def show_continuous():
"""Show a variety of continuous distributions"""
x = linspace(-10, 10, 201)
# Normal distribution
showDistribution(x, stats.norm, stats.norm(loc=2, scale=4), "Normal Distribution", "Z", "P(Z)", "")
# Exponential distribution
showDistribution(x, stats.expon, stats.expon(loc=-2, scale=4), "Exponential Distribution", "X", "P(X)", "")
# Students' T-distribution
# ... with 4, and with 10 degrees of freedom (DOF)
plot(x, stats.norm.pdf(x), "g")
hold(True)
showDistribution(x, stats.t(4), stats.t(10), "T-Distribution", "X", "P(X)", ["normal", "t=4", "t=10"])
# F-distribution
# ... with (3,4) and (10,15) DOF
showDistribution(x, stats.f(3, 4), stats.f(10, 15), "F-Distribution", "F", "P(F)", ["(3,4) DOF", "(10,15) DOF"])
# Weibull distribution
# ... with the shape parameter set to 1 and 2
# Don't worry that in Python it is called "weibull_min": the "weibull_max" is
# simply mirrored about the origin.
showDistribution(
arange(0, 5, 0.02),
stats.weibull_min(1),
stats.weibull_min(2),
"Weibull Distribution",
"X",
"P(X)",
["k=1", "k=2"],
xmin=0,
xmax=4,
)
# Uniform distribution
showDistribution(x, stats.uniform, "", "Uniform Distribution", "X", "P(X)", "")
# Logistic distribution
showDistribution(x, stats.norm, stats.logistic, "Logistic Distribution", "X", "P(X)", ["Normal", "Logistic"])
# Lognormal distribution
x = logspace(-9, 1, 1001) + 1e-9
showDistribution(x, stats.lognorm(2), "", "Lognormal Distribution", "X", "lognorm(X)", "", xmin=-0.1)
# The log-lin plot has to be done by hand:
plot(log(x), stats.lognorm.pdf(x, 2))
xlim(-10, 4)
title("Lognormal Distribution")
xlabel("log(X)")
ylabel("lognorm(X)")
show()
def ftest(data1, data2, alpha=0.05):
alpha1 = alpha
Sd1 = np.var(data1)
Sd2 = np.var(data2)
n1 = len(data1)
n2 = len(data2)
F = Sd1 / Sd2 #F统计量
if F > stats.f(n1 - 1, n2 - 1).ppf(1 - alpha / 2) or F < stats.f(
n1 - 1, n2 - 1).ppf(alpha / 2):
print("Reject H0 at the significance level of", alpha1, ".")
else:
print("Accept H0 at the significance level of", alpha1, ".")
def show_continuous():
"""Show a variety of continuous distributions"""
x = linspace(-10,10,201)
# Normal distribution
showDistribution(x, stats.norm, stats.norm(loc=2, scale=4),
'Normal Distribution', 'Z', 'P(Z)','')
# Exponential distribution
showDistribution(x, stats.expon, stats.expon(loc=-2, scale=4),
'Exponential Distribution', 'X', 'P(X)','')
# Students' T-distribution
# ... with 4, and with 10 degrees of freedom (DOF)
plot(x, stats.norm.pdf(x), 'g-.')
hold(True)
showDistribution(x, stats.t(4), stats.t(10),
'T-Distribution', 'X', 'P(X)',['normal', 't=4', 't=10'])
# F-distribution
# ... with (3,4) and (10,15) DOF
showDistribution(x, stats.f(3,4), stats.f(10,15),
'F-Distribution', 'F', 'P(F)',['(3,4) DOF', '(10,15) DOF'])
# Weibull distribution
# ... with the shape parameter set to 1 and 2
# Don't worry that in Python it is called "weibull_min": the "weibull_max" is
# simply mirrored about the origin.
showDistribution(arange(0,5,0.02), stats.weibull_min(1), stats.weibull_min(2),
'Weibull Distribution', 'X', 'P(X)',['k=1', 'k=2'], xmin=0, xmax=4)
# Uniform distribution
showDistribution(x, stats.uniform,'' ,
'Uniform Distribution', 'X', 'P(X)','')
# Logistic distribution
showDistribution(x, stats.norm, stats.logistic,
'Logistic Distribution', 'X', 'P(X)',['Normal', 'Logistic'])
# Lognormal distribution
x = logspace(-9,1,1001)+1e-9
showDistribution(x, stats.lognorm(2), '',
'Lognormal Distribution', 'X', 'lognorm(X)','', xmin=-0.1)
# The log-lin plot has to be done by hand:
plot(log(x), stats.lognorm.pdf(x,2))
xlim(-10, 4)
title('Lognormal Distribution')
xlabel('log(X)')
ylabel('lognorm(X)')
show()
def show_continuous():
"""Show a variety of continuous distributions"""
x = np.linspace(-10,10,201)
# Normal distribution
showDistribution(x, stats.norm, stats.norm(loc=2, scale=4),
'Normal Distribution', 'Z', 'P(Z)','')
# Exponential distribution
showDistribution(x, stats.expon, stats.expon(loc=-2, scale=4),
'Exponential Distribution', 'X', 'P(X)','')
# Students' T-distribution
# ... with 4, and with 10 degrees of freedom (DOF)
plt.plot(x, stats.norm.pdf(x), 'g-.')
plt.hold(True)
showDistribution(x, stats.t(4), stats.t(10),
'T-Distribution', 'X', 'P(X)',['normal', 't=4', 't=10'])
# F-distribution
# ... with (3,4) and (10,15) DOF
showDistribution(x, stats.f(3,4), stats.f(10,15),
'F-Distribution', 'F', 'P(F)',['(3,4) DOF', '(10,15) DOF'])
