R: Regression Modeling Strategies

# Regression Modeling Strategies

## Documentation for package ‘rms’ version 8.1-1

- DESCRIPTION file
- Code demos. Use demo() to run them.
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N O P Q R S U V W X misc

## -- A --

adapt_orm | Adaptive orm Fit For a Single Continuous Predictor
AIC.rms | Miscellaneous Design Attributes and Utility Functions
anova.rms | Analysis of Variance (Wald, LR, and F Statistics)
as.data.frame.Ocens | Convert 'Ocens' Object to Data Frame to Facilitate Subset
asis | rms Special Transformation Functions

## -- B --

bj | Buckley-James Multiple Regression Model
bj.fit | Buckley-James Multiple Regression Model
bjplot | Buckley-James Multiple Regression Model
bootBCa | BCa Bootstrap on Existing Bootstrap Replicates
bootcov | Bootstrap Covariance and Distribution for Regression Coefficients
bootplot | Bootstrap Covariance and Distribution for Regression Coefficients
bootplot.bootcov | Bootstrap Covariance and Distribution for Regression Coefficients
bplot | 3-D Plots Showing Effects of Two Continuous Predictors in a Regression Model Fit

## -- C --

calibrate | Resampling Model Calibration
calibrate.cph | Resampling Model Calibration
calibrate.default | Resampling Model Calibration
calibrate.orm | Resampling Model Calibration
calibrate.psm | Resampling Model Calibration
calibrate.rms | Miscellaneous Design Attributes and Utility Functions
catg | rms Special Transformation Functions
combineRelatedPredictors | Miscellaneous Design Attributes and Utility Functions
confplot | Bootstrap Covariance and Distribution for Regression Coefficients
confplot.bootcov | Bootstrap Covariance and Distribution for Regression Coefficients
contrast | General Contrasts of Regression Coefficients
contrast.rms | General Contrasts of Regression Coefficients
cph | Cox Proportional Hazards Model and Extensions
cr.setup | Continuation Ratio Ordinal Logistic Setup

## -- D --

datadist | Distribution Summaries for Predictor Variables
Design | rms Methods and Generic Functions
DesignAssign | Miscellaneous Design Attributes and Utility Functions
dxy.cens | Validation of a Fitted Cox or Parametric Survival Model's Indexes of Fit

## -- E --

effective.df | Trace AIC and BIC vs. Penalty
ExProb | Function Generators For Exceedance and Survival Probabilities
ExProb.orm | Function Generators For Exceedance and Survival Probabilities

## -- F --

fastbw | Fast Backward Variable Selection
formatNP | Miscellaneous Design Attributes and Utility Functions
Function.cph | Compose an S Function to Compute X beta from a Fit
Function.rms | Compose an S Function to Compute X beta from a Fit

## -- G --

gendata | Generate Data Frame with Predictor Combinations
Getlim | Miscellaneous Design Attributes and Utility Functions
Getlimi | Miscellaneous Design Attributes and Utility Functions
ggplot | Exported Functions That Were Imported From Other Packages
ggplot.npsurv | Title Plot npsurv Nonparametric Survival Curves Using ggplot2
ggplot.Predict | Plot Effects of Variables Estimated by a Regression Model Fit Using ggplot2
gIndex | Calculate Total and Partial g-indexes for an rms Fit
Glm | rms Version of glm
Gls | Fit Linear Model Using Generalized Least Squares
groupkm | Kaplan-Meier Estimates vs. a Continuous Variable
gTrans | rms Special Transformation Functions

## -- H --

Hazard | Parametric Survival Model
Hazard.psm | Parametric Survival Model
hazard.ratio.plot | Hazard Ratio Plot
histdensity | Bootstrap Covariance and Distribution for Regression Coefficients
html.anova.rms | Analysis of Variance (Wald, LR, and F Statistics)
html.naprint.delete | Miscellaneous Design Attributes and Utility Functions
html.summary.rms | Summary of Effects in Model
html.validate | Resampling Validation of a Fitted Model's Indexes of Fit

## -- I --

ie.setup | Intervening Event Setup
impactPO | Impact of Proportional Odds Assumpton
infoMxop | Operate on Information Matrices
intCalibration | Check Parallelism Assumption of Ordinal Semiparametric Models
interactions.containing | Miscellaneous Design Attributes and Utility Functions
is.na.Ocens | is.na Method for Ocens Objects

