Пример #1
0
 def sample(self, n=1):
     left, right = self.low, self.high
     mode = sqrt(left * right)
     c = (mode - left) / (right - left)
     loc = left
     scale = right - left
     return triang.rvs(c=c, loc=loc, scale=scale, size=n)
Пример #2
0
	def sample(self, n=1):
		left, right = self.low, self.high
		mode = sqrt(left * right)
		c = (mode - left) / (right - left)
		loc = left
		scale = right - left
		return triang.rvs(c=c, loc=loc, scale=scale, size=n)
Пример #3
0
def generateToy():

  np.random.seed(12345)

  fig,ax = plt.subplots(4,sharex=True)
  #fig,ax = plt.subplots(2)

  powerlaw_arg = 2
  triang_arg=0.7
  n_samples = 500
  #generate simple line with slope 1, from 0 to 1
  frozen_powerlaw = powerlaw(powerlaw_arg) #powerlaw.pdf(x, a) = a * x**(a-1)
  #generate triangle with peak at 0.7
  frozen_triangle = triang(triang_arg) #up-sloping line from loc to (loc + c*scale) and then downsloping for (loc + c*scale) to (loc+scale).
  frozen_uniform = uniform(0.2,0.5)
  frozen_uniform2 = uniform(0.3,0.2)

  x = np.linspace(0,1)

  signal = np.random.normal(0.5, 0.1, n_samples/2)

  data_frame = pd.DataFrame({'powerlaw':powerlaw.rvs(powerlaw_arg,size=n_samples),
    'triangle':triang.rvs(triang_arg,size=n_samples),
    'uniform':np.concatenate((uniform.rvs(0.2,0.5,size=n_samples/2),uniform.rvs(0.3,0.2,size=n_samples/2))),
    'powerlaw_signal':np.concatenate((powerlaw.rvs(powerlaw_arg,size=n_samples/2),signal))})

  ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
  hist(data_frame['powerlaw'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[0])
  #hist(data_frame['powerlaw'],bins='blocks',fitness='poly_events',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[0])
  ax[0].legend(loc = 'best')

  ax[1].plot(x, frozen_triangle.pdf(x), 'k-', lw=2, label='triangle pdf')
  hist(data_frame['triangle'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[1])
  hist(data_frame['triangle'],bins='blocks',fitness='poly_events',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[1])
  ax[1].legend(loc = 'best')

  #ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
  hist(data_frame['powerlaw_signal'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[2])
  #hist(data_frame['powerlaw_signal'],bins='blocks',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[2])
  ax[2].legend(loc = 'best')

  ax[3].plot(x, frozen_uniform.pdf(x)+frozen_uniform2.pdf(x), 'k-', lw=2, label='uniform pdf')
  hist(data_frame['uniform'],bins=100,normed=True,histtype='stepfilled',alpha=0.2,label='100 bins',ax=ax[3])
  #hist(data_frame['uniform'],bins='blocks',fitness = 'poly_events',p0=0.05,normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[3])
  ax[3].legend(loc = 'best')

  plt.show()
  fig.savefig('plots/toy_plots.png')
Пример #4
0
	def sample(self):
		left, right, mode = self.low90, self.high90, self.geomean
		c = (mode - left) / (right - left)
		loc = left
		scale = right - left
		return triang.rvs(c=c, loc=loc, scale=scale)
Пример #5
0
                    fontweight='bold')
ax.set_ylabel("Count", fontweight='bold')
ax.set_xlabel("h, m", fontweight='bold')

# Skin will be uniformly distributed
skin_dist = uniform.rvs(loc=0, scale=10, size=n_trials, random_state=seed)
ax = sns.distplot(skin_dist, kde=False, ax=axs[1, 0])
axs[1, 0].set_title("Input distribution for skin damage \n", fontweight='bold')
ax.set_ylabel("Count", fontweight='bold')
ax.set_xlabel("S", fontweight='bold')

