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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, |
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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; |
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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** |
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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." |
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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], |
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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], |
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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], |
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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], |
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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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