## -- L --

latex.anova.rms | Analysis of Variance (Wald, LR, and F Statistics)
latex.bj | LaTeX Representation of a Fitted Model
latex.cph | LaTeX Representation of a Fitted Cox Model
latex.Glm | LaTeX Representation of a Fitted Model
latex.Gls | LaTeX Representation of a Fitted Model
latex.lrm | LaTeX Representation of a Fitted Cox Model
latex.naprint.delete | Miscellaneous Design Attributes and Utility Functions
latex.ols | LaTeX Representation of a Fitted Cox Model
latex.orm | LaTeX Representation of a Fitted Cox Model
latex.pphsm | LaTeX Representation of a Fitted Cox Model
latex.psm | LaTeX Representation of a Fitted Cox Model
latex.Rq | rms Package Interface to quantreg Package
latex.summary.rms | Summary of Effects in Model
latex.validate | Resampling Validation of a Fitted Model's Indexes of Fit
latexrms | LaTeX Representation of a Fitted Model
legend.nomabbrev | Draw a Nomogram Representing a Regression Fit
lines.residuals.psm.censored.normalized | Parametric Survival Model
logLik.Gls | Miscellaneous Design Attributes and Utility Functions
logLik.ols | Miscellaneous Design Attributes and Utility Functions
logLik.rms | Miscellaneous Design Attributes and Utility Functions
lrm | Logistic Regression Model
lrm.fit | lrm.fit
lrtest | Miscellaneous Design Attributes and Utility Functions
LRupdate | LRupdate
lsp | rms Special Transformation Functions

## -- M --

makepredictcall.rms | rms Special Transformation Functions
matinv | Total and Partial Matrix Inversion using Gauss-Jordan Sweep Operator
matrx | rms Special Transformation Functions
Mean.cph | Cox Proportional Hazards Model and Extensions
Mean.lrm | Predicted Values for Binary and Ordinal Logistic Models
Mean.orm | Predicted Values for Binary and Ordinal Logistic Models
Mean.psm | Parametric Survival Model
modelData | rms Methods and Generic Functions

## -- N --

Newlabels | Miscellaneous Design Attributes and Utility Functions
Newlabels.rms | Miscellaneous Design Attributes and Utility Functions
Newlevels | Miscellaneous Design Attributes and Utility Functions
Newlevels.rms | Miscellaneous Design Attributes and Utility Functions
nobs.rms | Miscellaneous Design Attributes and Utility Functions
nomogram | Draw a Nomogram Representing a Regression Fit
npsurv | Nonparametric Survival Estimates for Censored Data

## -- O --

Ocens | Censored Ordinal Variable
Ocens2ord | Recode Censored Ordinal Variable
Ocens2Surv | Ocens2Surv
Olinks | Likehood-Based Statistics for Other Links for orm Fits
ols | Linear Model Estimation Using Ordinary Least Squares
oos.loglik | Miscellaneous Design Attributes and Utility Functions
oos.loglik.cph | Miscellaneous Design Attributes and Utility Functions
oos.loglik.Glm | Miscellaneous Design Attributes and Utility Functions
oos.loglik.lrm | Miscellaneous Design Attributes and Utility Functions
oos.loglik.ols | Miscellaneous Design Attributes and Utility Functions
oos.loglik.psm | Miscellaneous Design Attributes and Utility Functions
ordESS | ordESS
ordParallel | Check Parallelism Assumption of Ordinal Semiparametric Models
orm | Ordinal Regression Model
orm.fit | Ordinal Regression Model Fitter