# Reservoir pressure will be use the triangular distribution
# See https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.triang.html
pres_dist = triang.rvs(c=0.5,
                       loc=2750,
                       scale=500,
                       size=n_trials,
                       random_state=seed)
ax = sns.distplot(pres_dist, kde=False, ax=axs[1, 1])
axs[1, 1].set_title("Input distribution for reservoir pressure \n",
                    fontweight='bold')
ax.set_ylabel("Count", fontweight='bold')
ax.set_xlabel("P, psia", fontweight='bold')

plt.tight_layout()
plt.show()


# Custom function for performing PROSPER calculation
def calc_OPR(OpenServe, k, h, S, P):
    DoSet(OpenServe, "PROSPER.SIN.IPR.Single.ResPerm", k)
Пример #6
0
 def sample(self):
     left, right, mode = self.low90, self.high90, self.geomean
     c = (mode - left) / (right - left)
     loc = left
     scale = right - left
     return triang.rvs(c=c, loc=loc, scale=scale)
# Generate three Bernoulli random numbers
print(bernoulli.rvs(p, size=3))  # [0 1 0]

# Poisson
lmda = 2
x = 5
print(poisson.pmf(x, lmda))
print(poisson.cdf(x, lmda))
print(poisson.rvs(lmda, size=3))

# Uniform
a = 3
b = 10
x = 10
print(uniform.pdf(x, loc=a, scale=(b - a)))  # = 1 / 7
print(uniform.cdf(x, loc=a, scale=(b - a)))  # = 1.0
print(uniform.rvs(loc=3, scale=(b - a), size=3))

# Exponential
mu = 2
x = 2
print(expon.pdf(x, scale=(1 / mu)))
print(expon.cdf(x, scale=(1 / mu)))
print(expon.rvs(scale=(1 / mu), size=3))

# Triangular
a = 1
b = 10
c = 7
print(triang.rvs(c, loc=a, scale=(b - a), size=3))
Пример #8
0
def distribution_compared_individual(data, sample_size= 10000):
    '''
    This function works to compare the degree distribution at the individual and group mean level to
    a number of standard distribution: Uniform, Normal, Gamma, Exponential, Poisson, Triangular,
    LogNormal, and Weibull. Further, the comparison is made using a one-way
    Kolmogorov-Smirnov test for goodness of fit and a p-value is computed at the individual
    and group level.

    params:
    sample size = number of random values to generate per distribution test--default val = 10000
    data = list of degree distributions
     '''
    from scipy import stats
    from scipy.stats import uniform, norm, gamma, expon, poisson, triang, lognorm, weibull_min
    import numpy as np
    from numpy.random import weibull



    #####################################
    #####################################
    # Individual level comparison
    for jj, ll in zip(graphs['Subject'], graphs['Degree_dist']):
        path = jj[0]
        deg_dist = ll

        centered_deg_mean = np.asarray(deg_dist) - np.mean(deg_dist)

        data_uniform = uniform.rvs(size=sample_size, loc = np.min(centered_deg_mean), scale=np.max(centered_deg_mean))

        data_normal = norm.rvs(size=sample_size,loc=np.median(centered_deg_mean),scale=1)

        data_gamma = gamma.rvs(a=5, size= sample_size)

        data_expon = expon.rvs(scale=1,loc= np.median(centered_deg_mean),size= sample_size)

        mu=3
        data_poisson = poisson.rvs(mu=mu, size= sample_size)

        c= 0.158
        data_triang = triang.rvs(c=c, size = sample_size)

        s = 0.954
        data_lognorm = lognorm.rvs(s=s, size = sample_size)

        a = 5.0
        data_weibull = np.random.weibull(a = a, size = sample_size)