# Weibull distribution
# ... with the shape parameter set to 1 and 2
# Don't worry that in Python it is called "weibull_min": the "weibull_max" is
# simply mirrored about the origin.
showDistribution(np.arange(0,5,0.02), stats.weibull_min(1), stats.weibull_min(2),
'Weibull Distribution', 'X', 'P(X)',['k=1', 'k=2'], xmin=0, xmax=4)
# Uniform distribution
showDistribution(x, stats.uniform,'' ,
'Uniform Distribution', 'X', 'P(X)','')
# Logistic distribution
showDistribution(x, stats.norm, stats.logistic,
'Logistic Distribution', 'X', 'P(X)',['Normal', 'Logistic'])
# Lognormal distribution
x = np.logspace(-9,1,1001)+1e-9
showDistribution(x, stats.lognorm(2), '',
'Lognormal Distribution', 'X', 'lognorm(X)','', xmin=-0.1)
# The log-lin plot has to be done by hand:
plt.plot(np.log(x), stats.lognorm.pdf(x,2))
plt.xlim(-10, 4)
plt.title('Lognormal Distribution')
plt.xlabel('log(X)')
plt.ylabel('lognorm(X)')
plt.show()
def twoway_anova(data, alpha):
'''
双因素方差分析：涉及两个分类型自变量时的方差分析，这里只写一份无重复双因素的代码
Parameters
----------
data : R(m*n) 该自变量的多个水平的观测值表，标准的 m * n 二维矩阵
alpha: 执行F统计量假设检验的置信度
Returns
-------
R: 自变量与因变量之间的关系强度， R**2 = SSR + SSC / SST
'''
data = np.array(data)
k, r = np.shape(data) # k为行数，r为列数
n = k * r # 总观测值
mrs = np.mean(data, axis=1) # 每行的均值
mcs = np.mean(data, axis=0) # 每列的均值
mt = np.mean(data) # 总体均值
sst = (np.var(data) * k * r).round(4) # 总体平方和
ssr = (np.sum((mrs - mt)**2) * r).round(4) # 行间平方和
ssc = (np.sum((mcs - mt)**2) * k).round(4) # 列间平方和
sse = (sst - ssr - ssc).round(4) # 随机误差
msr = (ssr / (k - 1)).round(4)
msc = (ssc / (r - 1)).round(4)
mse = (sse / ((k - 1) * (r - 1))).round(4)
rvr = st.f(k - 1, (k - 1) * (r - 1))
fr = (msr / mse).round(4) # 检验行因素
fr_crit = rvr.ppf(1 - alpha).round(4) # 在当前置信度下的F临界值
pr = (1 - rvr.cdf(fr)).round(4) # P值
rvc = st.f(r - 1, (k - 1) * (r - 1))
fc = (msc / mse).round(4) # 检验行因素
fc_crit = rvc.ppf(1 - alpha).round(4) # 在当前置信度下的F临界值
pc = (1 - rvc.cdf(fc)).round(4) # P值
print('{0:-^97}'.format(''))
print('{0:^10}|{1:^15}|{2:^10}|{3:^15}|{4:^15}|{5:^15}|{6:^15}'.format(\
'Source', 'SS', 'df', 'MS', 'F', 'P-Value', 'F crit'))
print('{0:-^97}'.format(''))
print('{0:^10}|{1:^15}|{2:^10}|{3:^15}|{4:^15}|{5:^15}|{6:^15}'.format(\
'Rows', ssr, k - 1, msr, fr, pr, fr_crit))
print('{0:^10}|{1:^15}|{2:^10}|{3:^15}|{4:^15}|{5:^15}|{6:^15}'.format(\
'Cols', ssc, r - 1, msc, fc, pc, fc_crit))
print('{0:^10}|{1:^15}|{2:^10}|{3:^15}|'.format('Errors', sse,
(k - 1) * (r - 1), mse))
print('{0:^10}|{1:^15}|{2:^10}|'.format('Total', sst, k * r - 1))
return (ssr + ssc) / sst
def blocked_anova(file, reps):
data, _, treat_sums, block_sums, grand_total, n, n_treats, obs_per_treat = prep_data(
file, reps)
n_blocks = obs_per_treat // reps
obs_per_block = n // n_blocks
anova = {}
sources = ['treats', 'blocks', 'err', 'total']
for item in sources:
anova[item] = {}
# DF's
anova['total']['DF'] = n - 1
anova['treats']['DF'] = n_treats - 1
anova['blocks']['DF'] = n_blocks - 1
anova['err']['DF'] = anova['total']['DF'] - anova['treats']['DF'] - anova[
'blocks']['DF']
# SS's
anova['total']['SS'] = sum_xsq(data) - ((sum_x(data)**2) / n)
ssTreats = 0
for i in range(n_treats):
ssTreats += (treat_sums[i]**2) / obs_per_treat
ssTreats -= (grand_total**2) / n
anova['treats']['SS'] = ssTreats
ssBlocks = 0
for i in range(n_blocks):
ssBlocks += (block_sums[i]**2) / obs_per_block
ssBlocks -= (grand_total**2) / n
anova['blocks']['SS'] = ssBlocks
anova['err']['SS'] = anova['total']['SS'] - anova['treats']['SS'] - anova[
'blocks']['SS']
# MS's
anova['treats']['MS'] = anova['treats']['SS'] / anova['treats']['DF']
anova['blocks']['MS'] = anova['blocks']['SS'] / anova['blocks']['DF']
anova['err']['MS'] = anova['err']['SS'] / anova['err']['DF']
# F
anova['treats']['F'] = anova['treats']['MS'] / anova['err']['MS']
anova['blocks']['F'] = anova['blocks']['MS'] / anova['err']['MS']
# p
anova['treats']['p'] = stats.f(anova['treats']['DF'],
anova['err']['DF']).sf(anova['treats']['F'])
anova['blocks']['p'] = stats.f(anova['blocks']['DF'],
anova['err']['DF']).sf(anova['blocks']['F'])
pretty_anova_tbl(anova, sources)
def F_test(s1, s2, n1, n2, H0, alpha=0.05):
'''
F-Test for comparison of two variances.
H0: σ1 ≤, ≥, = σ2.
In slides 458.
REQUIRE: H0 can take three values: "equal", "less", "greater".
RETURN: Test statistics, critical value, p-value.
'''
F = s1**2 / s2**2
if H0 == "less":
c_value = stats.f(n1 - 1, n2 - 1).ppf(1 - alpha)
p_value = 1 - stats.f(n1 - 1, n2 - 1).cdf(F)
elif H0 == "greater":
c_value = stats.f(n1 - 1, n2 - 1).ppf(alpha)
p_value = stats.f(n1 - 1, n2 - 1).cdf(F)
elif H0 == "equal":
F1, F2 = F, 1 / F
c_value1, c_value2 = stats.f(n1 - 1,
n2 - 1).ppf(1 - alpha / 2), stats.f(
n2 - 1, n1 - 1).ppf(1 - alpha / 2)
F = (F1, F2)
c_value = (c_value1, c_value2)
p_value = 2 * min(1 - stats.f(n1 - 1, n2 - 1).cdf(F1),
1 - stats.f(n2 - 1, n1 - 1).cdf(F2))
return F, c_value, p_value
def FProbabilitiesLowerTail(values, dfn, dfd):
if len(values) > 0 and dfn > 0 and dfd > 0:
outputStr = ""
areas = []
for val in values:
outputStr += str(val)
rv = stats.f(dfn, dfd, loc=0, scale=1)
area = rv.cdf(val)
area = "{0:.5f}".format(area)
areas.append(area)
if len(values) > 1 and values.index(val) < len(values) - 1:
outputStr += ", "
else:
outputStr += ""
outputStr += ", serbestlik derecesi (pay): " + str(
dfn) + ", serbestlik derecesi (payda): " + str(dfd)
return outputStr, areas
elif dfn <= 0 or dfd <= 0:
return False, "Serbestlik dereceleri 0'dan kucuk olamaz."
else:
return False, "Hesaplama icin gecerli degerler girilmelidir."
def FQuantilesLowerTail(probs, dfn, dfd):
if len(probs) > 0 and dfn > 0 and dfd > 0:
outputStr = ""
yArray = []
for prob in probs:
outputStr += str(prob)
if prob > 0 and prob < 1:
rv = stats.f(dfn, dfd, loc=0, scale=1)
y = rv.ppf(prob)
y = "{0:.5f}".format(y)
yArray.append(y)
else:
yArray.append("NaN")
if len(probs) > 1 and probs.index(prob) < len(probs) - 1:
outputStr += ", "
else:
outputStr += ""
outputStr += ", serbestlik derecesi (pay): " + str(
dfn) + ", serbestlik derecesi (payda): " + str(dfd)
return outputStr, yArray
elif dfn <= 0 or dfd <= 0:
return False, "Serbestlik dereceleri 0'dan kucuk olamaz."
else:
return False, "Gecerli olasilik degeri girilmelidir."
