# "Risk Model Regression and Analysis with Complex Non-Linear Models"

## Documentation for package ‘Colossus’ version 1.5.1

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

## Help Pages

CaseControlRun | Fully runs a case-control regression model, returning the model and results
ColossusCoxSurv | Interprets basic cox survival formula RHS
ColossusLogitSurv | Interprets basic logistic survival formula RHS with no grouping
ColossusPoisSurv | Interprets basic poisson survival formula RHS
CoxRun | Fully runs a cox or fine-gray regression model, returning the model and results
CoxRunMulti | Fully runs a cox or fine-gray regression model with multiple column realizations, returning the model and results
Date_Shift | Automates creating a date difference column
EventAssignment | Generic background/excess event calculation function
EventAssignment.default | Predicts how many events are due to baseline vs excess
EventAssignment.poisres | Predicts how many events are due to baseline vs excess for a completed poisson model
EventAssignment.poisresbound | Predicts how many events are due to baseline vs excess for a completed poisson likelihood boundary regression
Event_Count_Gen | uses a table, list of categories, and list of event summaries to generate person-count tables
Event_Time_Gen | uses a table, list of categories, list of summaries, list of events, and person-year information to generate person-time tables
factorize | Splits a parameter into factors
gen_time_dep | Applies time dependence to parameters
get_form | Interprets a Colossus formula and makes necessary changes to data
get_form_joint | Interprets a Poisson joint formula and makes necessary changes to data
Joint_Multiple_Events | Automates creating data for a joint competing risks analysis
LikelihoodBound | Generic likelihood boundary calculation function
LikelihoodBound.coxres | Calculates the likelihood boundary for a completed cox model
LikelihoodBound.default | Generic likelihood boundary calculation function, default option
LikelihoodBound.poisres | Calculates the likelihood boundary for a completed Poisson model
Likelihood_Ratio_Test | Defines the likelihood ratio test
Linked_Dose_Formula | Calculates Full Parameter list for Special Dose Formula
Linked_Lin_Exp_Para | Calculates The Additional Parameter For a linear-exponential formula with known maximum
LogisticRun | Fully runs a logistic regression model, returning the model and results
OMP_Check | Checks the OMP flag
plot.coxres | Performs Cox Proportional Hazard model plots
plotMartingale | Generic Martingale Residual Plotting function
plotMartingale.coxres | Performs Cox Proportional Hazard model martingale residual plots
plotMartingale.default | Generic Martingale Residual Plotting function, default option
plotRisk | Generic Risk Plotting function
plotRisk.coxres | Performs Cox Proportional Hazard model hazard ratio plots
plotRisk.default | Generic Risk Plotting function, default option
plotSchoenfeld | Generic Schoenfeld Residual Plotting function
plotSchoenfeld.coxres | Performs Cox Proportional Hazard model schoenfeld residual plots
plotSchoenfeld.default | Generic Schoenfeld Residual Plotting function, default option
plotSurvival | Generic Survival Plotting function
plotSurvival.coxres | Performs Cox Proportional Hazard model survival plots
plotSurvival.default | Generic Survival Plotting function, default option
PoisRun | Fully runs a poisson regression model, returning the model and results
PoisRunJoint | Fully runs a joint poisson regression model, returning the model and results
PoisRunMulti | Fully runs a poisson regression model with multiple column realizations, returning the model and results
print.caseconres | Prints a case-control regression output clearly
print.coxres | Prints a cox regression output clearly
print.coxresbound | Prints a cox likelihood boundary regression output clearly
print.logitres | Prints a logistic regression output clearly
print.poisres | Prints a poisson regression output clearly
print.poisresbound | Prints a poisson likelihood boundary regression output clearly
RelativeRisk | Generic relative risk calculation function
RelativeRisk.coxres | Calculates hazard ratios for a reference vector
RelativeRisk.default | Generic relative risk calculation function, default option
Replace_Missing | Automatically assigns missing values in listed columns
Residual | Generic Residual calculation function
Residual.default | Generic Residual calculation function, default option
Residual.poisres | Calculates the Residuals for a completed poisson model
System_Version | Checks OS, compilers, and OMP
Time_Since | Automates creating a date since a reference column