        Distributions = [data_uniform, data_normal, data_gamma, data_expon, data_poisson, data_triang, data_lognorm, data_weibull]
        dist_names = ['Uniform', 'Normal', 'Gamma', 'Exponential', 'Poisson', 'Triangular', 'LogNormal', 'Weibull']


        uniform_test = list(['Uniform:', stats.kstest(centered_deg_mean, data_uniform)])
        normal_test = list(['Normal', stats.kstest(centered_deg_mean, data_normal)])
        gamma_test = list(['Gamma', stats.kstest(centered_deg_mean, data_gamma)])
        exponential_test = list(['Exponential', stats.kstest(centered_deg_mean, data_expon)])
        poisson_test = list(['Poisson', stats.kstest(centered_deg_mean, data_poisson)])
        triang_test = list(['Triang', stats.kstest(centered_deg_mean, data_triang)])
        lognormal_test = list(['Lognormal', stats.kstest(centered_deg_mean, data_lognorm)])
        weibull_test = list(['Weibull', stats.kstest(centered_deg_mean, data_weibull)])

        for ii, kk  in zip(Distributions, dist_names):
            sns.set_context('talk')
            ax = sns.histplot(ii,
                             bins = 50,
                             kde= True,
                            color = 'skyblue')
                            #hist_kws={'linewidth':15, 'alpha':1})
            ax.set(title= kk + ' Sample Degree Distribution', ylabel = 'Frequency')
            aj = sns.histplot(centered_deg_mean,
                      bins= 50,
                      kde=True,
                      color='forestgreen')
            plt.savefig( path + '/reports/' + kk +  ' Sample Degree Distribution.png')
            plt.clf()





        ks_test_results_individual= [uniform_test, normal_test, gamma_test, exponential_test, poisson_test,
                                     triang_test, lognormal_test, weibull_test]

        with open(path + '/reports/' +'ks_test_results' + jj[0] +'.txt', 'w') as filehandle:
            for listitem in ks_test_results_individual:
                filehandle.write('%s\n' % listitem)

    return
Пример #9
0
def generateToy():

    np.random.seed(12345)

    fig, ax = plt.subplots(4, sharex=True)
    #fig,ax = plt.subplots(2)

    powerlaw_arg = 2
    triang_arg = 0.7
    n_samples = 500
    #generate simple line with slope 1, from 0 to 1
    frozen_powerlaw = powerlaw(
        powerlaw_arg)  #powerlaw.pdf(x, a) = a * x**(a-1)
    #generate triangle with peak at 0.7
    frozen_triangle = triang(
        triang_arg
    )  #up-sloping line from loc to (loc + c*scale) and then downsloping for (loc + c*scale) to (loc+scale).
    frozen_uniform = uniform(0.2, 0.5)
    frozen_uniform2 = uniform(0.3, 0.2)

    x = np.linspace(0, 1)

    signal = np.random.normal(0.5, 0.1, n_samples / 2)

    data_frame = pd.DataFrame({
        'powerlaw':
        powerlaw.rvs(powerlaw_arg, size=n_samples),
        'triangle':
        triang.rvs(triang_arg, size=n_samples),
        'uniform':
        np.concatenate((uniform.rvs(0.2, 0.5, size=n_samples / 2),
                        uniform.rvs(0.3, 0.2, size=n_samples / 2))),
        'powerlaw_signal':
        np.concatenate((powerlaw.rvs(powerlaw_arg,
                                     size=n_samples / 2), signal))
    })

    ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
    hist(data_frame['powerlaw'],
         bins=100,
         normed=True,
         histtype='stepfilled',
         alpha=0.2,
         label='100 bins',
         ax=ax[0])
    #hist(data_frame['powerlaw'],bins='blocks',fitness='poly_events',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[0])
    ax[0].legend(loc='best')

    ax[1].plot(x, frozen_triangle.pdf(x), 'k-', lw=2, label='triangle pdf')
    hist(data_frame['triangle'],
         bins=100,
         normed=True,
         histtype='stepfilled',
         alpha=0.2,
         label='100 bins',
         ax=ax[1])
    hist(data_frame['triangle'],
         bins='blocks',
         fitness='poly_events',
         normed=True,
         histtype='stepfilled',
         alpha=0.2,
         label='b blocks',
         ax=ax[1])
    ax[1].legend(loc='best')

