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Russell Neches
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documentation updates (and a cute little logo!)
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‎docs/SuchTree_API.md‎

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---
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title: SuchTree's API
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subtitle: A somewhat consice description of the core features of SuchTree.
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icon: material/file-document-outline
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---
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# SuchTree Class API Reference
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## Overview

‎docs/api.md‎

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---
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title: API Reference
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subtitle: A complete, always up-to-date reference of SuchTree's API.
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icon: material/qrcode-scan
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---
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# API Reference
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This reference is automatically generated from the [source code](https://github.com/ryneches/SuchTree)
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and docstrings using [`mkdockstrings`](https://mkdocstrings.github.io/). This page will always
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be up to date to the latest git commit, but you may prefer [documentation written by an actual
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human](SuchTree_API.md) to be somewhat more palatable.
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Because `SuchTree` and `SuchLinkedTrees` are written in Cython and compiled into a shared library,
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the `mkdocstrings` is not (yet) able to extract the function implementations for documentation purposes.
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Sorry about that. You can always look in the source code.
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## SuchTree.SuchTree
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::: SuchTree.MuchTree.SuchTree

‎docs/assets/cpu-tree.svg‎

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‎docs/benchmarks.md‎

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---
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title: Benchmarks
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subtitle: Get a general idea of how SuchTree performs.
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icon: material/gauge
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---
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### Benchmarks
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`SuchTree` is motivated by the observation that the memory usage of distance

‎docs/datasets.md‎

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### Example datasets
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---
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title: Example datasets
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subtitle: Data from the scientific literature that you can use with SuchTree.
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icon: material/bee-flower
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---
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For analysis of ecological interactions, `SuchTree` is distributed
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with a curated collection of several different examples from the
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for generating them, is also included. Interactions are registered in
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a JSON object (`data/studies.json`).
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#### Host/Parasite
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## Host/Parasite
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* **gopher-louse** Hafner, M.S. & Nadler, S.A. 1988. *Phylogenetic trees support the coevolution of parasites and their hosts.* Nature 332: 258-259)
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* **dove-louse** Dale H. Clayton, Sarah E. Bush, Brad M. Goates, and Kevin P. Johnson. 2003. *Host defense reinforces host–parasite cospeciation.* PNAS.
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Floris C. Breman, Stephan Koblmüller, Christian Sturmbauer, Jos Snoeks,
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Filip A. M. Volckaert & Tine Huyse. 2015. *Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites*, Scientific Reports.
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#### Plant/Pollinator (visitor) interactions
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## Plant/Pollinator (visitor) interactions
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These were originally collected by Enrico Rezende *et al.* :
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* **smal** Small, E. 1976. *Insect pollinators of the Mer Bleue peat bog of Ottawa.* Canadian Field Naturalist 90:22-28.
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* **smra** Smith-Ramírez C., P. Martinez, M. Nuñez, C. González and J. J. Armesto 2005 *Diversity, flower visitation frequency and generalism of pollinators in temperate rain forests of Chiloé Island,Chile.* Botanical Journal of the Linnean Society, 2005, 147, 399–416.
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#### Frugivory interactions
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## Frugivory interactions
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* **bair** Baird, J.W. 1980. *The selection and use of fruit by birds in an eastern forest.* Wilson Bulletin 92: 63-73.
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* **beeh** Beehler, B. 1983. *Frugivory and polygamy in birds of paradise.* Auk, 100: 1-12.

‎docs/examples/SuchLinkedTree_examples.ipynb‎

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{
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"metadata": {},
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"source": [
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"---\n",
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"title: SuchLinkedTrees, with working examples\n",
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"subtitle: Worked examples illustrating some basic applications of SuchLinkedTrees. This file is available as a Jupyter Notebook in the project repository under docs/examples.\n",
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"icon: material/notebook-outline\n",
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"---"
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]
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},
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‎docs/examples/SuchLinkedTree_examples.md‎

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# SuchLinkedTree_examples
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---
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title: SuchLinkedTrees, with working examples
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subtitle: Worked examples illustrating some basic applications of SuchLinkedTrees. This file is available as a Jupyter Notebook in the project repository under docs/examples.
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icon: material/notebook-outline
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---
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# SuchLinkedTrees
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‎docs/examples/SuchTree_examples.ipynb‎

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"slideshow": {
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"tags": []
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},
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"source": [
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"---\n",
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"title: SuchTree, with working examples\n",
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"subtitle: Worked examples illustrating some basic applications of SuchTree. This file is available as a Jupyter Notebook in the project repository under docs/examples.\n",
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"icon: material/notebook-outline\n",
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"---"
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]
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‎docs/examples/SuchTree_examples.md‎

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# SuchTree_examples
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---
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title: SuchTree, with working examples
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subtitle: Worked examples illustrating some basic applications of SuchTree. This file is available as a Jupyter Notebook in the project repository under docs/examples.
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icon: material/notebook-outline
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---
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# SuchTree
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