Giter Club home page Giter Club logo

c060's Introduction

c060

Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models

Maintainer F. Bertrand

Lifecycle: stable Project Status: Active โ€“ The project has reached a stable, usable state and is being actively developed. R-CMD-check Codecov test coverage CRAN status CRAN RStudio mirror downloads GitHub Repo stars DOI

The goal of the c060 package is to provide additional functions to perform stability selection, model validation and parameter tuning for glmnet models.

Installation

You can install the released version of c060 from CRAN with:

install.packages("c060")

And the development version from GitHub with:

install.packages("devtools")
devtools::install_github("fbertran/c060")

c060's People

Contributors

fbertran avatar

Stargazers

Samuel Granjeaud avatar Cornelius Hennch avatar  avatar

Watchers

James Cloos avatar Samuel Granjeaud avatar  avatar

c060's Issues

object 'km.apparent' not found

Hello,

I'm not sure if this is due to something I am doing, but I am trying to follow along with the example from your Journal of Statistical Software paper, but I am using my own dataset as the one in the paper seems to not be available. I hit a problem when I try to use peperr to create prediction error curves with this code:

obj <- peperr(response = Surv(sample$fu_time, sample$outcome),
x = mat, fit.fun = fit.glmnet,
args.fit = list(standardize = FALSE, family = "cox",
penalty.factor = rep(1, times = c(dim(mat)[1]))),
complexity = complexity.glmnet,
args.complexity = list(standardize = FALSE, nfolds = 10,
family = "cox", penalty.factor = rep(1, times = c(dim(mat)[1]))),
RNG = "fixed", seed = 0815, cpus = 3, parallel = TRUE,
clustertype = "SOCK", load.list = list(packages = "c060"),
indices = resample.indices(n = dim(mat)[2], sample.n = 1000,
method = "sub632"))

which is just the code you provide on pages 10-11 of the manuscript, modified to reflect my dataset. When I run this I get the following error:

Explicit sfStop() is missing: stop now.
snowfall 1.84-6.1 initialized (using snow 0.4-3): parallel execution on 3 CPUs.

Library peperr loaded.
Library peperr loaded in cluster.

Library c060 loaded.
Library c060 loaded in cluster.

Error in checkForRemoteErrors(val) : 
  3 nodes produced errors; first error: object 'km.apparent' not found

I've tried this on Mac and a Linux RHEL7 server and got the same error - and I guess km.apparent is an internal function because I can't find it when I google. Can someone help me understand what is going on? Please let me know if you need additional information and thank you so much!

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.