## -- P --

pantext | Plot Effects of Variables Estimated by a Regression Model Fit
param.order | Miscellaneous Design Attributes and Utility Functions
Penalty.matrix | Miscellaneous Design Attributes and Utility Functions
Penalty.setup | Miscellaneous Design Attributes and Utility Functions
pentrace | Trace AIC and BIC vs. Penalty
perimeter | 3-D Plots Showing Effects of Two Continuous Predictors in a Regression Model Fit
perlcode | Compose an S Function to Compute X beta from a Fit
plot.anova.rms | Analysis of Variance (Wald, LR, and F Statistics)
plot.calibrate | Resampling Model Calibration
plot.calibrate.default | Resampling Model Calibration
plot.contrast.rms | plot.contrast.rms
plot.ExProb | Function Generators For Exceedance and Survival Probabilities
plot.gIndex | Calculate Total and Partial g-indexes for an rms Fit
plot.lrm.partial | Residuals from an 'lrm' or 'orm' Fit
plot.nomogram | Draw a Nomogram Representing a Regression Fit
plot.pentrace | Trace AIC and BIC vs. Penalty
plot.Predict | Plot Effects of Variables Estimated by a Regression Model Fit
plot.rexVar | plot.rexVar
plot.sensuc | Sensitivity to Unmeasured Covariables
plot.summary.rms | Summary of Effects in Model
plot.val.prob | Validate Predicted Probabilities
plot.val.surv | Validate Predicted Probabilities Against Observed Survival Times
plot.val.survh | Validate Predicted Probabilities Against Observed Survival Times
plot.validate.rpart | Dxy and Mean Squared Error by Cross-validating a Tree Sequence
plot.xmean.ordinaly | Plot Mean X vs. Ordinal Y
plotIntercepts | Plot Intercepts
plotp.Predict | Plot Effects of Variables Estimated by a Regression Model Fit Using plotly
pol | rms Special Transformation Functions
poma | Examine proportional odds and parallelism assumptions of 'orm' and 'lrm' model fits.
pphsm | Parametric Proportional Hazards form of AFT Models
predab.resample | Predictive Ability using Resampling
Predict | Compute Predicted Values and Confidence Limits
predict.bj | Predicted Values from Model Fit
predict.cph | Predicted Values from Model Fit
predict.Glm | Predicted Values from Model Fit
predict.Gls | Predicted Values from Model Fit
predict.lrm | Predicted Values for Binary and Ordinal Logistic Models
predict.ols | Predicted Values from Model Fit
predict.orm | Predicted Values for Binary and Ordinal Logistic Models
predict.psm | Predicted Values from Model Fit
predict.rms | Predicted Values from Model Fit
predict.Rq | rms Package Interface to quantreg Package
predictrms | Predicted Values from Model Fit
print.anova.rms | Analysis of Variance (Wald, LR, and F Statistics)
print.bj | Buckley-James Multiple Regression Model
print.calibrate | Resampling Model Calibration
print.calibrate.default | Resampling Model Calibration
print.contrast.rms | General Contrasts of Regression Coefficients
print.cph | Print cph Results
print.datadist | Distribution Summaries for Predictor Variables
print.fastbw | Fast Backward Variable Selection
print.gIndex | Calculate Total and Partial g-indexes for an rms Fit
print.Glm | print.glm
print.Gls | Fit Linear Model Using Generalized Least Squares
print.impactPO | Print Result from impactPO
print.lrm | Logistic Regression Model
print.lrtest | Miscellaneous Design Attributes and Utility Functions
print.nomogram | Draw a Nomogram Representing a Regression Fit
print.Ocens | print Method for Ocens Objects
print.ols | Print ols
print.orm | Ordinal Regression Model
print.pentrace | Trace AIC and BIC vs. Penalty
print.pphsm | Parametric Proportional Hazards form of AFT Models
print.Predict | Compute Predicted Values and Confidence Limits
print.psm | Parametric Survival Model
print.rexVar | print.rexVar
print.rms | Miscellaneous Design Attributes and Utility Functions
print.Rq | rms Package Interface to quantreg Package
print.specs.rms | rms Specifications for Models
print.summary.rms | Summary of Effects in Model
print.survest.psm | Parametric Survival Estimates
print.val.prob | Validate Predicted Probabilities
print.val.survh | Validate Predicted Probabilities Against Observed Survival Times
print.validate | Resampling Validation of a Fitted Model's Indexes of Fit
print.validate.rpart | Dxy and Mean Squared Error by Cross-validating a Tree Sequence
prmiInfo | prmiInfo
prModFit | Miscellaneous Design Attributes and Utility Functions
processMI | processMI
processMI.fit.mult.impute | processMI.fit.mult.impute
prStats | Miscellaneous Design Attributes and Utility Functions
psm | Parametric Survival Model
Punits | Prepare units for Printing and Plotting

## -- Q --

Quantile.cph | Cox Proportional Hazards Model and Extensions
Quantile.orm | Ordinal Regression Model
Quantile.psm | Parametric Survival Model

