View pareto-bm-noodling.R
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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) |
View out.json
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{ | |
"conf": { | |
"circular": { | |
"tickSize": 5 | |
}, | |
"features": { | |
"fallbackStyle": { | |
"color": "#787878", | |
"form": "rect", | |
"height": 30, |
View extract_protraits.pl
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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; |
View FENNEC_Individual_CLA
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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** |
View extract_scales_bee_traits_from_html.py
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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." |
View phinchFilterBug.biom
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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], |
View phinchDonutScale.biom
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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], |
View phinchSampleList.biom
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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], |
View phinchHideOTU.biom
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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], |
View rich_dense.biom
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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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