Markus J. Ankenbrand iimog
iimog
/ pareto-bm-noodling.R
Created
November 5, 2021 17:55
— forked from willpearse/pareto-bm-noodling.R
Distributions of body mass noodling for sDevTraits
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| # Rough-and-ready body-mass/species-number estimation in mammals and birds | |
| # Will Pearse - 2021-09-19 | |
| ########################## | |
| # Load data ############## | |
| ########################## | |
| library(caper) | |
| library(ape) | |
| library(Pareto) |
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| { | |
| "conf": { | |
| "circular": { | |
| "tickSize": 5 | |
| }, | |
| "features": { | |
| "fallbackStyle": { | |
| "color": "#787878", | |
| "form": "rect", | |
| "height": 30, |
iimog
/ extract_protraits.pl
Created
April 18, 2018 15:35
Perl script to combine multiple columns from the protraits table to a single categorical traitType for FENNEC
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| #!/usr/bin/perl | |
| # USAGE: perl extract_traits.pl <ProTraits_binaryIntegrated_File> <columns ...> | |
| # EXAMPLE: perl extract_traits.pl ProTraits_binaryIntegratedPr0.90.txt 275 276 277 292 >oxygenreq.tsv | |
| use strict; | |
| use warnings; | |
| my $file = shift(@ARGV); | |
| my @columns = @ARGV; |
iimog
/ FENNEC_Individual_CLA
Created
September 14, 2017 08:48
Individual Contributor License Agreement for FENNEC
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| ###Individual Contributor License Agreement | |
| Thank you for Your interest in FENNEC. This document clarifies the terms under which You, the person signing this agreement, may make Contributions — which may include without limitation, software, bug fixes, configuration changes, documentation, or any other materials — to the FENNEC project. | |
| Please read this agreement carefully. If You have questions about these terms, please contact us via [GitHub](https://github.com/molbiodiv/fennec). | |
| You accept and agree to the following terms and conditions for Your present and future Contributions submitted to FENNEC. Except for the license granted herein to Us, You reserve all right, title, and interest in and to Your Contributions. | |
| **Licenses** |
iimog
/ extract_scales_bee_traits_from_html.py
Created
August 23, 2017 07:55
A python script (using beautiful soup) to extract bee traits from the html pages at http://scales.ckff.si/scaletool/?menu=6&submenu=3 and save as FENNEC compatible tsv files
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| # coding: utf-8 | |
| from bs4 import BeautifulSoup | |
| import glob | |
| trait_types = dict() | |
| trait_values_numeric = dict() | |
| trait_values_categorical = dict() | |
| general_citation = "Budrys, E., Budriene., A. and Orlovskyte. S. 2014. Cavity-nesting wasps and bees database." |
iimog
/ phinchFilterBug.biom
Created
April 11, 2017 15:45
Minimal biom file to demonstrate [a bug](https://github.com/PitchInteractiveInc/Phinch/issues/73) in Phinch.
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| { | |
| "id": "No Table ID", | |
| "format": "Biological Observation Matrix 2.1.0", | |
| "format_url": "http://biom-format.org", | |
| "matrix_type": "sparse", | |
| "generated_by": "BIOM-Format 2.1", | |
| "date": "2017-04-11T17:40:40.014828", | |
| "type": "OTU table", | |
| "matrix_element_type": "float", | |
| "shape": [3, 3], |
iimog
/ phinchDonutScale.biom
Created
March 16, 2017 18:33
Minimal biom file to demonstrate [a bug](https://github.com/PitchInteractiveInc/Phinch/issues/72) in Phinch.
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| { | |
| "id": "No Table ID", | |
| "format": "Biological Observation Matrix 2.1.0", | |
| "format_url": "http://biom-format.org", | |
| "matrix_type": "sparse", | |
| "generated_by": "BIOM-Format 2.1", | |
| "date": "2016-05-03T08:13:41.848780", | |
| "type": "OTU table", | |
| "matrix_element_type": "float", | |
| "shape": [3, 3], |
iimog
/ phinchSampleList.biom
Created
January 11, 2017 10:07
Minimal biom file to demonstrate [a bug](https://github.com/PitchInteractiveInc/Phinch/issues/70) in Phinch.
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| { | |
| "id": "No Table ID", | |
| "format": "Biological Observation Matrix 2.1.0", | |
| "format_url": "http://biom-format.org", | |
| "matrix_type": "sparse", | |
| "generated_by": "BIOM-Format 2.1", | |
| "date": "2016-05-03T08:13:41.848780", | |
| "type": "OTU table", | |
| "matrix_element_type": "float", | |
| "shape": [3, 3], |
iimog
/ phinchHideOTU.biom
Last active
January 5, 2017 15:26
Minimal biom file to demonstrate [a bug](https://github.com/PitchInteractiveInc/Phinch/issues/69) in Phinch.
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| { | |
| "id": "No Table ID", | |
| "format": "Biological Observation Matrix 2.1.0", | |
| "format_url": "http://biom-format.org", | |
| "matrix_type": "sparse", | |
| "generated_by": "BIOM-Format 2.1", | |
| "date": "2016-05-03T08:13:41.848780", | |
| "type": "OTU table", | |
| "matrix_element_type": "float", | |
| "shape": [3, 3], |
iimog
/ rich_dense.biom
Created
September 7, 2016 08:47
Rich dense OTU table - Example biom file from http://biom-format.org/documentation/format_versions/biom-1.0.html
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| { | |
| "id":null, | |
| "format": "Biological Observation Matrix 0.9.1-dev", | |
| "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", | |
| "type": "OTU table", | |
| "generated_by": "QIIME revision 1.4.0-dev", | |
| "date": "2011-12-19T19:00:00", | |
| "rows":[ | |
| {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, | |
| {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, |
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