Timothée Poisot tpoisot
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tpoisot
/ lv-comp.c
Created
August 28, 2013 15:36
Model to reproduce the Box 2 of Gravel et al. 2011. C, uses the GSL, makefile included. Compiles on Arch 3.10.1 with clang and gcc. Gravel D., Guichard F. & Hochberg M.E. 2011. Coexistence in a variable world. Ecology Letters doi: 10.1111/j.1461-0248.2011.01643.x
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| // Compile with make | |
| // Change the comp variable to gcc or clang | |
| #include <stdio.h> | |
| #include <stdlib.h> | |
| #include <math.h> | |
| #include <time.h> | |
| #include <string.h> | |
| #include <gsl/gsl_rng.h> |
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| prog = logstoch | |
| source = stoch.c | |
| comp = gcc | |
| flags = -lgsl -lgslcblas -O3 -DHAVE_INLINE | |
| $(prog): $(source) | |
| $(comp) $(source) -o $(prog) $(flags) |
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| pdyn = function(N, r, K, t) | |
| { | |
| for(i in c(1:(t-1))) N[i+1] = N[i] + r*N[i]*(1-N[i]/K) | |
| return(N) | |
| } | |
| getNs = function(N, r, K, t, record) | |
| { | |
| N = pdyn(N, r, K, t) | |
| Ns = unique(N[(length(N)-record):length(N)]) |
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| #!/bin/bash/env python2 | |
| # -*- coding: utf-8 -*- | |
| zotdb = "zot.sqlite" | |
| import json | |
| import sys | |
| import sqlite3 as lite | |
| def count(array): | |
| counts = {} |
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| #!/usr/bin/python | |
| ### Blast a list of fasta files | |
| ### Returns the results and measure similarity IGNORING gaps | |
| ### | |
| ### Tim Poisot - [email protected] | |
| ### May 20, 2013 | |
| ### This code is in the public domain | |
| from Bio.Blast import NCBIXML |
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| // clang nb-sp.c -o nb -lgsl -lgslcblas -O3 -DHAVE_INLINE | |
| #include <stdio.h> | |
| #include <stdlib.h> | |
| #include <math.h> | |
| #include <time.h> | |
| #include <sys/time.h> | |
| #include <string.h> | |
| #include <gsl/gsl_rng.h> | |
| #include <gsl/gsl_randist.h> |
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| import numpy as np | |
| import scipy as sp | |
| import matplotlib.pyplot as plt | |
| from progressbar import * | |
| # Simulation time | |
| SimTime = 500 | |
| # A spatial version of the NB model | |
| # Make a movie with |
tpoisot
/ zotero-standalone.desktop
Last active
September 27, 2018 21:40
zotero desktop file for the standalone version in fedora -- https://developer.gnome.org/integration-guide/stable/desktop-files.html.en
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| [Desktop Entry] | |
| Name=Zotero Standalone | |
| Exec=/usr/local/bin/Zotero_linux-x86_64/zotero | |
| Icon=/usr/local/bin/Zotero_linux-x86_64/chrome/icons/default/default48.png | |
| Type=Application | |
| Categories=Education; |
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| // gcc niche.c -o nm -lgsl -lgslcblas -O3 -DHAVE_INLINE | |
| // clang niche.c -o nm -lgsl -lgslcblas -O3 -DHAVE_INLINE | |
| #include <stdio.h> | |
| #include <stdlib.h> | |
| #include <math.h> | |
| #include <time.h> | |
| #include <string.h> | |
| #include <gsl/gsl_rng.h> | |
| #include <gsl/gsl_randist.h> |
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| def niche_foodweb(S, C): | |
| G = nx.DiGraph() | |
| G.add_nodes_from([n for n in xrange(S)]) | |
| ## Step 1 - create random species | |
| for n in G: | |
| G.node[n]['n'] = np.round(np.random.uniform(),2) | |
| G.node[n]['r'] = np.random.beta(1, 1/float(2*C)-1) * G.node[n]['n'] | |
| G.node[n]['c'] = np.random.uniform(G.node[n]['r']/float(2),G.node[n]['n']) | |
| ## Step 2 - smallest species are basal | |
| Smallest = np.min([G.node[n]['n'] for n in G]) |