def sediff(sv1, sv2, n1, n2, alpha, bilateral=True):
"""
Calculate the interval estimation of the difference of 2 population variance
(两个总体方差比的区间估计)
sv1**2 pv2**2
------ * -------- ~ F(n1-1, n2-1)
sv2**2 pv1**2
Parameters
----------
sv1 : sample mean, 总体1的样本标准差
sv2 : sample mean, 总体2的样本标准差
n1 : sample count, 总体1的样本容量
n2 : sample count, 总体2的样本容量
alpha: confidence level, 置信水平
bilateral: 是否是双侧检验
Returns
-------
tuple(pm1, pm2) : interval estimation of diff of population proportion,
两个总体方差比的区间估计
"""
rv = st.f(n1 - 1, n2 - 1)
f1 = rv.ppf((1 - alpha) / 2)
f2 = rv.ppf((1 + alpha) / 2)
svdiff = sv1**2 / sv2**2
# print(svsum)
return tuple([svdiff / f2, svdiff / f1])
def calc_det_thresh(fstat_vals,
det_p_val,
TB_prod,
channel_cnt,
fstat_ref_peak=None):
fstat_min = np.min(fstat_vals)
fstat_max = np.max(fstat_vals)
# compute reference threshold if not provided
if fstat_ref_peak:
fstat_peak = fstat_ref_peak
else:
def temp_fstat(f):
return -stats.f(TB_prod, TB_prod * (channel_cnt - 1)).pdf(f)
fstat_peak = minimize_scalar(temp_fstat,
bracket=(fstat_min, fstat_max)).x
# compute
kde = stats.gaussian_kde(fstat_vals)
def temp_kde(f):
return -kde.pdf(f)[0]
kde_peak = minimize_scalar(temp_kde,
bracket=(fstat_min, fstat_max),
options={
'maxiter': 250
}).x
return stats.f(TB_prod, TB_prod *
(channel_cnt - 1)).ppf(det_p_val) * (kde_peak / fstat_peak)
def plotFDistribution(FCrit, FValue, dfModel, dfError):
mu = 0
x = np.linspace(0, FValue + 2, 1001)[1:]
fig, ax = plt.subplots(figsize=(5, 3.75))
dist = stats.f(dfModel, dfError, mu)
plt.plot(x,
dist.pdf(x),
ls='-',
c='black',
label=r'$d_1=%i,\ d_2=%i$' % (dfModel, dfError))
plt.xlim(0, FValue + 2)
plt.ylim(0.0, 1.0)
plt.annotate('F Crit\n (%s)' % FCrit,
xy=(FCrit, 0),
xytext=(FCrit - 1, 0.4),
arrowprops=dict(facecolor='red', shrink=0.05))
plt.annotate('F Value\n (%s)' % FValue,
xy=(FValue, 0),
xytext=(FValue - 2, 0.2),
arrowprops=dict(facecolor='blue', shrink=0.05))
plt.xlabel('$x$')
plt.ylabel(r'$p(x|d_1, d_2)$')
plt.title("Fisher's Distribution")
plt.legend()
plt.show()
def PlotFDistributionDistributionFunction(dfn, dfd):
if dfn>0 and dfd>0:
main_frame = QtGui.QWidget()
dpi = 100
fig = Figure((5.0, 4.0), dpi=dpi)
canvas = FigureCanvas(fig)
canvas.setParent(main_frame)
axes = fig.add_subplot(111)
mpl_toolbar = NavigationToolbar(canvas, main_frame)
hbox = QtGui.QHBoxLayout()
vbox = QtGui.QVBoxLayout()
vbox.addWidget(canvas)
vbox.addWidget(mpl_toolbar)
vbox.addLayout(hbox)
main_frame.setLayout(vbox)
alpha = 0.0005
sequence = stats.f.isf(alpha, dfn, dfd)
x = np.linspace(-sequence, sequence, 1000)
rv = stats.f(dfn, dfd)
y = rv.cdf(x)
axes.plot(x,y)
canvas.draw()
return main_frame
else:
return False, "Serbestlik derecesi 0'dan kucuk olamaz."
#---/F DISTRIBUTION
def FProbabilitiesLowerTail(values, dfn, dfd):
if len(values)>0 and dfn>0 and dfd>0:
outputStr = ""
areas = []
for val in values:
outputStr += str(val)
rv = stats.f(dfn, dfd, loc = 0, scale=1)
area = rv.cdf(val)
area = "{0:.5f}".format(area)
areas.append(area)
if len(values) >1 and values.index(val) < len(values) - 1 :
outputStr += ", "
else:
outputStr += ""
outputStr += ", serbestlik derecesi (pay): " + str(dfn) + ", serbestlik derecesi (payda): " + str(dfd)
return outputStr, areas
elif dfn<=0 or dfd<=0:
return False, "Serbestlik dereceleri 0'dan kucuk olamaz."
else:
return False, "Hesaplama icin gecerli degerler girilmelidir."
def PlotFDistributionDistributionFunction(dfn, dfd):
if dfn > 0 and dfd > 0:
main_frame = QtGui.QWidget()
dpi = 100
fig = Figure((5.0, 4.0), dpi=dpi)
canvas = FigureCanvas(fig)
canvas.setParent(main_frame)
axes = fig.add_subplot(111)
mpl_toolbar = NavigationToolbar(canvas, main_frame)
hbox = QtGui.QHBoxLayout()
vbox = QtGui.QVBoxLayout()
vbox.addWidget(canvas)
vbox.addWidget(mpl_toolbar)
vbox.addLayout(hbox)
main_frame.setLayout(vbox)
alpha = 0.0005
sequence = stats.f.isf(alpha, dfn, dfd)
x = np.linspace(-sequence, sequence, 1000)
rv = stats.f(dfn, dfd)
y = rv.cdf(x)
axes.plot(x, y)
canvas.draw()
return main_frame
else:
return False, "Serbestlik derecesi 0'dan kucuk olamaz."
#---/F DISTRIBUTION
def param_table(results, title, pad_bottom=False):
"""Formatted standard parameter table"""
param_data = np.c_[results.params.values[:, None],
results.std_errors.values[:, None],
results.tstats.values[:, None],
results.pvalues.values[:, None],
results.conf_int()]
data = []
for row in param_data:
txt_row = []
for i, v in enumerate(row):
f = _str
if i == 3:
f = pval_format
txt_row.append(f(v))
data.append(txt_row)
header = [
'Parameter', 'Std. Err.', 'T-stat', 'P-value', 'Lower CI', 'Upper CI'
]
table_stubs = list(results.params.index)
if pad_bottom:
# Append blank row for spacing
data.append([''] * 6)
table_stubs += ['']
return SimpleTable(data,
stubs=table_stubs,
txt_fmt=fmt_params,
headers=header,
title=title)
def three_sampling_dis():
"""
三大抽样分布与标准正态分布
:return:
"""
nor_dis = stats.norm()
chi2_dis = stats.chi2(df=app.df1)
t_dis = stats.t(df=app.df2)
f_dis = stats.f(dfn=app.df3, dfd=app.df4)
x1 = np.linspace(nor_dis.ppf(0.001), nor_dis.ppf(0.999), 1000)
x2 = np.linspace(chi2_dis.ppf(0.001), chi2_dis.ppf(0.999), 1000)
x3 = np.linspace(t_dis.ppf(0.001), t_dis.ppf(0.999), 1000)
x4 = np.linspace(f_dis.ppf(0.001), f_dis.ppf(0.999), 1000)
fig, ax = plt.subplots(1, 1, figsize=(16, 8))
ax.plot(x1, nor_dis.pdf(x1), 'r-', lw=2, label=r'N(0, 1)')
ax.plot(x2, chi2_dis.pdf(x2), 'g-', lw=2, label=f'$\chi^2$({app.df1})')
ax.plot(x3, t_dis.pdf(x3), 'b-', lw=2, label=f't({app.df2})')
ax.plot(x4,
f_dis.pdf(x4),
'm-',
lw=2,
label=f'F({app.df3}, {app.df4 * 2})')
plt.ylabel('Probability')
plt.title(r'PDF of Three Sampling Distribution')
ax.legend(loc='best', frameon=False)
plt.show()
def calculateSampleData(self, data):
self.l_mean = data.groupby(level=0).mean().T.mean()
self.l_ss = ((self.l_mean - self.total_mean) ** 2).sum() * self.r * self.t
self.l_ms = self.l_ss / (self.s - 1)
self.l_f = self.l_ms / self.e_ms
self.l_f_distribute = f(self.s - 1, self.r * self.s * (self.t - 1))
self.l_p = self.l_f_distribute.sf(self.l_f)
def __init__(self, d1, d2):
self.d1 = d1
self.d2 = d2
# set dist before calling super's __init__
self.dist = st.f(d1, d2)
super(F, self).__init__()
def anova_byHand():
""" Calculate the ANOVA by hand. While you would normally not do that, this function shows
how the underlying values can be calculated.
