コード例 #1
0
        elif figure == '3':
            gf.fig3()
        elif figure == '4':
            gf.fig4()
        elif figure == 'S1':
            gf.figS1()
        elif figure == 'S2':
            gf.figS2()
        elif figure == 'S3':
            gf.figS3()
        else:
            print "Command not recognized"
    else:
        gd.HMP_OTU_to_sparese_SbyS()
        gd.Match_NAP_to_sparse_SbyS()
        gd.get_SADs_HMP()
        gd.get_SADs_mgrast()
        gd.merge_SADs_mgrast()

        methods = ['geom','lognorm', 'mete','zipf']
        gd.generate_obs_pred_data(['EMPclosed','HMP', 'MGRAST'], methods, remove_obs = 0)
        gd.generate_obs_pred_data(['EMPclosed','HMP', 'MGRAST'], methods, remove_obs = 1)
        gd.generate_obs_pred_data(['95','97', '99'], methods, remove_obs = 0)
        gd.stratifyDataOnce(['EMPclosed','HMP', 'MGRAST'], remove_obs = 0)
        gd.stratifyDataOnce(['EMPclosed','HMP', 'MGRAST'], remove_obs = 1)
        gd.stratifyDataBootstrap(remove_obs = 0)
        gd.stratifyDataBootstrap(remove_obs = 1)
        gd.stratifyDataBootstrap(remove_obs = 0, seqSim = '95')
        gd.stratifyDataBootstrap(remove_obs = 0, seqSim = '97')
        gd.stratifyDataBootstrap(remove_obs = 0, seqSim = '99')
コード例 #2
0
from __future__ import division
import mete as mete
import os, math
import numpy as np
import modelsAndMetrics as mo
import macroeco_distributions as md
from scipy import stats
import generateData as gd

mydir = os.path.expanduser("~/github/MicroMETE/")

import importData as im


gd.stratifyDataBootstrap(remove_obs = 0)
#gd.stratifyDataBootstrap(remove_obs = 1)
#gd.stratifyDataBootstrap(remove_obs = 0, seqSim = '95')
#gd.stratifyDataBootstrap(remove_obs = 0, seqSim = '97')
#gd.stratifyDataBootstrap(remove_obs = 0, seqSim = '99')
#gd.stratifyDataOnce(['EMPclosed', 'MGRAST', 'HMP'], remove_obs = 0)
コード例 #3
0
        elif figure == 'TS4':
            gf.tableS4()
        elif figure == 'TS5':
            gf.tableS5()
        elif figure == 'TS6':
            gf.tableS6()
        else:
            print "Command not recognized"
    else:
        gd.HMP_OTU_to_sparese_SbyS()
        gd.Match_NAP_to_sparse_SbyS()
        gd.get_SADs_HMP()
        gd.get_SADs_mgrast()
        gd.merge_SADs_mgrast()

        methods = ['geom', 'lognorm', 'mete', 'zipf']
        gd.generate_obs_pred_data(['EMPclosed', 'HMP', 'MGRAST'],
                                  methods,
                                  remove_obs=0)
        gd.generate_obs_pred_data(['EMPclosed', 'HMP', 'MGRAST'],
                                  methods,
                                  remove_obs=1)
        gd.generate_obs_pred_data(['95', '97', '99'], methods, remove_obs=0)
        gd.stratifyDataOnce(['EMPclosed', 'HMP', 'MGRAST'], remove_obs=0)
        gd.stratifyDataOnce(['EMPclosed', 'HMP', 'MGRAST'], remove_obs=1)
        gd.stratifyDataBootstrap(remove_obs=0)
        gd.stratifyDataBootstrap(remove_obs=1)
        gd.stratifyDataBootstrap(remove_obs=0, seqSim='95')
        gd.stratifyDataBootstrap(remove_obs=0, seqSim='97')
        gd.stratifyDataBootstrap(remove_obs=0, seqSim='99')