    #ax[0].plot(x, frozen_powerlaw.pdf(x), 'k-', lw=2, label='powerlaw pdf')
    hist(data_frame['powerlaw_signal'],
         bins=100,
         normed=True,
         histtype='stepfilled',
         alpha=0.2,
         label='100 bins',
         ax=ax[2])
    #hist(data_frame['powerlaw_signal'],bins='blocks',normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[2])
    ax[2].legend(loc='best')

    ax[3].plot(x,
               frozen_uniform.pdf(x) + frozen_uniform2.pdf(x),
               'k-',
               lw=2,
               label='uniform pdf')
    hist(data_frame['uniform'],
         bins=100,
         normed=True,
         histtype='stepfilled',
         alpha=0.2,
         label='100 bins',
         ax=ax[3])
    #hist(data_frame['uniform'],bins='blocks',fitness = 'poly_events',p0=0.05,normed=True,histtype='stepfilled',alpha=0.2,label='b blocks',ax=ax[3])
    ax[3].legend(loc='best')

    plt.show()
    fig.savefig('plots/toy_plots.png')
Пример #10
0
x = np.linspace(triang.ppf(0.01, c),
                triang.ppf(0.99, c), 100)
ax.plot(x, triang.pdf(x, c),
       'r-', lw=5, alpha=0.6, label='triang pdf')

# Alternatively, the distribution object can be called (as a function)
# to fix the shape, location and scale parameters. This returns a "frozen"
# RV object holding the given parameters fixed.

# Freeze the distribution and display the frozen ``pdf``:

rv = triang(c)
ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf')

# Check accuracy of ``cdf`` and ``ppf``:

vals = triang.ppf([0.001, 0.5, 0.999], c)
np.allclose([0.001, 0.5, 0.999], triang.cdf(vals, c))
# True

# Generate random numbers:

r = triang.rvs(c, size=1000)

# And compare the histogram:

ax.hist(r, normed=True, histtype='stepfilled', alpha=0.2)
ax.legend(loc='best', frameon=False)
plt.show()
Пример #11
0
def distribution_compared_group(data, sample_size=10000, reports_path='.'):
    '''
    This function works to compare the degree distribution at the individual and group mean level to
    a number of standard distribution: Uniform, Normal, Gamma, Exponential, Poisson, Triangular,
    LogNormal, and Weibull. Further, the comparison is made using a one-way
    Kolmogorov-Smirnov test for goodness of fit and a p-value is computed at the individual
    and group level.

    params:
    sample size = number of random values to generate per distribution test--default val = 10000
    data = list of degree distributions
     '''
    from scipy import stats
    from scipy.stats import uniform, norm, gamma, expon, poisson, triang, lognorm, weibull_min
    import numpy as np
    from numpy.random import weibull
    import os
    import statistics

    #####################################
    # Group level comparison
    group_deg_mean = []
    for jj in data['Degree_dist']:
        group_deg_mean.append(statistics.mean(jj))

    group_deg_array = np.array(group_deg_mean)
    group_centered_deg_mean = group_deg_array - np.mean(group_deg_array)

    data_uniform = uniform.rvs(size=sample_size,
                               loc=np.min(group_centered_deg_mean),
                               scale=np.max(group_centered_deg_mean))

    data_normal = norm.rvs(size=sample_size,
                           loc=np.median(group_centered_deg_mean),
                           scale=1)

    data_gamma = gamma.rvs(a=5, size=sample_size)

    data_expon = expon.rvs(scale=1,
                           loc=np.median(group_centered_deg_mean),
                           size=sample_size)

    mu = 3
    data_poisson = poisson.rvs(mu=mu, size=sample_size)

    c = 0.158
    data_triang = triang.rvs(c=c, size=sample_size)

    s = 0.954
    data_lognorm = lognorm.rvs(s=s, size=sample_size)

    a = 5.0
    data_weibull = np.random.weibull(a=a, size=sample_size)