"""
# Get the data
data = getData("altman_910.txt", subDir="..\Data\data_altman")
# Convert them to pandas-forman and group them by their group value
df = pd.DataFrame(data, columns=["values", "group"])
groups = df.groupby("group")
# The "total sum-square" is the squared deviation from the mean
ss_total = np.sum((df["values"] - df["values"].mean()) ** 2)
# Calculate ss_treatment and ss_error
(ss_treatments, ss_error) = (0, 0)
for val, group in groups:
ss_error += sum((group["values"] - group["values"].mean()) ** 2)
ss_treatments += len(group) * (group["values"].mean() - df["values"].mean()) ** 2
df_groups = len(groups) - 1
df_residuals = len(data) - len(groups)
F = (ss_treatments / df_groups) / (ss_error / df_residuals)
df = stats.f(df_groups, df_residuals)
p = df.sf(F)
print(("ANOVA-Results: F = {0}, and p<{1}".format(F, p)))
return (F, p)
def anova_byHand():
"""Calculate the ANOVA by hand"""
# Get the data
data = getData('altman_910.txt', subDir='..\Data\data_altman')
# Convert them to pandas-forman and group them by their group value
df = pd.DataFrame(data, columns=['values', 'group'])
groups = df.groupby('group')
# The "total sum-square" is the squared deviation from the mean
ss_total = np.sum((df['values'] - df['values'].mean())**2)
# Calculate ss_treatment and ss_error
(ss_treatments, ss_error) = (0, 0)
for val, group in groups:
ss_error += sum((group['values'] - group['values'].mean())**2)
ss_treatments += len(group) * (
group['values'].mean() - df['values'].mean())**2
df_groups = len(groups) - 1
df_residuals = len(data) - len(groups)
F = (ss_treatments / df_groups) / (ss_error / df_residuals)
df = stats.f(df_groups, df_residuals)
p = df.sf(F)
print('ANOVA-Results: F = {0}, and p<{1}'.format(F, p))
return (F, p)
def FQuantilesLowerTail(probs,dfn,dfd):
if len(probs)>0 and dfn>0 and dfd>0:
outputStr = ""
yArray = []
for prob in probs:
outputStr += str(prob)
if prob> 0 and prob<1:
rv = stats.f(dfn,dfd, loc = 0, scale = 1)
y = rv.ppf(prob)
y = "{0:.5f}".format(y)
yArray.append(y)
else:
yArray.append("NaN")
if len(probs) >1 and probs.index(prob) < len(probs) - 1 :
outputStr += ", "
else:
outputStr += ""
outputStr += ", serbestlik derecesi (pay): " + str(dfn) + ", serbestlik derecesi (payda): " + str(dfd)
return outputStr, yArray
elif dfn<=0 or dfd <=0:
return False, "Serbestlik dereceleri 0'dan kucuk olamaz."
else:
return False, "Gecerli olasilik degeri girilmelidir."
def tt(A, B):
f_p = f(A, B).pvalue
if f_p <= 0.05:
t_p = ttest(A, B, equal_var=False).pvalue
elif f_p > 0.05:
t_p = ttest(A, B, equal_var=True).pvalue
return t_p
def __init__(self, groups):
k = groups.num_groups()
n = groups.n()
dist = stats.f(k - 1, n - k)
super(LinearContrastHyp, self).__init__(dist=dist,
kind=AltHypKind.TWO_SIDED)
self._groups = groups
def statistic(self, alpha=0.05):
x = self.train_x[:, 1]
y = self.train_y
y_pred = self.predict(self.train_x, add_const=False)
k = self.num_features
n = self.num_samples
SSE = np.sum((y - y_pred)**2)
SST = np.sum((y - y.mean()) * y)
SSR = np.sum((y_pred - y_pred.mean())**2)
sigma_e = SSE / (n - k - 1)
F_test = SSR * (n - k - 1) / SSE / k
F_q = stats.f(k, n - k - 1).ppf(1 - alpha)
test_result = 'NO SIGNIFICANT LINEAR DEPENDENCE!' if F_test < F_q else 'SIGNIFICANT LINEAR DEPENDENCE!'
print_list = [('k', k), ('n', n), ('SSE', SSE), ('SSR', SSR),
('SST', SST), ('sigma_e', sigma_e)]
if k == 1:
Lxx = np.sum((x - x.mean()) * x)
Lyy = SST
Lxy = np.sum((y - y.mean()) * x)
print_list.extend([('Lxx', Lxx), ('Lxy', Lxy), ('Lyy', Lyy)])
print_list.extend([('F_test', F_test), ('F_q', F_q),
('test_result', test_result)])
print('=' * 30, 'statistics', '=' * 30)
utils.pair_print(print_list)
print('=' * (len('statistics') + 62), end='\n\n')
def test_Normal_to_F(self):
A, B, C, V, W, X, Y, Z = RV(Normal(mean=0, var=1)**8)
sims = ((((A**2) + (B**2) + (C**2)) / 3) /
(((V**2) + (W**2) + (X**2) + (Y**2) + (Z**2)) / 5)).sim(Nsim)
cdf = stats.f(dfn=3, dfd=5).cdf
pval = stats.kstest(sims, cdf).pvalue
self.assertTrue(pval > .01)
def fix_alpha(alpha, Sigma, Sigma_star):
p = Sigma.shape[0]
Sigma_12 = fractional_matrix_power(Sigma, 0.5)
matrix = Sigma_12.T @ np.linalg.inv(Sigma_star) @ Sigma_12
lambdas = np.real(np.linalg.eigvals(matrix))
factorials = [1, 1, 2, 8]
k = np.asarray([factorials[r] * np.sum(lambdas**r) for r in [1,1,2,3]])
t1 = 4*k[1]*k[2]**2 + k[3]*(k[2]-k[1]**2)
t2 = k[3]*k[1] - 2*k[2]**2
chi_quantile = sps.chi2(p).ppf(1-alpha)
if t1 < 10**(-5):
a_new = 2 + (k[1]**2)/(k[2]**2)
b_new = (k[1]**3)/k[2] + k[1]
s1 = 2*k[1]*(k[3]*k[1] + k[2]*k[1]**2 - k[2]**2)
s2 = 3*t2 + 2*k[2]*(k[2] + k[1]**2)
alpha_star = 1 - sps.invgamma(a_new, scale = b_new).cdf(chi_quantile)
elif t2 < 10**(-5):
a_new = (k[1]**2)/k[2]
b_new = k[2]/k[1]
alpha_star = 1 - sps.gamma(a_new, scale = b_new).cdf(chi_quantile)
else:
a1 = 2*k[1]*(k[3]*k[1] + k[2]*k[1]**2 - k[2]**2)/t1
a2 = 3 + 2*k[2]*(k[2] + k[1]**2)/t2
alpha_star = 1 - sps.f(2*a1, 2*a2).cdf(a2*t2*chi_quantile/(a1*t1))
return alpha_star
def anova_byHand():
""" Calculate the ANOVA by hand. While you would normally not do that, this function shows
how the underlying values can be calculated.
"""
# Get the data
inFile = 'altman_910.txt'
data = np.genfromtxt(inFile, delimiter=',')
# Convert them to pandas-forman and group them by their group value
df = pd.DataFrame(data, columns=['values', 'group'])
groups = df.groupby('group')
# The "total sum-square" is the squared deviation from the mean
ss_total = np.sum((df['values']-df['values'].mean())**2)
# Calculate ss_treatment and ss_error
(ss_treatments, ss_error) = (0, 0)
for val, group in groups:
ss_error += sum((group['values'] - group['values'].mean())**2)
ss_treatments += len(group) * (group['values'].mean() - df['values'].mean())**2
df_groups = len(groups)-1
df_residuals = len(data)-len(groups)
F = (ss_treatments/df_groups) / (ss_error/df_residuals)
df = stats.f(df_groups,df_residuals)
p = df.sf(F)
print(('ANOVA-Results: F = {0}, and p<{1}'.format(F, p)))
return (F, p)
def LoF_test(N, X, Y, alpha=0.05):
'''
Test for Lack of Fit.
H0: the linear regression model is appropriate.
In slides 608.
