コード例 #1
0
ファイル: test_coal.py プロジェクト: xysheep/compbio
    def test_plot_prob_bounded_coal(self):
        n = 1000
        k = 4
        t = 800
        alltimes = []

        # sample times
        for i in xrange(5000):
            while True:
                times = [0]
                for j in xrange(k, 1, -1):
                    times.append(times[-1] + coal.sample_coal(j, n))
                    if times[-1] >= t:
                        break
                if times[-1] < t:
                    break
            alltimes.append(times)

        p = Gnuplot()
        for i in range(1, 2):
            x, y = distrib([q[i] - q[i-1] for q in alltimes], width=20)
            p.plot(x, y, style="lines", xmax=500)

        x = list(frange(0, 500, 10))
        #for i in range(1, 2): #k):
        y2 = [coal.prob_bounded_coal(j, k, n, t) for j in x]
        p.plot(x, y2, style="lines", xmax=500)

        fequals(y, y2, rel=.05, eabs=.01)
コード例 #2
0
ファイル: test_coal.py プロジェクト: xysheep/compbio
    def test_prob_coal2(self):

        outdir = 'test/tmp/test_coal/Coal_test_prob_coal2/'
        make_clean_dir(outdir)

        k = 2
        n = 1000
        p = Gnuplot()
        p.enableOutput(False)
        p.plotfunc(lambda t: coal.prob_coal(t, k, n), 0, 4000, 10,
                   ymin=0)

        # draw single coal samples
        x = [coal.sample_coal(k, n) for i in xrange(200)]
        plotdistrib(x, 40, plot=p)
        p.enableOutput(True)
        p.save(outdir + 'plot.png')

        eq_sample_pdf(x, lambda t: coal.prob_coal(t, k, n), 40)
コード例 #3
0
ファイル: test_coal.py プロジェクト: xysheep/compbio
    def test_fast_sample_bounded_coal(self):

        # sample bounded coal times efficiently
        n = 1000
        k = 5
        t = 500
        alltimes = []

        # sample times
        for i in xrange(5000):
            while True:
                times = [0]
                for j in xrange(k, 1, -1):
                    times.append(times[-1] + coal.sample_coal(j, n))
                    if times[-1] >= t:
                        break
                if times[-1] < t:
                    break
            alltimes.append(times)

        p = Gnuplot()
        for i in range(1, k):
            x, y = distrib([q[i] - q[i-1] for q in alltimes], width=30)
            p.plot(x, y, style="lines", xmax=500)
        p.enableOutput(True)
        p.replot()

        # sample times efficently
        alltimes2 = []
        for i in xrange(5000):
            times = [0]
            for j in xrange(k, 1, -1):
                times.append(times[-1] +
                             coal.sample_bounded_coal(j, n, t-times[-1]))
            alltimes2.append(times)

        #p = Gnuplot()
        for i in range(1, k):
            x, y = distrib([q[i] - q[i-1] for q in alltimes2], width=30)
            p.plot(x, y, style="lines", xmax=500)
        p.enableOutput(True)
        p.replot()