    Distributions = [
        data_uniform, data_normal, data_gamma, data_expon, data_poisson,
        data_triang, data_lognorm, data_weibull
    ]
    dist_names = [
        'Uniform', 'Normal', 'Gamma', 'Exponential', 'Poisson', 'Triangular',
        'LogNormal', 'Weibull'
    ]

    group_uniform = [
        'Uniform:',
        stats.kstest(group_centered_deg_mean, data_uniform)
    ]
    group_normal = [
        'Normal', stats.kstest(group_centered_deg_mean, data_normal)
    ]
    group_gamma = ['Gamma', stats.kstest(group_centered_deg_mean, data_gamma)]
    group_exponential = [
        'Exponential',
        stats.kstest(group_centered_deg_mean, data_expon)
    ]
    group_poisson = [
        'Poisson',
        stats.kstest(group_centered_deg_mean, data_poisson)
    ]
    group_traing = [
        'Triang', stats.kstest(group_centered_deg_mean, data_triang)
    ]
    group_lognormal = [
        'Lognormal',
        stats.kstest(group_centered_deg_mean, data_lognorm)
    ]
    group_weibull = [
        'Weibull',
        stats.kstest(group_centered_deg_mean, data_weibull)
    ]

    for ii, jj in zip(Distributions, dist_names):
        sns.set_context('talk')
        ax = sns.histplot(ii, bins=50, kde=True, color='skyblue')
        #hist_kws={'linewidth':15, 'alpha':1})
        ax.set(title=jj + ' Sample Degree Distribution', ylabel='Frequency')
        aj = sns.histplot(group_centered_deg_mean,
                          bins=50,
                          kde=True,
                          color='forestgreen')
        plt.savefig(reports_path + '/' + jj +
                    ' Sample Degree Distribution.png')
        plt.clf()

    ks_test_results_group = [
        group_uniform, group_normal, group_gamma, group_exponential,
        group_poisson, group_traing, group_lognormal, group_weibull
    ]

    with open(reports_path + '/' + 'ks_test_results_group.txt',
              'w') as filehandle:
        for listitem in ks_test_results_group:
            filehandle.write('%s\n' % listitem)

    return ks_test_results_group
Пример #12
0
	for x in range(0, random.randint(0, 6) ):
		S[Z[x]]=0
FC, FA, r, sC, sA, z1, z2=S

File2.write( "@NAME:SCAFFOLDS	VERSION:0.4.1	FORMAT:TEXT	CONCATENATED\n")
File2.write( "@NAME       	LENGTH\n")
File2.write( "scaffold_1	100000\n")
File2.write( "@END_TABLE\n")
File2.write( "@NAME:GENOTYPES	VERSION:0.4.1	FORMAT:TEXT	CONCATENATED	INDEXED\n")
File2.write( "@SCFNAME	POS	MN_FREQ	Sample_1	Sample_2\n")


for x in range(0, MAX):
	P=0
	while(P<MINP or P>MAXP):
		P = round(triang.rvs(0.1), 2)
	Q=1-P
	td=random.random()

	mmmm, Mmmm, MMmm, mmMm, MmMm, MMMm, mmMM, MmMM, MMMM=getMs(P, S)

	if( min([mmmm, Mmmm, MMmm, mmMm, MmMm, MMMm, mmMM, MmMM, MMMM])<-0.0001):
		skipped+=1
		continue