REQUIRE: multiple sampling for single x. N, X are 1-D lists. Y is a 2-D list.
RETURN: (SSE, SSE_pe, SSE_if), (Test statistics and critical value).
'''
k = len(N)
n = sum(N)
print(n, k)
mean_Y = [sum(Y[i]) / N[i] for i in range(k)]
SSE_pe = sum(
sum([(Y[i][j] - mean_Y[i])**2 for j in range(N[i])]) for i in range(k))
x = []
for i in range(k):
x.extend([X[i]] * N[i])
y = []
for i in range(k):
y.extend(Y[i])
model = SLR(n, x, y)
SSE = model.SSE
SSE_if = SSE - SSE_pe
F = (SSE_if / (k - 2)) / (SSE_pe / (n - k))
f = stats.f(k - 2, n - k).ppf(1 - alpha)
return (SSE, SSE_pe, SSE_if), (F, f)
def fun7():
print("open三大抽样分布")
#绘制 正态分布 卡方分布 t分布 F分布
nor_dis = stats.norm()
chi2_dis = stats.chi2(df=eval(k_1.get()))
t_dis = stats.t(df=eval(t_1.get()))
f_dis = stats.f(dfn=eval(f_1.get()), dfd=eval(f_2.get()))
x1 = np.linspace(nor_dis.ppf(0.001), nor_dis.ppf(0.999), 1000)
x2 = np.linspace(chi2_dis.ppf(0.001), chi2_dis.ppf(0.999), 1000)
x3 = np.linspace(t_dis.ppf(0.001), t_dis.ppf(0.999), 1000)
x4 = np.linspace(f_dis.ppf(0.001), f_dis.ppf(0.999), 1000)
fig, ax = plt.subplots(1, 1, figsize=(16, 8))
ax.plot(x1, nor_dis.pdf(x1), 'r-', lw=2, label=r'N(0, 1)')
ax.plot(x2,
chi2_dis.pdf(x2),
'g-',
lw=2,
label=r'$\chi^2$(%d)' % eval(k_1.get()))
ax.plot(x3, t_dis.pdf(x3), 'b-', lw=2, label='t(%d)' % eval(t_1.get()))
ax.plot(x4,
f_dis.pdf(x4),
'm-',
lw=2,
label='F(%d, %d)' % (eval(f_1.get()), eval(f_2.get())))
plt.xlabel("x")
plt.ylabel('Probability')
plt.title(r'PDF of Three Sampling Distribution')
ax.legend(loc='best', frameon=False)
plt.grid()
plt.show()
def f_threshold_twoway_rm(n_subjects, factor_levels, effects='A*B',
pvalue=0.05):
""" Compute f-value thesholds for a two-way ANOVA
Parameters
----------
n_subjects : int
The number of subjects to be analyzed.
factor_levels : list-like
The number of levels per factor.
effects : str
A string denoting the effect to be returned. The following
mapping is currently supported:
'A': main effect of A
'B': main effect of B
'A:B': interaction effect
'A+B': both main effects
'A*B': all three effects
pvalue : float
The p-value to be thresholded.
Returns
-------
f_threshold : list | float
list of f-values for each effect if the number of effects
requested > 2, else float.
"""
effect_picks = _check_effects(effects)
f_threshold = []
for _, df1, df2 in _iter_contrasts(n_subjects, factor_levels,
effect_picks):
f_threshold.append(stats.f(df1, df2).isf(pvalue))
return f_threshold if len(f_threshold) > 1 else f_threshold[0]
def anova_byHand():
""" Calculate the ANOVA by hand. While you would normally not do that, this function shows
how the underlying values can be calculated.
"""
# Get the data
data = getData('altman_910.txt', subDir='.')
# Convert them to pandas-forman and group them by their group value
df = pd.DataFrame(data, columns=['values', 'group'])
groups = df.groupby('group')
# The "total sum-square" is the squared deviation from the mean
ss_total = np.sum((df['values'] - df['values'].mean())**2)
# Calculate ss_treatment and ss_error
(ss_treatments, ss_error) = (0, 0)
for val, group in groups:
ss_error += sum((group['values'] - group['values'].mean())**2)
ss_treatments += len(group) * (group['values'].mean() -
df['values'].mean())**2
df_groups = len(groups) - 1
df_residuals = len(data) - len(groups)
F = (ss_treatments / df_groups) / (ss_error / df_residuals)
df = stats.f(df_groups, df_residuals)
p = df.sf(F)
print(('ANOVA-Results: F = {0}, and p<{1}'.format(F, p)))
return (F, p)
def calculateColumnData(self, data):
self.c_mean = data.mean()
self.c_ss = ((self.c_mean - self.total_mean) ** 2).sum() * self.s * self.t
self.c_ms = self.c_ss / (self.r - 1)
self.c_f = self.c_ms / self.e_ms
self.c_f_distribute = f(self.r - 1, self.r * self.s * (self.t - 1))
self.c_p = self.c_f_distribute.sf(self.c_f)
def p_value(t2):
'''
Calculate the p-value of the F distribution at t2
'''
T2 = (sample_size-dimension)/(dimension*(sample_size-1)) * t2
f = stats.f( dimension, sample_size-dimension)
return f.cdf(T2)
def generate_matrix():
def f(X1, X2, X3):
from random import randrange
y = 8.4+8.5*x1+5.7*x2+9.7*x3+8.9*x1*x1+0.2*x2*x2+0.5*x3*x3+2.0*x1*x2+0.7*x1*x3+4.3*x2*x3+9.7*x1*x2*x3 + randrange(0, 10) - 5
return y
matrix_with_y = [[f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for i in range(m)] for j in range(N)]
return matrix_with_y
def calculateCorrData(self, data):
l_mean = pd.concat([self.l_mean] * self.r, axis=1, keys=self.corr_mean.columns)
c_mean = pd.concat([self.c_mean] * self.s, axis=1, keys=self.corr_mean.index).T
self.corr_ss = ((self.corr_mean - l_mean - c_mean + self.total_mean) ** 2).sum().sum() * self.t
self.corr_ms = self.corr_ss / ((self.s - 1) * (self.r - 1))
self.corr_f = self.corr_ms / self.e_ms
self.corr_f_distribute = f((self.s - 1) * (self.r - 1), self.r * self.s * (self.t - 1))
self.corr_p = self.corr_f_distribute.sf(self.corr_f)
def Chow_Dickey(pd_series,
split,
reg_type='c',
auto_lag='AIC',
max_lag=4,
verbose=False):
if isinstance(pd_series, pd.DataFrame):
temp_index = pd_series.index
pd_series = pd.Series(pd_series, index=temp_index)
if isinstance(split, pd._libs.tslib.Timestamp) | isinstance(split, str):
mask = pd_series.index <= pd.to_datetime(split)
split1 = pd_series[mask]
split2 = pd_series[~mask]
else:
mask = pd_series.index.year <= split
split1 = pd_series[mask]
split2 = pd_series[~mask]
nr_adf = adfuller(pd_series,
regression=reg_type,
autolag=auto_lag,
maxlag=max_lag,
regresults=True)[3]
nr_lag = nr_adf.usedlag
nr_model = nr_adf.resols
nr_ssr = nr_model.ssr * nr_model.nobs
param_length = nr_model.df_model + 1
adf1 = adfuller(split1,
regression=reg_type,
autolag=None,
maxlag=max_lag,
regresults=True)[3]
adf1_model = adf1.resols
N1 = adf1_model.nobs
adf1_ssr = adf1_model.ssr * N1
adf2 = adfuller(split2,
regression=reg_type,
autolag=None,
maxlag=max_lag,
regresults=True)[3]
adf2_model = adf2.resols
N2 = adf2_model.nobs
adf2_ssr = adf2_model.ssr * N2
numerator = (nr_ssr - (adf1_ssr + adf2_ssr)) / param_length
denominator = (adf1_ssr + adf2_ssr) / (N1 + N2 - 2 * param_length)
F_stat = numerator / denominator
