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Commit7291024

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Merge pull request#18 from ericgiunta/main
Update dev branch to current main
2 parents10e3bd8 +49a8230 commit7291024

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‎.Rbuildignore‎

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‎.github/.gitignore‎

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‎.github/workflows/OS_TEST.yml‎

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@@ -23,29 +23,12 @@ jobs:
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with:
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Ncpus:2
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remove-openmp-macos:false
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-name:enable homebrew to allow OpenMP
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run:|
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curl -OL https://mac.r-project.org/openmp/openmp-19.1.0-darwin20-Release.tar.gz
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sudo tar fvxz openmp-19.1.0-darwin20-Release.tar.gz -C /
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-name:move to package and install
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run:|
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export PKG_CPPFLAGS='-Xclang -fopenmp'
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export PKG_LIBS=-lomp
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Rscript -e "install.packages(c('devtools'))"
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Rscript -e "devtools::install_deps(dependencies = TRUE)"
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Rscript -e "devtools::install_dev_deps(dependencies = TRUE)"
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Rscript -e "devtools::install()"
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-name:check detected OS and OpenMP
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run:|
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Rscript -e "a=Colossus::System_Version()
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print(a)
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if (a['OpenMP Enabled']!='TRUE'){
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stop()
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}
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if (a['Operating System']!='osx'){
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stop()
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}
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"
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-name:move to package and build examples
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run:|
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brew install pandoc

‎.github/workflows/YAML_LINT.yml‎

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‎.github/workflows/pkgdown.yaml‎

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‎.github/workflows/rhub.yaml‎

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‎.github/workflows/test-coverage.yaml‎

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‎.gitignore‎

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‎DESCRIPTION‎

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@@ -1,7 +1,8 @@
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Package: Colossus
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Type: Package
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Title: "Risk Model Regression and Analysis with Complex Non-Linear Models"
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Version: 1.4.1
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Title: "Risk Model Regression and Analysis with Complex Non-Linear
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Models"
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Version: 1.4.3
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Authors@R: c(
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person("Eric", "Giunta", email="egiunta@ksu.edu", role=c("aut", "cre"), comment = c(ORCID = "0000-0002-1577-766X")),
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person("Amir", "Bahadori", role=c("ctb"), comment = c(ORCID = "0000-0002-4589-105X")),
@@ -15,42 +16,35 @@ Authors@R: c(
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person("NCRP", role=c("fnd")),
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person("NRC", role=c("fnd"))
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)
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URL: https://ericgiunta.github.io/Colossus/, https://github.com/ericgiunta/Colossus
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URL: https://ericgiunta.github.io/Colossus/,
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https://github.com/ericgiunta/Colossus
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BugReports: https://github.com/ericgiunta/Colossus/issues
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Description: 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.
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License: GPL (>= 3)
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Imports:
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Rcpp,
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data.table,
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parallel,
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stats,
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utils,
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rlang,
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methods,
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callr,
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stringr,
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processx,
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dplyr,
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tibble,
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lubridate
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Imports: Rcpp, data.table, parallel, stats, utils, rlang, methods,
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callr, stringr, processx, dplyr, tibble, lubridate
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LinkingTo: Rcpp, RcppEigen, testthat
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SystemRequirements: make
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RoxygenNote: 7.3.2
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SystemRequirements: make, C++17
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RoxygenNote: 7.3.3
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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Suggests:
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knitr,
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rmarkdown,
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testthat,
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xml2,
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ggplot2,
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pandoc,
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spelling,
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survival,
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splines,
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dtplyr
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Suggests: knitr, rmarkdown, testthat, xml2, ggplot2, pandoc, spelling,
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survival, splines, dtplyr
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Config/testthat/edition: 3
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VignetteBuilder:
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knitr
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VignetteBuilder: knitr
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Language: en-US
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Biarch: TRUE
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NeedsCompilation: yes
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Packaged: 2025-10-02 19:35:20 UTC; user
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Author: Eric Giunta [aut, cre] (ORCID: <https://orcid.org/0000-0002-1577-766X>),
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Amir Bahadori [ctb] (ORCID: <https://orcid.org/0000-0002-4589-105X>),
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Dan Andresen [ctb],
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Linda Walsh [ctb] (ORCID: <https://orcid.org/0000-0001-7399-9191>),
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Benjamin French [ctb] (ORCID: <https://orcid.org/0000-0001-9265-5378>),
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Lawrence Dauer [ctb],
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John Boice Jr [ctb] (ORCID: <https://orcid.org/0000-0002-8755-1299>),
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Kansas State University [cph],
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NASA [fnd],
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NCRP [fnd],
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NRC [fnd]
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Maintainer: Eric Giunta <egiunta@ksu.edu>

‎NAMESPACE‎

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@@ -12,14 +12,13 @@ S3method(Residual,poisres)
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S3method(plot,coxres)
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S3method(print,caseconres)
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S3method(print,coxres)
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S3method(print,coxresbound)
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S3method(print,logitres)
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S3method(print,poisres)
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S3method(print,poisresbound)
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export(CaseControlRun)
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export(ColossusCaseConStrataSurv)
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export(ColossusCaseConSurv)
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export(ColossusCaseConTimeStrataSurv)
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export(ColossusCaseConTimeSurv)
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export(ColossusCoxSurv)
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export(ColossusExpressionCall)
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export(ColossusLogitSurv)
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export(ColossusPoisSurv)
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export(CoxRun)
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export(CoxRunMulti)
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export(Likelihood_Ratio_Test)
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export(Linked_Dose_Formula)
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export(Linked_Lin_Exp_Para)
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export(LogisticRun)
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export(PoisRun)
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export(PoisRunJoint)
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export(PoissonCurveSolver)
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export(PoisRunMulti)
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export(RelativeRisk)
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export(Replace_Missing)
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export(Residual)
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export(RunCaseControlRegression_Omnibus)
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export(RunCoxRegression_Omnibus)
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export(RunLogisticRegression_Omnibus)
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export(RunPoissonRegression_Omnibus)
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export(RunPoissonRegression_Residual)
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export(System_Version)
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export(Time_Since)
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export(factorize)
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importFrom(dplyr,mutate)
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importFrom(dplyr,n)
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importFrom(dplyr,slice)
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importFrom(dplyr,summarise)
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importFrom(dplyr,summarize)
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importFrom(grDevices,colorRampPalette)
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importFrom(grDevices,dev.off)

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