method | Matrix and arithmetic operations for big.matrix objects
align_big_plscox | Align a GD fit to a PLS fit (optional refit)
Arith-method | Matrix and arithmetic operations for big.matrix objects
benchmark_deviance_residuals | Cox deviance residuals via C++ backends
bigmatrix-operations | Matrix and arithmetic operations for big.matrix objects
bigPLScox | bigPLScox-package
bigscale | Construct Scaled Design Matrices for Big Survival Models
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
component_information | Information criteria for component selection
component_information, | Information criteria for component selection
component_information.big_pls_cox | Information criteria for component selection
component_information.big_pls_cox, | Information criteria for component selection
component_information.big_pls_cox_gd | Information criteria for component selection
component_information.big_pls_cox_gd, | Information criteria for component selection
computeDR | Compute deviance residuals
coxDKgplsDR | Fitting a Direct Kernel group PLS model on the (Deviance) Residuals
coxDKgplsDR.default | Fitting a Direct Kernel group PLS model on the (Deviance) Residuals
coxDKgplsDR.formula | Fitting a Direct Kernel group PLS model on the (Deviance) Residuals
coxDKsgplsDR | Fitting a Direct Kernel group sparse PLS model on the (Deviance) Residuals
coxDKsgplsDR.default | Fitting a Direct Kernel group sparse PLS model on the (Deviance) Residuals
coxDKsgplsDR.formula | 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
coxDKspls_sgplsDR.default | Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals
coxDKspls_sgplsDR.formula | Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals
coxgpls | Fitting a Cox-Model on group PLSR components
coxgpls.default | Fitting a Cox-Model on group PLSR components
coxgpls.formula | Fitting a Cox-Model on group PLSR components
coxgplsDR | Fitting a Cox-Model on group PLSR components using the (Deviance) Residuals
coxgplsDR.default | Fitting a Cox-Model on group PLSR components using the (Deviance) Residuals
coxgplsDR.formula | Fitting a Cox-Model on group PLSR components using the (Deviance) Residuals
coxsgpls | Fitting a Cox-Model on group sparse PLSR components
coxsgpls.default | Fitting a Cox-Model on group sparse PLSR components
coxsgpls.formula | Fitting a Cox-Model on group sparse PLSR components
coxsgplsDR | Fitting a Cox-Model on group sparse PLSR components using the (Deviance) Residuals
coxsgplsDR.default | Fitting a Cox-Model on group sparse PLSR components using the (Deviance) Residuals
coxsgplsDR.formula | Fitting a Cox-Model on group sparse PLSR components using the (Deviance) Residuals
coxspls_sgpls | Fitting a Cox-Model on sparse PLSR components
coxspls_sgpls.default | Fitting a Cox-Model on sparse PLSR components
coxspls_sgpls.formula | Fitting a Cox-Model on sparse PLSR components
coxspls_sgplsDR | Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals
coxspls_sgplsDR.default | Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals
coxspls_sgplsDR.formula | Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals
cox_deviance_details | Cox deviance residuals via C++ backends
cox_deviance_residuals | Cox deviance residuals via C++ backends
cox_deviance_residuals_big | Cox deviance residuals via C++ backends
cox_partial_deviance_big | Cox deviance residuals via C++ backends
cv.big_pls_cox | Cross-validation for big-memory PLS-Cox models
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
dataCox | Cox Proportional Hazards Model Data Generation From Weibull Distribution
dCox_sim | Simulated survival dataset for Cox models
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.coxDKgplsDR | Predict survival summaries from legacy Cox-PLS fits
predict.coxDKsgplsDR | Predict survival summaries from legacy Cox-PLS fits
predict.coxDKspls_sgplsDR | Predict survival summaries from legacy Cox-PLS fits
predict.coxgpls | Predict survival summaries from legacy Cox-PLS fits
predict.coxgplsDR | Predict survival summaries from legacy Cox-PLS fits
predict.coxsgpls | Predict survival summaries from legacy Cox-PLS fits
predict.coxsgplsDR | Predict survival summaries from legacy Cox-PLS fits
predict.coxspls_sgpls | Predict survival summaries from legacy Cox-PLS fits
predict.gPLS | Predict responses and latent scores from PLS fits
predict.pls.cox | Predict responses and latent scores from PLS fits
predict.sgPLS | Predict responses and latent scores from PLS fits
predict.sPLS | Predict responses and latent scores from PLS fits
predict_cox_pls | Predict survival summaries from legacy Cox-PLS fits
predict_pls_latent | 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
select_ncomp | Information criteria for component selection
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
Xmicro.censure_compl_imp | Imputed Microsat features