f_dist = stat.f(param_length, N1 + N2 - 2 * param_length)
p_val = 1 - f_dist.cdf(F_stat)
return F_stat, p_val, nr_lag
def show_continuous():
"""Show a variety of continuous distributions"""
x = linspace(-10,10,201)
# Normal distribution
showDistribution(x, stats.norm, stats.norm(loc=2, scale=4),
'Normal Distribution', 'Z', 'P(Z)','')
# Exponential distribution
showDistribution(x, stats.expon, stats.expon(loc=-2, scale=4),
'Exponential Distribution', 'X', 'P(X)','')
# Students' T-distribution
# ... with 4, and with 10 degrees of freedom (DOF)
plot(x, stats.norm.pdf(x), 'g')
hold(True)
showDistribution(x, stats.t(4), stats.t(10),
'T-Distribution', 'X', 'P(X)',['normal', 't=4', 't=10'])
# F-distribution
# ... with (3,4) and (10,15) DOF
showDistribution(x, stats.f(3,4), stats.f(10,15),
'F-Distribution', 'F', 'P(F)',['(3,4) DOF', '(10,15) DOF'])
# Uniform distribution
showDistribution(x, stats.uniform,'' ,
'Uniform Distribution', 'X', 'P(X)','')
# Logistic distribution
showDistribution(x, stats.norm, stats.logistic,
'Logistic Distribution', 'X', 'P(X)',['Normal', 'Logistic'])
# Lognormal distribution
x = logspace(-9,1,1001)+1e-9
showDistribution(x, stats.lognorm(2), '',
'Lognormal Distribution', 'X', 'lognorm(X)','', xmin=-0.1)
# The log-lin plot has to be done by hand:
plot(log(x), stats.lognorm.pdf(x,2))
xlim(-10, 4)
title('Lognormal Distribution')
xlabel('log(X)')
ylabel('lognorm(X)')
show()
def generate_matrix():
def f(X1, X2, X3):
from random import randrange
y = 7.7 + 2.8 * X1 + 0.5 * X2 + 2.6 * X3 + 1.4 * X1 * X1 + 0.3 * X2 * X2 + 7.1 * X3 * X3 + 5.0 * X1 * X2 + \
0.3 * X1 * X3 + 9.3 * X2 * X3 + 4.1 * X1 * X2 * X3 + randrange(0, 10) - 5
return y
matrix_with_y = [[f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for i in range(m)] for j in range(N)]
return matrix_with_y
def generate_matrix():
def f(X1, X2, X3):
from random import randrange
y = 6.7 + 9.1 * X1 + 1.6 * X2 + 9.1 * X3 + 3.3 * X1 * X1 + 0.2 * X2 * X2 + 6.1 * X3 * X3 + 8.5 * X1 * X2 + \
0.7 * X1 * X3 + 6.6 * X2 * X3 + 8.1 * X1 * X2 * X3 + randrange(0, 10) - 5
return y
matrix_with_y = [[f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for i in range(m)] for j in range(N)]
return matrix_with_y
def generate_matrix():
def f(X1, X2, X3):
"""Генерація функції по варіанту"""
y = (5.6 + 8.0 * X1 + 4.8 * X2 + 6.2 * X3 + 5.9 * X1 * X1 + 1.0 * X2 * X2 + 8.7 * X3 * X3 + 2.0 * X1 * X2 + \
0.8 * X1 * X3 + 1.0 * X2 * X3 + 3.0 * X1 * X2 * X3 + randrange(0, 10) - 5)
return y
matrix_with_y = [[f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for i in range(m)] for j in range(N)]
return matrix_with_y
def generate_matrix():
def f(X1, X2, X3):
from random import randrange
y = 3.5 + 6.6 * X1 + 5.3 * X2 + 5.0 * X3 + 5.1 * X1 * X1 + 0.1 * X2 * X2 + 7.2 * X3 * X3 + 1.4 * X1 * X2 \
+ 0.7 * X1 * X3 + 4.2 * X2 * X3 + 7.7 * X1 * X2 * X3 + randrange(0, 10) - 5
return y
matrix_with_y = [[f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for _ in range(m)] for j in range(N)]
return matrix_with_y
def anova(arr):
a = seasonal_matrix(arr)
tau = a.shape[0]
zbar = a.mean(0)
v_zbar = zbar.var()
v = a.ravel().var()
stat = m * (tau - 1) / (m - 1) * v_zbar / (v - v_zbar)
i_a = stat > stats.f(m - 1, m * (tau - 1)).ppf(.9)
return i_a
def generate_matrix():
def f(X1, X2, X3):
# my function
y = 5.4 + 3.6 * X1 + 6.6 * X2 + 7.7 * X3 + 8.0 * X1 * X1 + 0.3 * X2 * X2 + 2.5 * X3 * X3 + 5.9 * X1 * X2 + \
0.3 * X1 * X3 + 7.2 * X2 * X3 + 5.3 * X1 * X2 * X3 + randrange(0, 10) - 5
return y
matrix_with_y = [[f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for i in range(m)] for j in range(N)]
return matrix_with_y
def __init__(self, data):
self.r = data.shape[1]
self.k = data.shape[0]
self.calculate_error_value(data)
columnAnalysis = SingleAnalysisVariance(data)
self.c_ss = columnAnalysis.between_group_ss
self.c_ms = columnAnalysis.between_group_ss / (self.r - 1)
self.c_f = self.c_ms / self.e_ms
self.c_statistics_info = columnAnalysis.statistics_info
self.c_f_distribute = f(self.r - 1, (self.r - 1) * (self.k - 1))
self.c_p_value = self.c_f_distribute.sf(self.c_f)
lineAnalysis = SingleAnalysisVariance(data.T)
self.l_ss = lineAnalysis.between_group_ss
self.l_ms = lineAnalysis.between_group_ss / (self.k - 1)
self.l_f = self.l_ms / self.e_ms
self.l_statistics_info = lineAnalysis.statistics_info
self.l_f_distribute = f(self.k - 1, (self.r - 1) * (self.k - 1))
self.l_p_value = self.l_f_distribute.sf(self.l_f)
def generate_matrix():
def f(X1, X2, X3):
y = 0.3 + 4.1 * X1 + 2.8 * X2 + 7.8 * X3 + 1.4 * X1 * X1 + 0.2 * X2 * X2 + 2.4 * X3 * X3 + 9.7 * X1 * X2 + \
0.6 * X1 * X3 + 4.4 * X2 * X3 + 3.4 * X1 * X2 * X3 + randrange(0, 10) - 5
return y
matrix_y = [[
f(matrix_x[j][0], matrix_x[j][1], matrix_x[j][2]) for i in range(m)
] for j in range(N)]
return matrix_y
def F(d1, d2, tag=None):
"""
An F (fisher) random variate
Parameters
----------
d1 : int
Numerator degrees of freedom
d2 : int
Denominator degrees of freedom
"""
assert isinstance(d1, int) and d1>1, 'd1 must be an int greater than 1'
assert isinstance(d2, int) and d2>1, 'd2 must be an int greater than 1'
return uv(rv=ss.f(d1, d2), tag=tag)
def Fisher(d1, d2, tag=None):
"""
An F (fisher) random variate
Parameters
----------
d1 : int
Numerator degrees of freedom
d2 : int
Denominator degrees of freedom
"""
assert int(d1)==d1 and d1>=1, 'Fisher (F) "d1" must be an integer greater than 0'
assert int(d2)==d2 and d2>=1, 'Fisher (F) "d2" must be an integer greater than 0'
return uv(ss.f(d1, d2), tag=tag)
def __init__(self):
self.dist_equivalents = [
#transf, stats.lognorm(1))
(lognormalg, stats.lognorm(1)),
#transf2
(squarenormalg, stats.chi2(1)),
(absnormalg, stats.halfnorm),
(absnormalg, stats.foldnorm(1e-5)), #try frozen
#(negsquarenormalg, 1-stats.chi2), # won't work as distribution
(squaretg(10), stats.f(1, 10))] #try both frozen
l,s = 0.0, 1.0
self.ppfq = [0.1,0.5,0.9]
self.xx = [0.95,1.0,1.1]
self.nxx = [-0.95,-1.0,-1.1]
def f_threshold_mway_rm(n_subjects, factor_levels, effects='A*B',
pvalue=0.05):
"""Compute F-value thresholds for a two-way ANOVA.