	Mmmm+=mmmm
	MMmm+=Mmmm

	mmMm+=MMmm
	MmMm+=mmMm
Пример #13
0
def WeightedRandom(sel, M, N, total, dist):
    if dist == "no":
        if sel == "exp":
            rand = []
            expvar = M
            ctr = 100
            final = (-float(M)) / math.log(0.05)
            while ctr < total and expvar > final:
                expvar = expvar - 500
                ctr += 100
            if expvar < final:
                expvar = final
            if total < 0:
                for i in range(0, N):
                    rand.append(random.randint(0, M - 1))
                    while rand.count(rand[i]) > 1:
                        rand[i] = random.randint(0, M - 1)
            else:
                for i in range(0, N):
                    rand.append(int(expon.rvs(scale=expvar)))
                    if rand[i] < 0:
                        rand[i] = -rand[i]
                    while rand[i] >= M or rand.count(rand[i]) > 1:
                        rand[i] = int(expon.rvs(scale=expvar))
                        if rand[i] < 0:
                            rand[i] = -rand[i]
        elif sel == "filter":
            rand = []
            epscale = M
            ctr = 100
            while ctr < total and epscale != 1000:
                epscale = epscale - 500
                ctr += 100
            if total < 0:
                for i in range(0, N):
                    rand.append(random.randint(0, M - 1))
                    while rand.count(rand[i]) > 1:
                        rand[i] = random.randint(0, M - 1)
            else:
                for i in range(0, N):
                    rand.append(int(gennorm.rvs(5, scale=epscale)))
                    if rand[i] < 0:
                        rand[i] = -rand[i]
                    while rand[i] >= M or rand.count(rand[i]) > 1:
                        rand[i] = int(gennorm.rvs(5, scale=epscale))
                        if rand[i] < 0:
                            rand[i] = -rand[i]
        elif sel == "triang":
            rand = []
            triscale = M * 2
            ctr = 100
            final = M
            while ctr < total and triscale > M:
                triscale = triscale - 1000
                ctr += 100
            if triscale <= M:
                triscale = M + int(round(M / 5))
            if total < 0:
                for i in range(0, N):
                    rand.append(random.randint(0, M - 1))
                    while rand.count(rand[i]) > 1:
                        rand[i] = random.randint(0, M - 1)
            else:
                for i in range(0, N):
                    rand.append(int(triang.rvs(0, loc=0, scale=triscale)))
                    if rand[i] < 0:
                        rand[i] = -rand[i]
                    while rand[i] >= M or rand.count(rand[i]) > 1:
                        rand[i] = int(triang.rvs(0, loc=0, scale=triscale))
                        if rand[i] < 0:
                            rand[i] = -rand[i]
    else:
        if sel == "exp":
            rand = []
            expvar = (-float(M)) / math.log(0.05)
            if total < 0:
                for i in range(0, N):
                    rand.append(random.randint(0, M - 1))
                    while rand.count(rand[i]) > 1:
                        rand[i] = random.randint(0, M - 1)
            else:
                for i in range(0, N):
                    rand.append(int(expon.rvs(scale=expvar)))
                    if rand[i] < 0:
                        rand[i] = -rand[i]
                    while rand[i] >= M or rand.count(rand[i]) > 1:
                        rand[i] = int(expon.rvs(scale=expvar))
                        if rand[i] < 0:
                            rand[i] = -rand[i]
        elif sel == "filter":
            rand = []
            epscale = M / 5
            if total < 0:
                for i in range(0, N):
                    rand.append(random.randint(0, M - 1))
                    while rand.count(rand[i]) > 1:
                        rand[i] = random.randint(0, M - 1)
            else:
                for i in range(0, N):
                    rand.append(int(gennorm.rvs(5, scale=epscale)))
                    if rand[i] < 0:
                        rand[i] = -rand[i]
                    while rand[i] >= M or rand.count(rand[i]) > 1:
                        rand[i] = int(gennorm.rvs(5, scale=epscale))
                        if rand[i] < 0:
                            rand[i] = -rand[i]
        elif sel == "triang":
            rand = []
            triscale = M + int(round(M / 10))
            if total < 0:
                for i in range(0, N):
                    rand.append(random.randint(0, M - 1))
                    while rand.count(rand[i]) > 1:
                        rand[i] = random.randint(0, M - 1)
            else:
                for i in range(0, N):
                    rand.append(int(triang.rvs(0, loc=0, scale=triscale)))
                    if rand[i] < 0:
                        rand[i] = -rand[i]
                    while rand[i] >= M or rand.count(rand[i]) > 1:
                        rand[i] = int(triang.rvs(0, loc=0, scale=triscale))
                        if rand[i] < 0:
                            rand[i] = -rand[i]

    return rand