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Posts tagged ‘matrix’

Weekly reading: A dynamic homology approach for morphological data

Following up on last week’s wide-ranging explorations of dynamic homology sensu Wheeler, this week’s original, inspiring, and overall excellent paper by Martín Ramírez applies the issue to the challenge of properly (read: parsimoniously) assigning one or two of three potentially available sclerite ‘identities’ to their homologous positions in the complex male spider pedipalps and ranging over variously simultaneous inferred clades. Complex, engaging, and well conceived material for thought and possible application.

Ramírez, M.J. 2007. Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 23: 588-612. Available here.

P.s.: Posted retrospectively for April 04, 2014.

Weekly reading: Missing values, inapplicable states and polymorphic taxa

The third and likely penultimate session in our “explore cladistic coding” series. A brief primer below; more during our discussions and practices.

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Authoring interactive identification keys in SCAN – an introduction

Most recent update: February 26, 2014.

SCAN has activated the module for authoring interactive identification keys, even though the keys themselves are not yet live for potential users. In what follows some of the basic interfaces and practices for authoring keys are introduced. Prospective SCAN members interested in preparing keys individually or in collaboration should contact Nico Franz.

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Weekly reading: Character types and coding methods

Second chapter in the “let’s get some practice” series. In this week’s reading practice we will explore the interaction of alternative coding schemes and tree/optimization outcomes, both “by hand” and with WinClada and NONA. In particular, we will apply and compare simple binary, non-additive multi-state, and complex additive character coding schemes. We will assess their effects on cladogram length and on the character state optimizations along the internal cladogram nodes. We will start by learning how to code complex character state hierarchies as additive binary as well as additive multi-state characters. Please do some reading of the handout beforehand.

Weekly reading: Introducing DELTA (DEscriptive Language for TAxonomy)

As part of the series on character coding and analysis, we will learn about the software DELTA during this week’s discussion (February 14, 2014). As stated on its website, “[t]he DELTA format (DEscription Language for TAxonomy) is a flexible and powerful method of recording taxonomic descriptions for computer processing”, and “[i]t was adopted as a standard for data exchange by Biodiversity Information Standards (TDWG).” Read more

Weekly reading: Cladistic matrices, Wagner trees, and optimizations “by hand”

This week our weekly lab discussion group shifts gears from the empiricism/realism debate to actual, and mostly still “manual” (as if hands could think), character matrix assembly, Wagner tree construction, and upward-/downward-pass parsimony-based character state optimization. Consistency and retention indices. And WinClada and NONA. Let’s see how far the first session will take us towards understanding the interaction between characters, parsimony, optimizations, and trees.

Worthwhile reads on cladistic character coding

Some pointers to literature relevant to one of the most intellectually engaging topics I can think of in systematics – how to properly “code” cladistic characters. “Code” in quotation marks because there is more to it than a single verb or action might denote. For what it is worth, Olivier Rieppel’s (2007) “performance” paper is a must read in my assessment; he talks about the process of character “scoping”. Though practically all papers can be considered sincere (yes, that can matter) and scholarly contributions to advance the field, occasionally in an intellectual discourse setting overshadowed by too-easy dichotomies of pattern versus process, supposed methodological rigor versus eclecticism, or total evidence versus cherry picking (as I said, too easy, and no improvement here either in such a stenographic account).

Franz, N.M. 2014. Anatomy of a cladistic analysis. Cladistics 30: 294-321. pdf

I will update this listing, from time to time. My own current take is here, with corresponding WHS 2012 presentation:

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