Package: Colossus 1.6.4

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

Performs risk 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_1.6.4.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Colossus/json (API)

# Install 'Colossus' in R:
install.packages('Colossus', repos = c('https://ericgiunta.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

7.89 score 2 stars 54 scripts 975 downloads 32 exports 41 dependencies

Last updated from:a14d39d685. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK284
linux-devel-x86_64OK247
source / vignettesOK545
linux-release-arm64OK267
linux-release-x86_64OK326
macos-release-arm64OK298
macos-release-x86_64OK856
macos-oldrel-arm64OK294
macos-oldrel-x86_64OK623
windows-devel-arm64OK425
windows-devel-x86_64OK372
windows-release-arm64OK392
windows-release-x86_64OK278
windows-oldrel-x86_64OK254
wasm-releaseOK185

Exports:CaseControlRunCoxRunCoxRunMultiDate_ShiftEvent_Count_GenEvent_Time_GenEventAssignmentfactorizegen_time_depget_formget_form_jointJoint_Multiple_EventsLikelihood_Ratio_TestLikelihoodBoundLinked_Dose_FormulaLinked_Lin_Exp_ParaLogisticRunLogisticRunMultiLogisticRunMultiOutplotMartingaleplotRiskplotSchoenfeldplotSurvivalPoisRunPoisRunJointPoisRunMultiPoisRunMultiOutRelativeRiskReplace_MissingResidualSystem_VersionTime_Since

Dependencies:briocallrclicpp11crayondata.tabledescdiffobjdplyrevaluatefsgenericsgluejsonlitelifecyclelubridatemagrittrotelpillarpkgbuildpkgconfigpkgloadpracmapraiseprocessxpsR6RcppRcppEigenrlangrprojrootstringistringrtestthattibbletidyselecttimechangeutf8vctrswaldowithr

Poisson and Logistic Residuals
Rate and Probability Residuals | Calculating Residuals for Poisson Models | Calculating Residuals for Logistic Regressions | Running the functions
Rendered fromResidual.Rmdusingknitr::rmarkdown

Last update: 2026-09-23
Started: 2026-08-26

Alternative Regression Options
General Options | Stratification | Cox Proportional Hazards | Poisson Regression | Logistic and Matched Case-Control Regression | Non-Derivative Calculation | Competing Risks | Fine-Gray | Poisson Joint Analysis | Linear Constraints | General Input | Application to gradient descent | Multiple Initial Parameter Sets
Rendered fromAlt_Run_Opt.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-07-26

Colossus Starting Description
Colossus Description | Model Structure | Using The Standard Model | Survival Time and Event Data | Control and Verbosity | Running the Regression and Output
Rendered fromStarting-Description.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-07-26

Confidence Interval Selection
Available Methods | Wald Method | Likelihood-Based Bound | Example and Comparison | Illustration of Issues with Likelihood-Boundary Algorithm | Likelihood Boundary Algorithm Alternative | Expected Information Matrix Derivation
Rendered fromWald_and_Log_Bound.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-06-21

Dose Response Formula Terms
Dose Response Formula | Using The Different subterms
Rendered fromDose_Formula_Inputs.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-07-26

Excess and Predicted Cases
General Theory
Rendered fromExcess_and_Predicted_Cases.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-10-09

Functions for Plotting and Analysis
Example Setup | Survival Function Approximation | Cox Proportional Hazards model assumptions | Schoenfeld Residuals | Martingale Residuals | General Evaluation of Risk
Rendered fromPlotting_And_Analysis.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-01-16

Generating Person-Count and Person-Time Tables
General Purpose | Person-Count Tables | Person-Time Tables | Calendar Time Scale | User Defined Time Scale | Additional summary options
Rendered fromcount_time_tables.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-10-25

Logistic Regression
Logistic Modeling for Binomial Odds and Binary Data | General Theory | Examples of Use
Rendered fromLogistic.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2025-10-13

Matched Case-Control Logistic Regression
Matched Case-Control Modeling | General Theory | Conditional Logistic Regression | Unconditional Logistic Regression | Examples of Use
Rendered fromMatched_Case_Control.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2025-03-21

SMR Analysis
External Rate Comparisons | SMR Calculation
Rendered fromSMR_Analysis.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-11-04

Time Dependent Covariate Use
General Usage | Multiplicative Interaction | Step Function Interaction | Examples of Use
Rendered fromTime_Dep_Cov.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2023-10-12

Unified Equation Representation
Equation Expression
Rendered fromEquation_Expression.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2024-11-20

Gradient and Hessian Approaches
Optimization Theory | Use in Practice | Hyper-parameter Tuning Examples
Rendered fromGrad_Hess.Rmdusingknitr::rmarkdown

Last update: 2026-08-28
Started: 2024-11-05

List of Control Options
General Use | Standard Control List | Other Control Lists
Rendered fromControl_Options.Rmdusingknitr::rmarkdown

Last update: 2026-08-28
Started: 2024-07-26

Multiple Realization Methods
Available Methods | Exposure Uncertainty | Specifics of Use | Outcome Uncertainty
Rendered fromMulti_Realization.Rmdusingknitr::rmarkdown

Last update: 2026-08-28
Started: 2024-07-24

Script comparisons with 32-bit Epicure
Introduction to Colossus | Example Epicure Analysis | Colossus Script
Rendered fromScript_Comparison_Epicure.Rmdusingknitr::rmarkdown

Last update: 2026-06-24
Started: 2024-08-23

Readme and manuals

Help Manual

Help pageTopics
Fully runs a case-control regression model, returning the model and resultsCaseControlRun
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 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
Calculates the likelihood boundary for a completed Logistic modelLikelihoodBound.logitres
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
Fully runs a logistic regression model with multiple column realizations, returning the model and resultsLogisticRunMulti
Fully runs a logistic regression model with multiple event realizations, returning the model and resultsLogisticRunMultiOut
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 Risk Plotting functionplotRisk
Performs Cox Proportional Hazard model hazard ratio plotsplotRisk.coxres
Generic Schoenfeld Residual Plotting functionplotSchoenfeld
Performs Cox Proportional Hazard model schoenfeld residual plotsplotSchoenfeld.coxres
Generic Survival Plotting functionplotSurvival
Performs Cox Proportional Hazard model survival plotsplotSurvival.coxres
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
Fully runs a poisson regression model with multiple event realizations, returning the model and resultsPoisRunMultiOut
Generic relative risk calculation functionRelativeRisk
Calculates hazard ratios for a reference vector and modelRelativeRisk.coxmodel
Calculates hazard ratios for a reference vectorRelativeRisk.coxres
Calculates hazard ratios for a reference vector and modelRelativeRisk.formula
Automatically assigns missing values in listed columnsReplace_Missing
Generic Residual calculation functionResidual
Calculates the Residuals for a logistic modelResidual.logitmodel
Calculates the Residuals for a completed logistic modelResidual.logitres
Calculates the Residuals for a poisson formulaResidual.poismodel
Calculates the Residuals for a completed poisson modelResidual.poisres
Checks OS, compilers, and OMPSystem_Version
Automates creating a date since a reference columnTime_Since