## -- R --

rbind.Predict | Compute Predicted Values and Confidence Limits
rcs | rms Special Transformation Functions
recode2integer | recode2integer
related.predictors | Miscellaneous Design Attributes and Utility Functions
reListclean | Miscellaneous Design Attributes and Utility Functions
removeFormulaTerms | Miscellaneous Design Attributes and Utility Functions
residuals.bj | Buckley-James Multiple Regression Model
residuals.cph | Residuals for a cph Fit
residuals.Glm | residuals.Glm
residuals.lrm | Residuals from an 'lrm' or 'orm' Fit
residuals.ols | Residuals for ols
residuals.orm | Residuals from an 'lrm' or 'orm' Fit
residuals.psm | Parametric Survival Model
rexVar | rexVar
rms | rms Methods and Generic Functions
rms.Overview | Overview of rms Package
rms.trans | rms Special Transformation Functions
rmsArgs | Miscellaneous Design Attributes and Utility Functions
rmsMisc | Miscellaneous Design Attributes and Utility Functions
rmsOverview | Overview of rms Package
robcov | Robust Covariance Matrix Estimates
Rq | rms Package Interface to quantreg Package
RqFit | rms Package Interface to quantreg Package

## -- S --

sascode | Compose an S Function to Compute X beta from a Fit
scored | rms Special Transformation Functions
sensuc | Sensitivity to Unmeasured Covariables
setPb | Progress Bar for Simulations
show.influence | Which Observations are Influential
specs | rms Specifications for Models
specs.rms | rms Specifications for Models
strat | rms Special Transformation Functions
summary.rms | Summary of Effects in Model
Surv | Exported Functions That Were Imported From Other Packages
survdiffplot | Plot Survival Curves and Hazard Functions
survest | Cox Survival Estimates
survest.cph | Cox Survival Estimates
survest.orm | Title survest.orm
survest.psm | Parametric Survival Estimates
survest.rms | Miscellaneous Design Attributes and Utility Functions
survfit.cph | Cox Predicted Survival
Survival | Parametric Survival Model
Survival.cph | Cox Proportional Hazards Model and Extensions
Survival.orm | Function Generators For Exceedance and Survival Probabilities
Survival.psm | Parametric Survival Model
survplot | Plot Survival Curves and Hazard Functions
survplot.npsurv | Plot Survival Curves and Hazard Functions
survplot.orm | Title Survival Curve Plotting
survplot.residuals.psm.censored.normalized | Parametric Survival Model
survplot.rms | Plot Survival Curves and Hazard Functions
survplotp | Plot Survival Curves and Hazard Functions
survplotp.npsurv | Plot Survival Curves and Hazard Functions

## -- U --

univarLR | Miscellaneous Design Attributes and Utility Functions

## -- V --

val.prob | Validate Predicted Probabilities
val.surv | Validate Predicted Probabilities Against Observed Survival Times
validate | Resampling Validation of a Fitted Model's Indexes of Fit
validate.bj | Buckley-James Multiple Regression Model
validate.cph | Validation of a Fitted Cox or Parametric Survival Model's Indexes of Fit
validate.lrm | Resampling Validation of a Logistic or Ordinal Regression Model
validate.ols | Validation of an Ordinary Linear Model
validate.orm | Resampling Validation of a Logistic or Ordinal Regression Model
validate.psm | Validation of a Fitted Cox or Parametric Survival Model's Indexes of Fit
validate.rpart | Dxy and Mean Squared Error by Cross-validating a Tree Sequence
validate.Rq | Validation of a Quantile Regression Model
vcov.cph | Miscellaneous Design Attributes and Utility Functions
vcov.Glm | Miscellaneous Design Attributes and Utility Functions
vcov.Gls | Miscellaneous Design Attributes and Utility Functions
vcov.lrm | Miscellaneous Design Attributes and Utility Functions
vcov.ols | Miscellaneous Design Attributes and Utility Functions
vcov.orm | Miscellaneous Design Attributes and Utility Functions
vcov.pphsm | Parametric Proportional Hazards form of AFT Models
vcov.psm | Miscellaneous Design Attributes and Utility Functions
vcov.rms | Miscellaneous Design Attributes and Utility Functions
vif | Variance Inflation Factors

## -- W --

which.influence | Which Observations are Influential

## -- X --

Xcontrast | Xcontrast

## -- misc --

%ia% | rms Special Transformation Functions
[.Ocens | Ocens