Package: Colossus 1.5.1

Eric King-Giunta

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

Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.

Authors:Eric King-Giunta [aut, cre], Amir Bahadori [ctb], Dan Andresen [ctb], Linda Walsh [ctb], Benjamin French [ctb], Lawrence Dauer [ctb], John Boice Jr [ctb], Kansas State University [cph], NASA [fnd], NCRP [fnd], NRC [fnd]

Colossus_1.5.1.tar.gz
Colossus_1.5.1.tar.gz(r-4.7-arm64)Colossus_1.5.1.tar.gz(r-4.7-x86_64)Colossus_1.5.1.tar.gz(r-4.6-arm64)Colossus_1.5.1.tar.gz(r-4.6-x86_64)
Colossus_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
Colossus/json (API)
NEWS

# Install 'Colossus' in R:
install.packages('Colossus', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ericgiunta/colossus/issues

Pkgdown/docs site:https://ericgiunta.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

cppopenmp

5.34 score 34 scripts 630 downloads 32 exports 39 dependencies

Last updated from:c46535b109. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK306
linux-devel-x86_64OK284
source / vignettesOK438
linux-release-arm64OK285
linux-release-x86_64OK307
wasm-releaseOK225

Exports:CaseControlRunColossusCoxSurvColossusLogitSurvColossusPoisSurvCoxRunCoxRunMultiDate_ShiftEvent_Count_GenEvent_Time_GenEventAssignmentfactorizegen_time_depget_formget_form_jointJoint_Multiple_EventsLikelihood_Ratio_TestLikelihoodBoundLinked_Dose_FormulaLinked_Lin_Exp_ParaLogisticRunplotMartingaleplotRiskplotSchoenfeldplotSurvivalPoisRunPoisRunJointPoisRunMultiRelativeRiskReplace_MissingResidualSystem_VersionTime_Since

Dependencies:briocallrclicpp11crayondata.tabledescdiffobjdplyrevaluatefsgenericsgluejsonlitelifecyclelubridatemagrittrpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6RcppRcppEigenrlangrprojrootstringistringrtestthattibbletidyselecttimechangeutf8vctrswaldowithr

Alternative Regression Options

Rendered fromAlt_Run_Opt.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

Colossus Description

Rendered fromStarting-Description.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

Confidence Interval Selection

Rendered fromWald_and_Log_Bound.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

Dose Response Formula Terms

Rendered fromDose_Formula_Inputs.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

Excess and Predicted Cases

Rendered fromExcess_and_Predicted_Cases.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-10-21

Functions for Plotting and Analysis

Rendered fromPlotting_And_Analysis.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-02-21

Generating Person-Count and Person-Time Tables

Rendered fromcount_time_tables.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2025-02-13

Gradient and Hessian Approaches

Rendered fromGrad_Hess.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2025-02-13

List of Control Options

Rendered fromControl_Options.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

Logistic Regression

Rendered fromLogistic.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2025-10-30

Matched Case-Control Logistic Regression

Rendered fromMatched_Case_Control.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2025-06-05

Multiple Realization Methods

Rendered fromMulti_Realization.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

Script comparisons with 32-bit Epicure

Rendered fromScript_Comparison_Epicure.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2024-09-07

SMR Analysis

Rendered fromSMR_Analysis.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2025-02-13

Time Dependent Covariate Use

Rendered fromTime_Dep_Cov.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2023-09-28

Unified Equation Representation

Rendered fromEquation_Expression.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2026-04-17
Started: 2025-02-13

Readme and manuals

Help Manual

Help pageTopics
Fully runs a case-control regression model, returning the model and resultsCaseControlRun
Interprets basic cox survival formula RHSColossusCoxSurv
Interprets basic logistic survival formula RHS with no groupingColossusLogitSurv
Interprets basic poisson survival formula RHSColossusPoisSurv
Fully runs a cox or fine-gray regression model, returning the model and resultsCoxRun
Fully runs a cox or fine-gray regression model with multiple column realizations, returning the model and resultsCoxRunMulti
Automates creating a date difference columnDate_Shift
uses a table, list of categories, and list of event summaries to generate person-count tablesEvent_Count_Gen
uses a table, list of categories, list of summaries, list of events, and person-year information to generate person-time tablesEvent_Time_Gen
Generic background/excess event calculation functionEventAssignment
Predicts how many events are due to baseline vs excessEventAssignment.default
Predicts how many events are due to baseline vs excess for a completed poisson modelEventAssignment.poisres
Predicts how many events are due to baseline vs excess for a completed poisson likelihood boundary regressionEventAssignment.poisresbound
Splits a parameter into factorsfactorize
Applies time dependence to parametersgen_time_dep
Interprets a Colossus formula and makes necessary changes to dataget_form
Interprets a Poisson joint formula and makes necessary changes to dataget_form_joint
Automates creating data for a joint competing risks analysisJoint_Multiple_Events
Defines the likelihood ratio testLikelihood_Ratio_Test
Generic likelihood boundary calculation functionLikelihoodBound
Calculates the likelihood boundary for a completed cox modelLikelihoodBound.coxres
Generic likelihood boundary calculation function, default optionLikelihoodBound.default
Calculates the likelihood boundary for a completed Poisson modelLikelihoodBound.poisres
Calculates Full Parameter list for Special Dose FormulaLinked_Dose_Formula
Calculates The Additional Parameter For a linear-exponential formula with known maximumLinked_Lin_Exp_Para
Fully runs a logistic regression model, returning the model and resultsLogisticRun
Checks the OMP flagOMP_Check
Performs Cox Proportional Hazard model plotsplot.coxres
Generic Martingale Residual Plotting functionplotMartingale
Performs Cox Proportional Hazard model martingale residual plotsplotMartingale.coxres
Generic Martingale Residual Plotting function, default optionplotMartingale.default
Generic Risk Plotting functionplotRisk
Performs Cox Proportional Hazard model hazard ratio plotsplotRisk.coxres
Generic Risk Plotting function, default optionplotRisk.default
Generic Schoenfeld Residual Plotting functionplotSchoenfeld
Performs Cox Proportional Hazard model schoenfeld residual plotsplotSchoenfeld.coxres
Generic Schoenfeld Residual Plotting function, default optionplotSchoenfeld.default
Generic Survival Plotting functionplotSurvival
Performs Cox Proportional Hazard model survival plotsplotSurvival.coxres
Generic Survival Plotting function, default optionplotSurvival.default
Fully runs a poisson regression model, returning the model and resultsPoisRun
Fully runs a joint poisson regression model, returning the model and resultsPoisRunJoint
Fully runs a poisson regression model with multiple column realizations, returning the model and resultsPoisRunMulti
Prints a case-control regression output clearlyprint.caseconres
Prints a cox regression output clearlyprint.coxres
Prints a cox likelihood boundary regression output clearlyprint.coxresbound
Prints a logistic regression output clearlyprint.logitres
Prints a poisson regression output clearlyprint.poisres
Prints a poisson likelihood boundary regression output clearlyprint.poisresbound
Generic relative risk calculation functionRelativeRisk
Calculates hazard ratios for a reference vectorRelativeRisk.coxres
Generic relative risk calculation function, default optionRelativeRisk.default
Automatically assigns missing values in listed columnsReplace_Missing
Generic Residual calculation functionResidual
Generic Residual calculation function, default optionResidual.default
Calculates the Residuals for a completed poisson modelResidual.poisres
Checks OS, compilers, and OMPSystem_Version
Automates creating a date since a reference columnTime_Since