R Observatory: Metrics for SRS version 0.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SRS

0.2.3

Scaling with Ranked Subsampling

3packages depend

5.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Lukas BeuleFirst published 2020-08-317 releasesCRAN page ↗

Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is a popular method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. An alternative to rarefying is scaling with ranked subsampling (SRS). SRS consists of two steps. In the first step, the total counts for all OTUs (operational taxonomic units) or species in each sample are divided by a scaling factor chosen in such a way that the sum of the scaled counts Cscaled equals Cmin. In the second step, the non-integer Cscaled values are converted into integers by an algorithm that we dub ranked subsampling. The Cscaled value for each OTU or species is split into the integer part Cint (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cints). Since the sum of Cint is smaller or equal to Cmin, additional delta C = Cmin - the sum of Cint counts have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values. Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches delta C and the sum of all counts in the normalized library equals Cmin. When the lowest Cfrag involved in picking delta C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. OTUs with identical Cfrag as well as Cint are sampled randomly without replacement. See Beule & Karlovsky (2020) doi:10.7717/peerj.9593 for details.

Install

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

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

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

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-srs

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-SRS

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-SRS

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: 1.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

5

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 100%

Downloads

5.7K

CRAN downloads in the past year

Rank #7,480 · ~16/day · ~478/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

1.1K90 days

5.7K1 year

Compare downloads with other packages →

Also on99 r2u10 autocran781 conda_forge

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (6)

R >= 3.4.0vegan shiny DT (>= 0.16)shinycssloaders shinybusy

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

CoreMicrobiomeR QsRutils MiscMetabar

Code & Tests

People & History

People (3)

Maintainer (1)

Lukas Beule

Author, Maintainer

Authors (3)

Lukas Beule

Author, Maintainer

Vitor Heidrich

Author · added in 0.1.1

Petr Karlovsky

Author

Listed in earlier versions (1)

Devon O'rourke

no longer listed · 0.1.2 to 0.2.2

Package Timeline

7 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
0.2.3Latest
2022-03-27 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.2
2021-02-10 · diff ↗
0.2.1
2020-11-17 · diff ↗
0.2.0
2020-11-14 · diff ↗
0.1.2
2020-10-29 · diff ↗
0.1.1
2020-10-02 · diff ↗
0.1.0
2020-08-31
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-31
Total releases: 7 / 6 yrs
License: CC BY-SA 4.0
Minimum R: ≥ 3.4.0
Download size: 11 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SRS")

Format

Beule, L., Heidrich, V., & Karlovsky, P. (2022). SRS: Scaling with Ranked Subsampling (Version 0.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.SRS

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 SRS version 0.2.3 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →