Package: Colossus 1.1.4.2

Eric 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-Grey competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grant 80NSSC19M0161 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 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_1.1.4.2.tar.gz
Colossus_1.1.4.2.tar.gz(r-4.5-noble)Colossus_1.1.4.2.tar.gz(r-4.4-noble)
Colossus_1.1.4.2.tgz(r-4.4-emscripten)Colossus_1.1.4.2.tgz(r-4.3-emscripten)
Colossus.pdf |Colossus.html
Colossus/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://ericgiunta.github.io

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

5.20 score 36 scripts 409 downloads 43 exports 30 dependencies

Last updated 2 months agofrom:2ca69db76a. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-linux-x86_64OKNov 21 2024

Exports:Check_Dupe_ColumnsCheck_TruncCorrect_Formula_OrderCox_Relative_RiskDate_ShiftDef_ControlDef_Control_GuessDef_model_controlDef_modelform_fixfactorizefactorize_parGather_Guesses_CPPgen_time_depGetCensWeightinteract_themJoint_Multiple_EventsLikelihood_Ratio_TestLinked_Dose_FormulaLinked_Lin_Exp_ParaReplace_MissingRunCoxNullRunCoxPlotsRunCoxRegressionRunCoxRegression_BasicRunCoxRegression_CRRunCoxRegression_Guesses_CPPRunCoxRegression_OmnibusRunCoxRegression_Omnibus_MultidoseRunCoxRegression_SingleRunCoxRegression_STRATARunCoxRegression_Tier_GuessesRunPoissonEventAssignmentRunPoissonEventAssignment_boundRunPoissonRegressionRunPoissonRegression_Guesses_CPPRunPoissonRegression_Joint_OmnibusRunPoissonRegression_OmnibusRunPoissonRegression_ResidualRunPoissonRegression_SingleRunPoissonRegression_STRATARunPoissonRegression_Tier_GuessesSystem_VersionTime_Since

Dependencies:briocallrclicrayondata.tabledescdiffobjdigestevaluatefsgluejsonlitelifecyclemagrittrpkgbuildpkgloadpraiseprocessxpsR6RcppRcppEigenrlangrprojrootstringistringrtestthatvctrswaldowithr

Alternative Regression Options

Rendered fromAlt_Run_Opt.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-21
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Colossus Description

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Confidence Interval Selection

Rendered fromWald_and_Log_Bound.Rmdusingknitr::rmarkdownon Nov 21 2024.

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Distributed Start Framework

Rendered fromAlt_Distrib_Starts.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-21
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Dose Response Formula Terms

Rendered fromDose_Formula_Inputs.Rmdusingknitr::rmarkdownon Nov 21 2024.

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Excess and Predicted Cases

Rendered fromExcess_and_Predicted_Cases.Rmdusingknitr::rmarkdownon Nov 21 2024.

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Functions for Plotting and Analysis

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List of Control Options

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Multiple Realization Methods

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Script comparisons with 32-bit Epicure

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Time Dependent Covariate Use

Rendered fromTime_Dep_Cov.Rmdusingknitr::rmarkdownon Nov 21 2024.

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Readme and manuals

Help Manual

Help pageTopics
checks for duplicated column namesCheck_Dupe_Columns
Applies time duration truncation limits to create columns for Cox modelCheck_Trunc
General purpose verbosity checkCheck_Verbose
Corrects the order of terms/formula/etcCorrect_Formula_Order
Calculates hazard ratios for a reference vectorCox_Relative_Risk
Automates creating a date difference columnDate_Shift
Automatically assigns missing control valuesDef_Control
Automatically assigns missing guessing control valuesDef_Control_Guess
Automatically assigns missing model control valuesDef_model_control
Automatically assigns geometric-mixture values and checks that a valid modelform is usedDef_modelform_fix
Splits a parameter into factorsfactorize
Splits a parameter into factors in parallelfactorize_par
Performs checks to gather a list of guesses and iterationsGather_Guesses_CPP
Checks default c++ compilergcc_version
Applies time dependence to parametersgen_time_dep
Checks system OSget_os
Calculates and returns data for time by hazard and survival to estimate censoring rateGetCensWeight
Defines Interactionsinteract_them
Automates creating data for a joint competing risks analysisJoint_Multiple_Events
Defines the likelihood ratio testLikelihood_Ratio_Test
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
Checks the OMP flagOMP_Check
Checks how R was compiledRcomp_version
Checks default R c++ compilerRcpp_version
Automatically assigns missing values in listed columnsReplace_Missing
Performs basic Cox Proportional Hazards regression with the null modelRunCoxNull
Performs Cox Proportional Hazard model plotsRunCoxPlots
Performs basic Cox Proportional Hazards regression without special optionsRunCoxRegression
Performs basic Cox Proportional Hazards regression with a multiplicative log-linear modelRunCoxRegression_Basic
Performs basic Cox Proportional Hazards regression with competing risksRunCoxRegression_CR
Performs basic Cox Proportional Hazards regression, Generates multiple starting guesses on c++ sideRunCoxRegression_Guesses_CPP
Performs Cox Proportional Hazards regression using the omnibus functionRunCoxRegression_Omnibus
Performs Cox Proportional Hazards regression using the omnibus function with multiple column realizationsRunCoxRegression_Omnibus_Multidose
Performs basic Cox Proportional Hazards calculation with no derivativeRunCoxRegression_Single
Performs basic Cox Proportional Hazards regression with strata effectRunCoxRegression_STRATA
Performs basic cox regression, with multiple guesses, starts with solving for a single termRunCoxRegression_Tier_Guesses
Predicts how many events are due to baseline vs excessRunPoissonEventAssignment
Predicts how many events are due to baseline vs excess at the confidence bounds of a single parameterRunPoissonEventAssignment_bound
Performs basic poisson regressionRunPoissonRegression
Performs basic Poisson regression, generates multiple starting guesses on c++ sideRunPoissonRegression_Guesses_CPP
Performs joint Poisson regression using the omnibus functionRunPoissonRegression_Joint_Omnibus
Performs basic Poisson regression using the omnibus functionRunPoissonRegression_Omnibus
Calculates poisson residualsRunPoissonRegression_Residual
Performs poisson regression with no derivative calculationsRunPoissonRegression_Single
Performs poisson regression with strata effectRunPoissonRegression_STRATA
Performs basic poisson regression, with multiple guesses, starts with a single termRunPoissonRegression_Tier_Guesses
Checks OS, compilers, and OMPSystem_Version
Automates creating a date since a reference columnTime_Since