R Observatory: Metrics for nestedcv version 0.9.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nestedcv

0.9.0

Nested Cross-Validation with 'glmnet' and 'caret'

0packages dependsuggested by 1

9.2Kdownloads / year

–test coverage

7/13flavors OK

Overview

About

Maintained by Myles LewisCRAN page ↗GitHub ↗Issues ↗

Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package doi:10.1093/bioadv/vbad048. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) doi:10.1111/j.2517-6161.1977.tb01603.x. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) doi:10.1214/17-EJS1337SI.

Changes in 0.9.0

13/07/2026

Added nestcv.explain(), a wrapper around shapr::explain()

for generating SHAP values from nestedcv models, replacing the

fastshap-based workflow due to the removal of fastshap from CRAN.

Returns the shapr object directly, so shapr print() and plot()

methods can be used; plot_shap_bar() and plot_shap_beeswarm() also accept

this object directly.

Fixed pred_train(), pred_train_class() and pred_SuperLearner()

erroring when called with a data.table (as shapr::explain() does

internally) by changing newdata to a data frame.

nestedcv still works with fastshap for users who prefer it; the

pred_* wrapper functions remain usable directly with fastshap::explain().

Show all changes in 0.9.0Hide the rest of the changes in 0.9.0

Small fixes to handle updates to ggplot2.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("nestedcv", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("myles-lewis/nestedcv")

Development version from myles-lewis/nestedcv. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-nestedcv

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-nestedcv

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-nestedcv

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

6NOTE7OK

Check messages

NOTERd cross-referencesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Unknown package ‘CORElearn’ in Rd xrefs

CRAN check page ↗

Slowest check: 12.0 min · r-oldrel-windows-x86_64

Status changes

NOTE7 OK, 6 NOTENow
NOTE8 OK, 1 NOTE2026-07-16
OK8 OK2026-07-15
ERROR11 OK, 2 ERROR2026-05-28
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.0

READMEYes · 240 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.9.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 66
Examples that run: 31%5 run in a plain check (2 of them under a condition) · 11 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 26%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 5%

Vignettes (3)

How these are measured

Downloads

9.2K

CRAN downloads in the past year

Rank #4,544 · ~25/day · ~770/mo

Releases R versions

Daily download trend is not available in this view yet.

70230 days

1.8K90 days

9.2K1 year

Compare downloads with other packages →

Also on131 r2u6 autocran49 c2d4u

How downloads are counted

Repository

myles-lewis/nestedcv ↗Account: myles-lewis

17Stars

8Forks

3Open issues

1Open PRs

16Releases

1,021Commits

6Commit identities

1,021 commits · Last activity 2026-07-13

Responsiveness

How these are sampled

PRs merged (all time): 87%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2026-07-15 · 72026-09-05 · 8

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/myles-lewis/nestedcv on 2026-10-11.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing nestedcv adds 78 packages (45 with compiled code, 60 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (16)

caret data.table doParallel foreach future.apply ggplot2 glmnet matrixStats matrixTestsmethodsparallelpROC Rfast RhpcBLASctl rlang ROCR

LinkingTo (0)

none

Suggests (17)

Boruta CORElearn gbm ggbeeswarm ggpubr hsstan mda mlbench pbapply pls randomForest ranger RcppEigen rmarkdown knitr shapr SuperLearner

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

multiDEGGs

How these are counted

Code & Tests

People & History

People (6)

Myles Lewis

Author, Maintainer since 0.2.3 (2022)

Athina Spiliopoulou

Author

Cankut Cubuk

Contributor · added in 0.7.8

Katriona Goldmann

Contributor

David Rios Santini

Contributor · added in 0.9.0

Ryan C. Thompson

Contributor · added in 0.8.0

Releases (20)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-07-14
0.9.0Latest
record
2026-07-14 · current release · diff ↗ ·
added 1 export
nestcv.explain
archivedRemoved from CRAN
2026-06-10
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-10
0.8.2
record
2026-04-10 · diff ↗
archivedRemoved from CRAN
2026-03-31
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
0.8.0
record
2025-03-10 · diff ↗ ·
removed 6 exports
pred_nestcv_glmnet_class1, pred_nestcv_glmnet_class2, pred_nestcv_glmnet_class3, pred_train_class1, pred_train_class2, pred_train_class3

added 2 exports
pred_nestcv_glmnet_class, pred_train_class
0.7.12
record
2024-11-27 · diff ↗ ·
added 3 exports
hist_var_ranks, plot_var_ranks, slim
0.7.10
record
2024-08-16 · diff ↗ ·
added 2 exports
mcc, mcc_multi
0.7.9
record
2024-07-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.7.8
record
2024-03-13 · diff ↗ ·
removed 1 export
layer_filter

added 3 exports
metrics, pls_filter, prc
0.7.4
record
2024-01-30 · diff ↗
0.7.3
record
2023-12-04 · diff ↗ ·
removed 1 export
boxplot_model

added 5 exports
boxplot_expression, pred_SuperLearner, repeatcv, repeatfolds, txtProgressBar2

Show 13 earlier eventsHide 13 earlier events

0.7.0
record
2023-10-26 · diff ↗
0.6.9
record
2023-08-22 · diff ↗
0.6.7
record
2023-07-02 · diff ↗ ·
added 5 exports
bin_stat_filter, class_stat_filter, cor_stat_filter, one_hot, stat_filter
0.6.6
record
2023-06-08 · diff ↗
0.6.4
record
2023-05-30 · diff ↗
0.6.2
record
2023-05-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.6.1
record
2023-04-16 · diff ↗ ·
added 17 exports
barplot_var_stability, cv_coef, cv_varImp, plot_shap_bar, plot_shap_beeswarm, plot_var_stability, pred_nestcv_glmnet, pred_nestcv_glmnet_class1, pred_nestcv_glmnet_class2, pred_nestcv_glmnet_class3, pred_train, pred_train_class1, pred_train_class2, pred_train_class3, ranger_filter, var_direction, var_stability
0.4.4
record
2022-12-05 · diff ↗ ·
added 5 exports
innercv_preds, innercv_summary, train_preds, train_roc, train_summary
0.4.0
record
2022-10-23 · diff ↗ ·
added 4 exports
layer_filter, nestcv.SuperLearner, supervisedPCA, weight
0.3.0
record
2022-09-10 · diff ↗ ·
added 11 exports
boot_anova, boot_correl, boot_filter, boot_lm, boot_ttest, boot_wilcoxon, class_balance, plot_varImp, randomsample, smote, summary_vars
0.2.3
record
2022-07-07
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-07-07
Total releases: 20 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 2.5 MB

Appears in task views

Machine Learning & Statistical Learning

Cite

Cite this package

Run in R for the authors' entry:

citation("nestedcv")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioadv/vbad048.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for nestedcv version 0.9.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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