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

## Documentation for package ‘Colossus’ version 1.3.0

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

## Help Pages

Check_Dupe_Columns | checks for duplicated column names
Check_Trunc | Applies time duration truncation limits to create columns for Cox model
Check_Verbose | General purpose verbosity check
Convert_Model_Eq | Converts a string equation to regression model inputs
Correct_Formula_Order | Corrects the order of terms/formula/etc
CoxCurveSolver | Calculates the likelihood curve for a cox model directly
Cox_Relative_Risk | Calculates hazard ratios for a reference vector
Date_Shift | Automates creating a date difference column
Def_Control | Automatically assigns missing control values
Def_Control_Guess | Automatically assigns missing guessing control values
Def_modelform_fix | Automatically assigns geometric-mixture values and checks that a valid modelform is used
Def_model_control | Automatically assigns missing model control values
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
factorize_par | Splits a parameter into factors in parallel
Gather_Guesses_CPP | Performs checks to gather a list of guesses and iterations
gcc_version | Checks default c++ compiler
gen_time_dep | Applies time dependence to parameters
GetCensWeight | Calculates and returns data for time by hazard and survival to estimate censoring rate
get_os | Checks system OS
interact_them | Defines Interactions
Interpret_Output | Prints a regression output clearly
Joint_Multiple_Events | Automates creating data for a joint competing risks analysis
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
OMP_Check | Checks the OMP flag
PoissonCurveSolver | Calculates the likelihood curve for a poisson model directly
Rcomp_version | Checks how R was compiled
Rcpp_version | Checks default R c++ compiler
Replace_Missing | Automatically assigns missing values in listed columns
RunCaseControlRegression_Omnibus | Performs Matched Case-Control Conditional Logistic Regression
RunCoxNull | Performs basic Cox Proportional Hazards regression with the null model
RunCoxPlots | Performs Cox Proportional Hazard model plots
RunCoxRegression | Performs basic Cox Proportional Hazards regression without special options
RunCoxRegression_Basic | Performs basic Cox Proportional Hazards regression with a multiplicative log-linear model
RunCoxRegression_CR | Performs basic Cox Proportional Hazards regression with competing risks
RunCoxRegression_Guesses_CPP | Performs basic Cox Proportional Hazards regression, Generates multiple starting guesses on c++ side
RunCoxRegression_Omnibus | Performs Cox Proportional Hazards regression using the omnibus function
RunCoxRegression_Omnibus_Multidose | Performs Cox Proportional Hazards regression using the omnibus function with multiple column realizations
RunCoxRegression_Single | Performs basic Cox Proportional Hazards calculation with no derivative
RunCoxRegression_Strata | Performs basic Cox Proportional Hazards regression with strata effect
RunCoxRegression_Tier_Guesses | Performs basic cox regression, with multiple guesses, starts with solving for a single term
RunPoissonEventAssignment | Predicts how many events are due to baseline vs excess
RunPoissonEventAssignment_bound | Predicts how many events are due to baseline vs excess at the confidence bounds of a single parameter
RunPoissonRegression | Performs basic poisson regression
RunPoissonRegression_Guesses_CPP | Performs basic Poisson regression, generates multiple starting guesses on c++ side
RunPoissonRegression_Joint_Omnibus | Performs joint Poisson regression using the omnibus function
RunPoissonRegression_Omnibus | Performs basic Poisson regression using the omnibus function
RunPoissonRegression_Residual | Calculates poisson residuals
RunPoissonRegression_Single | Performs poisson regression with no derivative calculations
RunPoissonRegression_Strata | Performs poisson regression with strata effect
RunPoissonRegression_Tier_Guesses | Performs basic poisson regression, with multiple guesses, starts with a single term
System_Version | Checks OS, compilers, and OMP
Time_Since | Automates creating a date since a reference column