paleoAM

1.0.1

Simulating Assemblage Models of Abundance for the Fossil Record

0packages depend

6.5Kdownloads / year

63.5%test coverage

13/13checks pass

Overview

About

Maintained by David W BapstFirst published 2024-09-171 releasesCRAN page ↗

Provides functions for fitting abundance distributions over environmental gradients to the species in ecological communities, and tools for simulating the fossil assemblages from those abundance models for such communities, as well as simulating assemblages across various patterns of sedimentary history and sampling. These tools are for particular use with fossil records with detailed age models and abundance distributions used for calculating environmental gradients from ordinations or other indices based on fossil assemblages.

Install

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

install.packages("paleoAM", 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-paleoam

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-paleoAM

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-paleoAM

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

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

63.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 162 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 93%
Return-value docs: 100%
References docs: 25%

Downloads

6.5K

CRAN downloads in the past year

Rank #7,461 · ~18/day · ~541/mo

Releases R versions

Daily download trend is not available in this view yet.

30330 days

1.4K90 days

6.5K1 year

Compare downloads with other packages →

Also on95 r2u24 autocran

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (3)

graphicsstatsvegan

LinkingTo (0)

none

Suggests (2)

spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,236 (73%)Rd 1,171 (27%)

Code characteristics

Cyclomatic complexity: 4.5 median / 15 max
Test cases: 2 / 0.04 per code line

Test coverage

Line coverage

63%

Expression

59.5%

Tests / Examples

63.5% / 13% ex

Functions

22 14 exported

Complexity

5.5 avg / 15 max

Call network

22 nodes / 16 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

22 functions

Function	Cyclo	Coverage
getRecoveredTransitionDuration exp	11	0%
plotGradientKDE exp	4	0%
plotHeatmapComparison exp	6	0%
simMixedAssemblageSample exp	1	0%
simulateGradientQuantile exp	1	0%
checkFossilSeriesAbundanceTable	8	0%

Datasets

Bundled datasets · 5

Name	Class	Rows × Cols	Also ships in
DCA1_GOA	vector	–	–
abundData_GOA	data.frame	355 × 48	–
fullDataTable_GOA	data.frame	355 × 53	–
graptCommData	data.frame	34 × 43	–
graptSampleInfo	data.frame	34 × 5	–

People & History

People (2)

Maintainer (1)

David W Bapst

Author, Maintainer

Authors (2)

David W Bapst

Author, Maintainer

Christina L Belanger

Author

Listed in earlier versions (2)

Bapst

no longer listed · 1.0.1

Belanger

no longer listed · 1.0.1

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-09-17
Total releases: 1 / 2 yrs
License: CC0
Minimum R: ≥ 4.1.0
Bundled data: 34 KB / 2 files
Download size: 86 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Paleontology

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