Parameters
----------
n_subjects : int
The number of subjects to be analyzed.
factor_levels : list-like
The number of levels per factor.
effects : str
A string denoting the effect to be returned. The following
mapping is currently supported:
* ``'A'``: main effect of A
* ``'B'``: main effect of B
* ``'A:B'``: interaction effect
* ``'A+B'``: both main effects
* ``'A*B'``: all three effects
pvalue : float
The p-value to be thresholded.
Returns
-------
F_threshold : list | float
list of F-values for each effect if the number of effects
requested > 2, else float.
See Also
--------
f_oneway
f_mway_rm
Notes
-----
.. versionadded:: 0.10
"""
from scipy.stats import f
effect_picks, _ = _map_effects(len(factor_levels), effects)
F_threshold = []
for _, df1, df2 in _iter_contrasts(n_subjects, factor_levels,
effect_picks):
F_threshold.append(f(df1, df2).isf(pvalue))
return F_threshold if len(F_threshold) > 1 else F_threshold[0]
def setup_class(cls):
cls.dist_equivalents = [
#transf, stats.lognorm(1))
#The below fails on the SPARC box with scipy 10.1
#(lognormalg, stats.lognorm(1)),
#transf2
(squarenormalg, stats.chi2(1)),
(absnormalg, stats.halfnorm),
(absnormalg, stats.foldnorm(1e-5)), #try frozen
#(negsquarenormalg, 1-stats.chi2), # won't work as distribution
(squaretg(10), stats.f(1, 10))
] #try both frozen
l,s = 0.0, 1.0
cls.ppfq = [0.1,0.5,0.9]
cls.xx = [0.95,1.0,1.1]
cls.nxx = [-0.95,-1.0,-1.1]
def f_oneway(self, *args):
if args[0]==None:
return [None,None]
result=[]
n=len(args)*len(args[0])
m=len(args)
fS=m-1
fe=n-m
SA=self.getSA(*args)
Se=self.getSe(*args)
VA=SA/fS
Ve=Se/fe
FA=VA/Ve
F=f(fS,fe)
p=F.sf(FA)
result.append(float('%.6f'%FA))
result.append(float('%.6f'%p))
return [float('%.6f'%FA),float('%.6f'%p)]
def __init__(self, data):
"""
:param data: the data to analysis, it'a a DataFrame
"""
self.n = data.notnull().sum().sum()
self.k = data.shape[1]
self.statistics_info = self._create_statistics_info(data)
self.total_mean = self.statistics_info["sum"].sum() / self.statistics_info["count"].sum()
self.between_group_ss = (
self.statistics_info["count"] * (self.statistics_info["mean"] - self.total_mean) ** 2
).sum()
self.ms_between_group = self.between_group_ss / (self.k - 1)
self.inside_group_ss = self.statistics_info["sumdiff"].sum()
self.ms_inside_group = self.inside_group_ss / (self.n - self.k)
self.f = self.ms_between_group / self.ms_inside_group
self.f_distribute = f(self.k - 1, self.n - self.k)
self.p_value = self.f_distribute.sf(self.f)
self.t_distribute = t(self.n - self.k)
def understand_f_fitting(sigma2):
"""
Test function: Understanding the F scaled fitting procedure.
"""
import matplotlib.pyplot as plt
prms = st.f.fit(sigma2, f0=19)#, floc=0)
print prms
dfn = prms[0]
dfd = prms[1]
scale_ = prms[3]
loc_ = prms[2]
x = np.linspace(st.f.ppf(0.01, dfn, dfd, scale=scale_, loc=loc_),
st.f.ppf(0.99, dfn, dfd, scale=scale_, loc=loc_), 100)
rv = st.f(dfn, dfd, scale=scale_)#, loc=loc_)
plt.plot(x, rv.pdf(x), color='#ee9041', lw=2)
h = plt.hist(sigma2, normed=True, color='#459db9')
def f_mway_rm(data, factor_levels, effects='all',
correction=False, return_pvals=True):
"""Compute M-way repeated measures ANOVA for fully balanced designs.
Parameters
----------
data : ndarray
3D array where the first two dimensions are compliant
with a subjects X conditions scheme where the first
factor repeats slowest::
A1B1 A1B2 A2B1 A2B2
subject 1 1.34 2.53 0.97 1.74
subject ... .... .... .... ....
subject k 2.45 7.90 3.09 4.76
The last dimensions is thought to carry the observations
for mass univariate analysis.
factor_levels : list-like
The number of levels per factor.
effects : str | list
A string denoting the effect to be returned. The following
mapping is currently supported (example with 2 factors):
* ``'A'``: main effect of A
* ``'B'``: main effect of B
* ``'A:B'``: interaction effect
* ``'A+B'``: both main effects
* ``'A*B'``: all three effects
* ``'all'``: all effects (equals 'A*B' in a 2 way design)
If list, effect names are used: ``['A', 'B', 'A:B']``.
correction : bool
The correction method to be employed if one factor has more than two
levels. If True, sphericity correction using the Greenhouse-Geisser
method will be applied.
return_pvals : bool
If True, return p-values corresponding to F-values.
Returns
-------
F_vals : ndarray
An array of F-statistics with length corresponding to the number
of effects estimated. The shape depends on the number of effects
estimated.
p_vals : ndarray
If not requested via return_pvals, defaults to an empty array.
See Also
--------
f_oneway
f_threshold_mway_rm
Notes
-----
.. versionadded:: 0.10
"""
from scipy.stats import f
if data.ndim == 2: # general purpose support, e.g. behavioural data
data = data[:, :, np.newaxis]
elif data.ndim > 3: # let's allow for some magic here.
data = data.reshape(
data.shape[0], data.shape[1], np.prod(data.shape[2:]))
effect_picks, _ = _map_effects(len(factor_levels), effects)
n_obs = data.shape[2]
n_replications = data.shape[0]
# put last axis in front to 'iterate' over mass univariate instances.
data = np.rollaxis(data, 2)
fvalues, pvalues = [], []
for c_, df1, df2 in _iter_contrasts(n_replications, factor_levels,
effect_picks):
y = np.dot(data, c_)
b = np.mean(y, axis=1)[:, np.newaxis, :]
ss = np.sum(np.sum(y * b, axis=2), axis=1)
mse = (np.sum(np.sum(y * y, axis=2), axis=1) - ss) / (df2 / df1)
fvals = ss / mse
fvalues.append(fvals)
if correction:
# sample covariances, leave off "/ (y.shape[1] - 1)" norm because
# it falls out.
v = np.array([np.dot(y_.T, y_) for y_ in y])
v = (np.array([np.trace(vv) for vv in v]) ** 2 /
(df1 * np.sum(np.sum(v * v, axis=2), axis=1)))
eps = v
df1, df2 = np.zeros(n_obs) + df1, np.zeros(n_obs) + df2
if correction:
# numerical imprecision can cause eps=0.99999999999999989
# even with a single category, so never let our degrees of
# freedom drop below 1.
df1, df2 = [np.maximum(d[None, :] * eps, 1.) for d in (df1, df2)]
if return_pvals:
pvals = f(df1, df2).sf(fvals)
else:
pvals = np.empty(0)
pvalues.append(pvals)
# handle single effect returns
return [np.squeeze(np.asarray(vv)) for vv in (fvalues, pvalues)]
def FandPV(df1, df2, fval):
rv = _ss.f(df1, df2)
return 1 - rv.cdf(fval)
def f_twoway_rm(data, factor_levels, effects='A*B', alpha=0.05,
correction=False, return_pvals=True):
""" 2 way repeated measures ANOVA for fully balanced designs
data : ndarray
3D array where the first two dimensions are compliant
with a subjects X conditions scheme:
first factor repeats slowest:
A1B1 A1B2 A2B1 B2B2
subject 1 1.34 2.53 0.97 1.74
subject ... .... .... .... ....
subject k 2.45 7.90 3.09 4.76
The last dimensions is thought to carry the observations
for mass univariate analysis.
factor_levels : list-like
The number of levels per factor.
effects : str
A string denoting the effect to be returned. The following
mapping is currently supported:
'A': main effect of A
'B': main effect of B
'A:B': interaction effect
'A+B': both main effects
'A*B': all three effects
alpha : float
The significance threshold.
correction : bool
The correction method to be employed if one factor has more than two
levels. If True, sphericity correction using the Greenhouse-Geisser
method will be applied.
return_pvals : bool
If True, return p values corresponding to f values.
