Colossus

Stores the R and C++ code being developed for the Colossus R package

https://github.com/ericgiunta/colossus

Science Score: 26.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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Scientific vocabulary similarity
Low similarity (18.1%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Stores the R and C++ code being developed for the Colossus R package

Basic Info

Host: GitHub
Owner: ericgiunta
Language: C++
Default Branch: main
Homepage: https://ericgiunta.github.io/Colossus/
Size: 106 MB

Statistics

Stars: 2
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created about 4 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing Codemeta

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# Colossus


[![](https://img.shields.io/github/languages/code-size/ericgiunta/Colossus.svg)](https://github.com/ericgiunta/Colossus)
[![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![codecov](https://codecov.io/gh/ericgiunta/Colossus/graph/badge.svg?token=NMH5R502W8)](https://app.codecov.io/gh/ericgiunta/Colossus)
[![pkgdown](https://github.com/ericgiunta/Colossus/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/ericgiunta/Colossus/actions/workflows/pkgdown.yaml)
[![OS_Checks](https://github.com/ericgiunta/Colossus/actions/workflows/OS_TEST.yml/badge.svg?branch=main)](https://github.com/ericgiunta/Colossus/actions/workflows/OS_TEST.yml)
[![](https://cranlogs.r-pkg.org/badges/grand-total/Colossus)](https://CRAN.R-project.org/package=Colossus)


The goal of Colossus is to provide an open-source means of performing survival analysis on big data with complex risk formulas. Colossus is designed to perform Cox Proportional Hazard regressions and Poisson regressions on datasets loaded as data.tables or data.frames. The risk models allowed are sums or products of linear, log-linear, or several other radiation dose response formulas highlighted in the vignettes. Additional plotting capabilities are available.


By default, a fully portable version of the code is compiled, which does not support OpenMP on every system. Note that Colossus requires OpenMP support to perform parallel calculations. The environment variable "R_COLOSSUS_NOT_CRAN" is checked to determine if OpenMP should be disabled for linux compiling with clang. The number of cores is set to 1 if the environment variable is empty, the operating system is detected as linux, and the default compiler or R compiler is clang. Colossus testing checks for the "NOT_CRAN" variable to determine if additional tests should be run. Setting "NOT_CRAN" to "false" will disable the longer tests. Currently, OpenMP support is not configured for linux compiling with clang.

## Example

This is a basic example which shows you how to solve a common problem:

```{r example}
library(data.table)
library(parallel)
library(Colossus)
## basic example code reproduced from the starting-description vignette

df <- data.table(
  "UserID" = c(112, 114, 213, 214, 115, 116, 117),
  "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
  "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
  "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
  "a" = c(0, 1, 1, 0, 1, 0, 1),
  "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
  "c" = c(10, 11, 10, 11, 12, 9, 11),
  "d" = c(0, 0, 0, 1, 1, 1, 1)
)
# For the interval case
time1 <- "Starting_Age"
time2 <- "Ending_Age"
event <- "Cancer_Status"

names <- c("a", "b", "c", "d")
term_n <- c(0, 1, 1, 2)
tform <- c("loglin", "lin", "lin", "plin")
modelform <- "M"

a_n <- c(0.1, 0.1, 0.1, 0.1)

keep_constant <- c(0, 0, 0, 0)
der_iden <- 0

control <- list(
  "lr" = 0.75, "maxiter" = 100, "halfmax" = 5, "epsilon" = 1e-9,
  "deriv_epsilon" = 1e-9, "abs_max" = 1.0,
  "verbose" = 2, "ties" = "breslow"
)

e <- RunCoxRegression(df, time1, time2, event, names, term_n, tform, keep_constant, a_n, modelform, control = control)
Interpret_Output(e)
```

Owner

Login: ericgiunta
Kind: user

Repositories: 1
Profile: https://github.com/ericgiunta

CodeMeta (codemeta.json)

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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 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.",
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Packages

Total packages: 1
Total downloads:
- cran 427 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 11
Total maintainers: 1

cran.r-project.org: Colossus

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

Homepage: https://ericgiunta.github.io/Colossus/
Documentation: http://cran.r-project.org/web/packages/Colossus/Colossus.pdf
License: GPL (≥ 3)
Latest release: 1.3.0
published about 1 year ago

Versions: 11
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 427 Last month

Rankings

Dependent packages count: 27.9%

Dependent repos count: 36.9%

Average: 50.3%

Downloads: 86.1%

Maintainers (1)

egiunta@ksu.edu

Last synced: 11 months ago

Dependencies

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