Evidence map›Paper›PMID 39695946›Full record

ArticleBMC bioinformatics2024

Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space.

Jeet Sukumaran, Marina Meila

Abstract read
In one paragraph

Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Jeet SukumaranBiology, San Diego State University, San Diego, CA, USA. jsukumaran@sdsu.edu.
Marina MeilaStatistics, University of Washington, Seattle, 10587, WA, USA.

Funding

Division of Environmental Biology 1937725
6 · The paper itself

Abstract

backgroundExisting software for comparison of species delimitation models do not provide a (true) metric or distance functions between species delimitation models, nor a way to compare these models in terms of relative clustering differences along a lattice of partitions.

resultsPiikun is a Python package for analyzing and visualizing species delimitation models in an information theoretic framework that, in addition to classic measures of information such as the entropy and mutual information [1], provides for the calculation of the Variation of Information (VI) criterion [2], a true metric or distance function for species delimitation models that is aligned with the lattice of partitions.

conclusionsPiikun is available under the MIT license from its public repository ( https://github.com/jeetsukumaran/piikun ), and can be installed locally using the Python package manager 'pip'.

Indexed as

SoftwareAlgorithmsComputational BiologyGenetic SpeciationInformation TheoryPhylogenyDistancesEvolutionary biologyInformation theoryMetricsSpecies delimitation

Identifiers

PMID39695946
PMCPMC11657818

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.