Package: Colossus 1.5.5

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]

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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

7.37 score 2 stars 64 scripts 634 downloads 32 exports 40 dependencies

Last updated from:819eaba9ef. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK326
linux-devel-x86_64OK313
source / vignettesOK471
linux-release-arm64OK313
linux-release-x86_64OK308
macos-release-arm64OK328
macos-release-x86_64OK436
macos-oldrel-arm64OK298
macos-oldrel-x86_64OK854
windows-develOK322
windows-releaseOK344
windows-oldrelOK320
wasm-releaseOK245

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.tabledescdiffobjdplyrevaluatefsgenericsgluejsonlitelifecyclelubridatemagrittrotelpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6RcppRcppEigenrlangrprojrootstringistringrtestthattibbletidyselecttimechangeutf8vctrswaldowithr

Alternative Regression Options
General Options | Stratification | Cox Proportional Hazards | Poisson Regression | Non-Derivative Calculation | Competing Risks | Fine-Gray | Poisson Joint Analysis

Last update: 2026-06-24
Started: 2024-07-26

Colossus Description
Model Structure | Using The Standard Model | Survival Time and Event Data | Control and Verbosity | Running the Regression and Output

Last update: 2026-06-24
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

Last update: 2026-06-24
Started: 2024-06-21

Dose Response Formula Terms
Dose Response Formula | Using The Different subterms

Last update: 2026-06-24
Started: 2024-07-26

Excess and Predicted Cases
General Theory

Last update: 2026-06-24
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

Last update: 2026-06-24
Started: 2024-01-16

Generating Person-Count and Person-Time Tables
General Purpose | Person-Count Tables | Person-Time Tables

Last update: 2026-06-24
Started: 2024-10-25

Gradient and Hessian Approaches
Optimization Theory | Use in Practice | Hyper-parameter Tuning Examples

Last update: 2026-06-24
Started: 2024-11-05

List of Control Options
General Use | Standard Control List | Other Control Lists

Last update: 2026-06-24
Started: 2024-07-26

Logistic Regression
Logistic Modeling for Binomial Odds and Binary Data | General Theory | Examples of Use

Last update: 2026-06-24
Started: 2025-10-13

Matched Case-Control Logistic Regression
Matched Case-Control Modeling | General Theory | Conditional Logistic Regression | Unconditional Logistic Regression | Examples of Use

Last update: 2026-06-24
Started: 2025-03-21

Multiple Realization Methods
Available Methods | Specifics of Use

Last update: 2026-06-24
Started: 2024-07-24

Script comparisons with 32-bit Epicure
Introduction to Colossus | Example Epicure Analysis | Colossus Script

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

SMR Analysis
External Rate Comparisons | SMR Calculation

Last update: 2026-06-24
Started: 2024-11-04

Time Dependent Covariate Use
General Usage | Multiplicative Interaction | Step Function Interaction | Examples of Use

Last update: 2026-06-24
Started: 2023-10-12

Unified Equation Representation
Equation Expression

Last update: 2026-06-24
Started: 2024-11-20

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 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
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
Generic relative risk calculation functionRelativeRisk
Calculates hazard ratios for a reference vectorRelativeRisk.coxres
Automatically assigns missing values in listed columnsReplace_Missing
Generic Residual calculation functionResidual
Calculates the Residuals for a completed poisson modelResidual.poisres
Checks OS, compilers, and OMPSystem_Version
Automates creating a date since a reference columnTime_Since