Returns
-------
f_vals : ndarray
An array of f values with length corresponding to the number
of effects estimated. The shape depends on the number of effects
estimated.
p_vals : ndarray
If not requested via return_pvals, defaults to an empty array.
"""
if data.ndim == 2: # general purpose support, e.g. behavioural data
data = data[:, :, np.newaxis]
elif data.ndim > 3: # let's allow for some magic here.
data = data.reshape(data.shape[0], data.shape[1],
np.prod(data.shape[2:]))
effect_picks = _check_effects(effects)
n_obs = data.shape[2]
n_replications = data.shape[0]
# pute last axis in fornt to 'iterate' over mass univariate instances.
data = np.rollaxis(data, 2)
fvalues, pvalues = [], []
for c_, df1, df2 in _iter_contrasts(n_replications, factor_levels,
effect_picks):
y = np.dot(data, c_)
b = np.mean(y, axis=1)[:, np.newaxis, :]
ss = np.sum(np.sum(y * b, axis=2), axis=1)
mse = (np.sum(np.sum(y * y, axis=2), axis=1) - ss) / (df2 / df1)
fvals = ss / mse
fvalues.append(fvals)
if correction:
# sample covariances, leave off "/ (y.shape[1] - 1)" norm because
# it falls out. the below line is faster than the equivalent:
# v = np.array([np.dot(y_.T, y_) for y_ in y])
v = np.array(map(np.dot, y.swapaxes(2, 1), y))
v = (np.array(map(np.trace, v)) ** 2 /
(df1 * np.sum(np.sum(v * v, axis=2), axis=1)))
eps = v
df1, df2 = np.zeros(n_obs) + df1, np.zeros(n_obs) + df2
if correction:
df1, df2 = [d[None, :] * eps for d in df1, df2]
if return_pvals:
pvals = stats.f(df1, df2).sf(fvals)
else:
pvals = np.empty(0)
pvalues.append(pvals)
# handle single effect returns
return [np.squeeze(np.asarray(v)) for v in fvalues, pvalues]
plt.figure(1)
plt.plot(support[ix], rv.pdf(support[ix]), label='Actual')
plt.plot(support[ix], dens_normal.pdf()[ix], label='Scott')
plt.plot(support[ix], dens_cvls.pdf()[ix], label='CV_LS')
plt.plot(support[ix], dens_cvml.pdf()[ix], label='CV_ML')
plt.title("Nonparametric Estimation of the Density of Beta Distributed " \
"Random Variable")
plt.legend(('Actual', 'Scott', 'CV_LS', 'CV_ML'))
# f distribution
df = 100
dn = 100
nobs = 250
support = np.random.f(dn, df, size=nobs)
rv = stats.f(df, dn)
ix = np.argsort(support)
dens_normal = KDEMultivariate(data=[support], var_type='c', bw='normal_reference')
dens_cvls = KDEMultivariate(data=[support], var_type='c', bw='cv_ls')
dens_cvml = KDEMultivariate(data=[support], var_type='c', bw='cv_ml')
plt.figure(2)
plt.plot(support[ix], rv.pdf(support[ix]), label='Actual')
plt.plot(support[ix], dens_normal.pdf()[ix], label='Scott')
plt.plot(support[ix], dens_cvls.pdf()[ix], label='CV_LS')
plt.plot(support[ix], dens_cvml.pdf()[ix], label='CV_ML')
plt.title("Nonparametric Estimation of the Density of f Distributed " \
"Random Variable")
plt.legend(('Actual', 'Scott', 'CV_LS', 'CV_ML'))
def test_causality(self, equation, variables, kind='f', signif=0.05,
verbose=True):
"""Compute test statistic for null hypothesis of Granger-noncausality,
general function to test joint Granger-causality of multiple variables
Parameters
----------
equation : string or int
Equation to test for causality
variables : sequence (of strings or ints)
List, tuple, etc. of variables to test for Granger-causality
kind : {'f', 'wald'}
Perform F-test or Wald (chi-sq) test
signif : float, default 5%
Significance level for computing critical values for test,
defaulting to standard 0.95 level
Notes
-----
Null hypothesis is that there is no Granger-causality for the indicated
variables. The degrees of freedom in the F-test are based on the
number of variables in the VAR system, that is, degrees of freedom
are equal to the number of equations in the VAR times degree of freedom
of a single equation.
Returns
-------
results : dict
"""
if isinstance(variables, (basestring, int, np.integer)):
variables = [variables]
k, p = self.neqs, self.k_ar
# number of restrictions
N = len(variables) * self.k_ar
# Make restriction matrix
C = np.zeros((N, k ** 2 * p + k), dtype=float)
eq_index = self.get_eq_index(equation)
vinds = mat([self.get_eq_index(v) for v in variables])
# remember, vec is column order!
offsets = np.concatenate([k + k ** 2 * j + k * vinds + eq_index
for j in range(p)])
C[np.arange(N), offsets] = 1
# Lutkepohl 3.6.5
Cb = np.dot(C, vec(self.params.T))
middle = L.inv(chain_dot(C, self.cov_params, C.T))
# wald statistic
lam_wald = statistic = chain_dot(Cb, middle, Cb)
if kind.lower() == 'wald':
df = N
dist = stats.chi2(df)
elif kind.lower() == 'f':
statistic = lam_wald / N
df = (N, k * self.df_resid)
dist = stats.f(*df)
else:
raise Exception('kind %s not recognized' % kind)
pvalue = dist.sf(statistic)
crit_value = dist.ppf(1 - signif)
conclusion = 'fail to reject' if statistic < crit_value else 'reject'
results = {
'statistic' : statistic,
'crit_value' : crit_value,
'pvalue' : pvalue,
'df' : df,
'conclusion' : conclusion,
'signif' : signif
}
if verbose:
summ = output.causality_summary(results, variables, equation, kind)
print summ
return results
'Normal Distribution', 'Z', 'P(Z)','')
# Exponential distribution
showDistribution(stats.expon, stats.expon(loc=-2, scale=4),
'Exponential Distribution', 'X', 'P(X)','')
# Students' T-distribution
# ... with 4, and with 10 degrees of freedom (DOF)
plot(x, stats.norm.pdf(x), 'g')
hold(True)
showDistribution(stats.t(4), stats.t(10),
'T-Distribution', 'X', 'P(X)',['normal', 't=4', 't=10'])
# F-distribution
# ... with (3,4) and (10,15) DOF
showDistribution(stats.f(3,4), stats.f(10,15),
'F-Distribution', 'F', 'P(F)',['(3,4) DOF', '(10,15) DOF'])
# Uniform distribution
showDistribution(stats.uniform,'' ,
'Uniform Distribution', 'X', 'P(X)','')
# Logistic distribution
showDistribution(stats.norm, stats.logistic,
'Logistic Distribution', 'X', 'P(X)',['Normal', 'Logistic'])
# Lognormal distribution
x = logspace(-9,1,1001)+1e-9
showDistribution(stats.lognorm(2), '',
'Lognormal Distribution', 'X', 'lognorm(X)','', xmin=-0.1)
