Package index • Colossus

All functions

CaseControlRun(): Fully runs a case-control regression model, returning the model and results

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

ColossusCaseConStrataSurv(): Interprets basic case-control survival formula RHS with grouping by strata

ColossusCaseConSurv(): Interprets basic case-control survival formula RHS with no grouping

ColossusCaseConTimeStrataSurv(): Interprets basic case-control survival formula RHS with grouping by strata and risk group

ColossusCaseConTimeSurv(): Interprets basic case-control survival formula RHS with grouping by risk group

ColossusCoxStrataSurv(): Interprets basic cox survival formula RHS with strata

ColossusCoxSurv(): Interprets basic cox survival formula RHS

ColossusExpressionCall(): Applies a list of function calls from a model evaluation

ColossusFineGrayStrataSurv(): Interprets basic fine-gray survival formula RHS with strata

ColossusFineGraySurv(): Interprets basic fine-gray survival formula RHS

ColossusPoisSurv(): Interprets basic poisson survival formula RHS

CoxCurveSolver(): Calculates the likelihood curve for a cox model directly

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

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_model_control(): Automatically assigns missing model control values

EventAssignment(): Generic background/excess event calculation function

EventAssignment(<default>): Predicts how many events are due to baseline vs excess

EventAssignment(<poisres>): Calculates the likelihood boundary for a completed cox model

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

Interpret_Output(): Prints a regression output clearly

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

OMP_Check(): Checks the OMP flag

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

PoissonCurveSolver(): Calculates the likelihood curve for a poisson model directly

Rcomp_version(): Checks how R was compiled

Rcpp_version(): Checks default R c++ compiler

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 likelihood boundary for a completed cox model

RunCaseControlRegression_Omnibus(): Performs Matched Case-Control Conditional Logistic Regression

RunCoxPlots(): Performs Cox Proportional Hazard model plots

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

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_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

System_Version(): Checks OS, compilers, and OMP

Time_Since(): Automates creating a date since a reference column

factorize(): Splits a parameter into factors

gcc_version(): Checks default c++ compiler

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

get_form_list(): Interprets a Colossus formula and makes necessary changes to data, returns list not class

get_form_risk(): Interprets the risk factor side of a formula

get_form_surv(): Interprets the survival side of a formula

get_os(): Checks system OS

interact_them(): Defines Interactions

nested_split(): Splits a string by commas, skipping over parenthesis sections

parse_literal_string(): converts a string of a vector/list to vector/list

plot(<coxres>): Performs Cox Proportional Hazard model plots

print(<caseconres>): Prints a case-control regression output clearly

print(<coxres>): Prints a cox regression output clearly

print(<poisres>): Prints a poisson regression output clearly