R Observatory: Metrics for pssmooth version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pssmooth

1.0.3

Flexible and Efficient Evaluation of Principal Surrogates/Treatment Effect Modifiers

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Michal JuraskaFirst published 2018-07-304 releasesCRAN page ↗GitHub ↗

Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB (2020), Inference on treatment effect modification by biomarker response in a three-phase sampling design, Biostatistics, 21(3): 545-560 doi:10.1093/biostatistics/kxy074. The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response (see the flexible three-phase sampling design in the paper for details). Bootstrap-based procedures are available for pointwise and simultaneous confidence intervals and testing of four relevant hypotheses. Summary and plotting functions are provided for estimation results.

Install

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

install.packages("pssmooth", 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("mjuraska/pssmooth")

Development version from mjuraska/pssmooth. 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-pssmooth

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-pssmooth

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-pssmooth

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 48 wordsVignettesNopkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 83%

Downloads

2.4K

CRAN downloads in the past year

Rank #18,303 · ~7/day · ~204/mo

Releases R versions

Daily download trend is not available in this view yet.

15130 days

60190 days

2.4K1 year

Compare downloads with other packages →

Also on96 r2u

Repository

GitHub ↗ mjuraska/pssmooth

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2020-11-18

Repository practices

Upstream repositoryBeta

Checks run against github.com/mjuraska/pssmooth on 2026-08-09.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

graphicsstatsosDesign np chngptMASS

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Michal Juraska

Author, Maintainer

Authors (1)

Michal Juraska

Author, Maintainer

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.3Latest
2020-11-18 · current release · diff ↗
unarchivedReturned to CRAN
2020-11-18
archivedRemoved from CRAN
2020-10-18
requires archived package 'osDesign'
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.2
2019-01-22 · diff ↗
1.0.1
2018-09-19 · diff ↗
1.0.0
2018-07-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-30
Total releases: 4 / 8 yrs
License: GPL-2 OSI
Download size: 19 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pssmooth")

Format

Juraska, M. (2020). pssmooth: Flexible and Efficient Evaluation of Principal Surrogates/Treatment Effect Modifiers (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.pssmooth

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 pssmooth version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-14. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-14, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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