Science Score: 20.0%
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Links to: arxiv.org -
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2 of 2 committers (100.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: lihualei71
- License: other
- Language: R
- Default Branch: master
- Size: 17.8 MB
Statistics
- Stars: 9
- Watchers: 4
- Forks: 6
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
adaptMT
Overview
This package implements Adaptive P-Value Thresholding in the paper: AdaPT: An interactive procedure for multiple testing with side information. It includes both a framework that allows the user to specify any algorithm to learn local FDR and a pool of convenient functions that implement specific algorithms:
adapt()provides a generic framework of AdaPT permitting any learning algorithm;adapt_glm(),adapt_gam()andadapt_glmnet()provide convenient wrappers of AdaPT using Generalized Linear Models (GLM), Generalized Additive Models (GAM) and L1-penalized GLMs;
Install the adaptMT package then read vignette("adapt_demo", package = "adaptMT").
Installation
```
install.packages("devtools")
devtools::install_github("lihualei71/adaptMT") ``` If one wants to access the vignette, run the following code to build the vignette. This might update other related packages and please be patient if so.
devtools::install_github("lihualei71/adaptMT", build_vignettes = TRUE)
An Example
We illustrate the usage of adaptMT package using the example discussed in Section 5.1 of the paper AdaPT: An interactive procedure for multiple testing with side information.
```
Load package
library("adaptMT")
Load data
data(estrogen) pvals <- as.numeric(estrogen$pvals) x <- data.frame(x = as.numeric(estrogen$ord_high))
Define the exponential family for AdaPT (Section 4)
dist <- beta_family()
Run adapt_glm
library("splines") formulas <- paste0("ns(x, df = ", 6:10, ")") res <- adaptglm(x = x, pvals = pvals, piformulas = formulas, mu_formulas = formulas, dist = dist, nfits = 10)
Plot the threshold curve and the level curves of local FDR
plot1dthresh(res, alpha = 0.1, "P-Value Thresholds") plot1dlfdr(res, alpha = 0.1, "Level Curves of Local FDR Estimates") ```
Owner
- Name: Lihua Lei
- Login: lihualei71
- Kind: user
- Company: Stanford University
- Website: https://lihualei71.github.io
- Twitter: lihua_lei_stat
- Repositories: 4
- Profile: https://github.com/lihualei71
Assistant Professor of Economics, Stanford GSB
GitHub Events
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Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| lihualei71 | l****i@b****u | 119 |
| lihualei71 | l****i@s****u | 4 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- cran 288 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 1
- Total maintainers: 1
cran.r-project.org: adaptMT
Adaptive P-Value Thresholding for Multiple Hypothesis Testing with Side Information
- Homepage: https://arxiv.org/abs/1609.06035
- Documentation: http://cran.r-project.org/web/packages/adaptMT/adaptMT.pdf
- License: MIT + file LICENSE
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Latest release: 1.0.0
published almost 8 years ago
Rankings
Maintainers (1)
Dependencies
- methods * imports
- HDtweedie * suggests
- dplyr * suggests
- glmnet * suggests
- knitr * suggests
- mgcv * suggests
- rmarkdown * suggests
- splines * suggests
- testthat * suggests