R Observatory: Metrics for PresenceAbsence version 1.1.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PresenceAbsence

1.1.11Package record

Presence-Absence Model Evaluation

4packages dependsuggested by 3

64.1Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Elizabeth FreemanCRAN page ↗

Provides a set of functions useful when evaluating the results of presence-absence models. Package includes functions for calculating threshold dependent measures such as confusion matrices, pcc, sensitivity, specificity, and Kappa, and produces plots of each measure as the threshold is varied. It will calculate optimal threshold choice according to a choice of optimization criteria. It also includes functions to plot the threshold independent ROC curves along with the associated AUC (area under the curve).

Install

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

install.packages("PresenceAbsence", 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-presenceabsence

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-PresenceAbsence

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-PresenceAbsence

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Elizabeth Freeman <elizabeth.a.freeman@usda.gov>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Elizabeth",
                    family = "Freeman",
                    role = c("aut", "cre"),
                    email = "elizabeth.a.freeman@usda.gov")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.3 min · r-release-macos-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.11

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 20includes a package overview page
Examples that run: 100%20 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 15%

Also includes 2 demo scripts (run with demo())

How these are measured

Downloads

64.1K

CRAN downloads in the past year

Rank #1,647 · ~176/day · ~5.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.9K30 days

13.5K90 days

64.1K1 year

Compare downloads with other packages →

Also on499 r2u6 autocran2.9K conda_forge99 c2d4u

How downloads are counted

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing PresenceAbsence adds no packages beyond those that come with R.

Depends (1)

R >= 2.2.0

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

5indirect

Imports 4

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

biomod2 ecospat ModelMap RRgeo

Suggests, most downloaded first

BiodiversityR ebirdst spind

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

Elizabeth Freeman

· added in 1.1.5

Maintainer since 1.0.0 (2007)

Listed in earlier versions (1)

Elizabeth Freeman.

no longer listed · 1.0.0 to 1.1.4

Releases (10)

Pick two releases to compare their code metrics.

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
1.1.11Latest
record
2023-01-07 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.10
record
2022-03-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03

Show 20 earlier eventsHide 20 earlier events

1.1.9
record
2012-08-17 · diff ↗ ·
added 1 export
pattern:.
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
1.1.5
record
2010-12-07 · diff ↗
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
1.1.4
record
2010-04-17 · diff ↗
R
R 2.10.0 released · 2009-10-26
R
R 2.9.0 released · 2009-04-17
1.1.3
record
2009-03-17 · diff ↗
R
R 2.8.0 released · 2008-10-20
R
R 2.7.0 released · 2008-04-22
1.1.2
record
2008-03-28 · diff ↗
1.1.1
record
2008-01-07 · diff ↗
R
R 2.6.0 released · 2007-10-03
1.1.0
record
2007-09-13 · diff ↗
R
R 2.5.0 released · 2007-04-24
1.0.0
record
2007-02-23
R
R 2.4.0 released · 2006-10-03

Package metadata

First published: 2007-02-23
Total releases: 10 / 19 yrs
License: Unlimited · relicensed from This code was written and prepared by a U.S. Government employee on official time, and therefore it is in the public domain and not subject to copyright. in 1.1.0
Minimum R: ≥ 2.2.0
Bundled data: 83 KB / 3 files
Download size: 136 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("PresenceAbsence")

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

It points to 10.18637/jss.v023.i11.

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 PresenceAbsence version 1.1.11 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, 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 →