R Observatory: Metrics for Claddis version 0.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Claddis

0.7.0Package record

Measuring Morphological Diversity and Evolutionary Tempo

1packages depend

8.6Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Graeme T. LloydCRAN page ↗

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) doi:10.1093/sysbio/46.4.590) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) doi:10.1111/j.1096-0031.2008.00217.x). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) doi:10.1111/j.1558-5646.2011.01460.x, Brusatte et al. (2014) doi:10.1016/j.cub.2014.08.034, Close et al. (2015) doi:10.1016/j.cub.2015.06.047, and Lloyd (2016) doi:10.1111/bij.12746, and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) doi:10.2307/2528823, Wills (1998) doi:10.1006/bijl.1998.0255, Lloyd (2016) doi:10.1111/bij.12746, and Hopkins and St John (2018) doi:10.1098/rspb.2018.1784. This also includes the GED correction from Lehmann et al. (2019) doi:10.1111/pala.12430. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) doi:10.1371/journal.pone.0039752, plot_morphospace() implements Wills et al. (1994) doi:10.1017/S009483730001263X, plot_changes_on_tree() implements Wang and Lloyd (2016) doi:10.1098/rspb.2016.0214, and plot_morphospace_stack() implements Foote (1993) doi:10.1017/S0094837300015864. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) doi:10.1093/sysbio/44.4.501, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) doi:10.1093/gbe/evy096, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) doi:10.1111/pala.12380. calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).

Install

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

install.packages("Claddis", 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-claddis

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-Claddis

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-Claddis

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

13OK

CRAN check page ↗

Slowest check: 3.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-10
WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.7.0

READMEYes · 299 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 92includes a package overview page
Examples that run: 94%84 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 89%
Help pages citing references: 39%

How these are measured

Downloads

8.6K

CRAN downloads in the past year

Rank #4,449 · ~24/day · ~719/mo

Releases R versions

Daily download trend is not available in this view yet.

85430 days

1.9K90 days

8.6K1 year

Compare downloads with other packages →

Also on199 r2u9 autocran77 c2d4u

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing Claddis adds 41 packages (21 with compiled code, 21 MB of source tarballs). Heaviest: igraph 4.8 MB, maps 2.2 MB, phangorn 1.9 MB.

Depends (4)

R >= 3.5.0ape phytools strap

Imports (9)

clipr geoscalegraphicsgrDevicesmethodsmulticool partitionsstatsutils

LinkingTo (0)

none

Suggests (2)

rgl testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

1indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

dispRity

How these are counted

Code & Tests

Datasets

People & History

People (5)

Graeme T. Lloyd

Thomas Guillerme

Author, Copyright holder · added in 0.3.0

Jen Hoyal Cuthill

Author, Copyright holder · added in 0.7.0

Emma Sherratt

Author, Copyright holder · added in 0.3.0

Steve C. Wang

Author, Copyright holder · added in 0.3.0

Releases (6)

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
0.7.0Latest
record
2024-09-03 · current release · diff ↗ ·
removed 3 exports
compactify_matrix, map_stochastic_changes, pattern:^[[:alpha:]]+

added 52 exports
add_polymorphisms_to_costmatrix, add_uncertainties_to_costmatrix, calculate_g, calculate_gmax, calculate_kardashian_index, calculate_MPD, calculate_tree_length, calculate_WMPD, check_cladisticMatrix, check_costMatrix, check_stateGraph, check_taxonGroups, check_timeBins, classify_costmatrix, compactify_cladistic_matrix, convert_adjacency_matrix_to_costmatrix, convert_costmatrix_to_stategraph, convert_state_tree_to_adjacency_matrix, convert_stategraph_to_costmatrix, count_cherries, drop_time_tip, estimate_squared_change_ancestors, find_costmatrix_minimum_span, find_shortest_costmatrix_path, find_stategraph_minimum_span, find_time_bin_midpoints, find_unique_trees, fix_costmatrix, is_graph_connected, is.cladisticMatrix and 22 more
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
0.6.3
record
2020-09-26 · diff ↗ ·
added 2 exports
print.cladisticMatrix, trim_marginal_whitespace
0.6.1
record
2020-08-27 · diff ↗ ·
removed 31 exports
AncStateEstMatrix, BlockAligner, ChangesInBins, ChronoPhyloMorphospacePlot, CompactifyMatrix, CorrectRootTime, DiscreteCharacterRate, DolloSCM, EdgeLengthsInBins, EdgeMatch, FindAncestor, FindLinkedEdges, GetAllStateChanges, GetDescendantEdges, GetNodeAges, MakeMorphMatrix, MatrixPruner, MinSpanTreeEdges, MorphDistMatrix, MorphMatrix2PCoA, MorphospacePlot, MultiMorphospacePlot, PhyloCharCompletenessInBins, PlotCharacterChanges, ReadMorphNexus, SafeTaxonomicReduction, SafeTaxonomicReinsertion, StackPlot, TrimMorphDistMatrix, WriteMorphNexus and 1 more

added 36 exports
align_matrix_block, assign_taxa_to_bins, bin_changes, bin_character_completeness, bin_edge_lengths, build_cladistic_matrix, calculate_morphological_distances, compactify_matrix, date_nodes, estimate_ancestral_states, find_descendant_edges, find_linked_edges, find_minimum_spanning_edges, find_mrca, fix_root_time, map_dollo_changes, map_stochastic_changes, match_tree_edges, ordinate_cladistic_matrix, partition_time_bins, plot_changes_on_tree, plot_chronophylomorphospace, plot_morphospace, plot_morphospace_stack, plot_multi_morphospace, plot_rates_character, plot_rates_time, plot_rates_tree, prune_cladistic_matrix, read_nexus_matrix and 6 more
R
R 4.0.0 released · 2020-04-24
0.3.4
record
2019-12-05 · diff ↗ ·
added 1 export
BlockAligner
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-02-12
0.3.0
record
2019-02-12 · diff ↗ ·
added 24 exports
ChangesInBins, ChronoPhyloMorphospacePlot, CompactifyMatrix, CorrectRootTime, DiscreteCharacterRate, DolloSCM, EdgeLengthsInBins, EdgeMatch, FindLinkedEdges, GetAllStateChanges, GetDescendantEdges, GetNodeAges, MakeMorphMatrix, MatrixPruner, MinSpanTreeEdges, MorphMatrix2PCoA, MorphospacePlot, MultiMorphospacePlot, PhyloCharCompletenessInBins, PlotCharacterChanges, SafeTaxonomicReinsertion, StackPlot, WriteMorphNexus, WriteMorphTNT
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 4 earlier eventsHide 4 earlier events

R
R 3.3.0 released · 2016-05-03
archivedRemoved from CRAN
2015-10-29
check problems were not corrected despite reminders
0.1
record
2015-04-28
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-04-28
Total releases: 6 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.8 KB / 3 files
Download size: 890 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("Claddis")

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

It points to 10.1111/bij.12746, 10.1111/pala.12380, 10.1111/pala.12430.

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 Claddis version 0.7.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, 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 →