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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
# 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)
@iimog
iimog / out.json
Created June 7, 2018 14:18
MRE for AliTVTeam/AliTV-perl-interface#155
{
"conf": {
"circular": {
"tickSize": 5
},
"features": {
"fallbackStyle": {
"color": "#787878",
"form": "rect",
"height": 30,
@iimog
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
#!/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
iimog / FENNEC_Individual_CLA
Created September 14, 2017 08:48
Individual Contributor License Agreement for FENNEC
###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
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
# 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
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.
{
"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
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.
{
"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
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.
{
"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
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.
{
"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
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
{
"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__"]}},