def iBootstrap(Data1,Data2,NumSims=1000):
"""
Conduct a bootstrap test (Tauxe, 2010) for a common mean on two declination,
inclination data sets
This function modifies code from PmagPy for use calculating and plotting
bootstrap statistics. Three plots are generated (one for x, one for y and
one for z). If the 95 percent confidence bounds for each component overlap
each other, the two directions are not significantly different.
Parameters
----------
Data1 : a list of directional data [dec,inc]
Data2 : a list of directional data [dec,inc]
NumSims : number of bootstrap samples (default is 1000)
"""
counter=0
BDI1=pmag.di_boot(Data1)
BDI2=pmag.di_boot(Data2)
print ""
print "==============="
print ""
print "Here are the results of the bootstrap test for a common mean"
CDF={'X':1,'Y':2,'Z':3}
pylab.figure(CDF['X'],figsize=(3,3),dpi=160)
pylab.figure(CDF['Y'],figsize=(3,3),dpi=160)
pylab.figure(CDF['Z'],figsize=(3,3),dpi=160)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,["",""])
def iBootstrap(Data1, Data2, NumSims=1000):
"""
Conduct a bootstrap test (Tauxe, 2010) for a common mean on two declination,
inclination data sets
This function modifies code from PmagPy for use calculating and plotting
bootstrap statistics. Three plots are generated (one for x, one for y and
one for z). If the 95 percent confidence bounds for each component overlap
each other, the two directions are not significantly different.
Parameters
----------
Data1 : a list of directional data [dec,inc]
Data2 : a list of directional data [dec,inc]
NumSims : number of bootstrap samples (default is 1000)
"""
counter = 0
BDI1 = pmag.di_boot(Data1)
BDI2 = pmag.di_boot(Data2)
print ""
print "==============="
print ""
print "Here are the results of the bootstrap test for a common mean"
CDF = {'X': 1, 'Y': 2, 'Z': 3}
pylab.figure(CDF['X'], figsize=(3, 3), dpi=160)
pylab.figure(CDF['Y'], figsize=(3, 3), dpi=160)
pylab.figure(CDF['Z'], figsize=(3, 3), dpi=160)
pmagplotlib.plotCOM(CDF, BDI1, BDI2, ["", ""])
def common_dir_boot(dir1,dir2,bootsteps=1000,plot='no'):
#test for a common direction using bootstrap method
#directions given as pandas Series listing mean direction/pole parameters
#this is assuming published means without input directions, so bootstrap is a little different from the one
#described in Tauxe: not a pseudoselection from specified points but drawing from fisher distribution directly.
#adds a level of abstraction which hopefully does not invalidate procedure
BDI1,BDI2=[],[]
for s in range(bootsteps):
fpars1=pmag.fisher_mean(get_fish(dir1))
fpars2=pmag.fisher_mean(get_fish(dir2))
BDI1.append([fpars1['dec'],fpars1['inc']])
BDI2.append([fpars2['dec'],fpars2['inc']])
bounds1=get_bounds(BDI1)
bounds2=get_bounds(BDI2)
#now want to check if is a pass or a fail - only pass if error bounds overlap in x,y,and z
bresult=[]
for b1,b2 in zip(bounds1,bounds2):
if (b1[0]>b2[1] or b1[1]<b2[0]):
bresult.append(0)
else: bresult.append(1)
if sum(bresult)==3: outcome='Pass'
else: outcome='Fail'
angle=pmag.angle((dir1['dec'],dir1['inc']),(dir2['dec'],dir2['inc']))
# set up plots - can run this if want to visually check what's going on.
if plot=='yes':
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],4,4)
pmagplotlib.plot_init(CDF['Y'],4,4)
pmagplotlib.plot_init(CDF['Z'],4,4)
# draw the cdfs
pmagplotlib.plotCOM(CDF,BDI1,BDI2,["",""])
pmagplotlib.drawFIGS(CDF)
return pd.Series([outcome,angle[0]],index=['Outcome','angle'])
def main():
"""
NAME
revtest.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
revtest.py [-h] [-i] [command line options]
OPTION
-h prints help message and quits
-i for interactive entry of file names from command line
-f FILE, sets input filename on command line
-fmt [svg,png,jpg], sets format for image output
"""
D,fmt=[],'svg'
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-i' in sys.argv: # ask for filename
file=raw_input("Enter file name with dec, inc data: ")
f=open(file,'rU')
data=f.readlines()
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
for line in data:
if '\t' in line:
rec=line.split('\t') # split each line on space to get records
else:
rec=line.split() # split each line on space to get records
Dec,Inc=float(rec[0]),float(rec[1])
D.append([Dec,Inc,1.])
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
print 'doing first mode, be patient'
BDI1=pmag.di_boot(D1)
print 'doing second mode, be patient'
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
pmagplotlib.drawFIGS(CDF)
ans= raw_input("s[a]ve plots, [q]uit: ")
if ans=='a':
files={}
for key in CDF.keys():
files[key]='REV'+'_'+key+'.'+fmt
pmagplotlib.saveP(CDF,files)
else:
print 'good bye'
sys.exit()
def main():
"""
NAME
revtest_magic.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc data from pmag_sites table
SYNTAX
revtest_magic.py [command line options]
OPTION
-h prints help message and quits
-f FILE, sets pmag_sites filename on command line
-crd [s,g,t], set coordinate system, default is geographic
-exc use pmag_criteria.txt to set acceptance criteria
-fmt [svg,png,jpg], sets format for image output
"""
D,fmt=[],'svg'
coord='0'
infile='pmag_sites.txt'
critfile='pmag_criteria.txt'
dir_path='.'
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
infile=sys.argv[ind+1]
if '-crd' in sys.argv:
ind=sys.argv.index('-crd')
coord=sys.argv[ind+1]
if coord=='s':coord='-1'
if coord=='g':coord='0'
if coord=='t':coord='100'
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
#
infile=dir_path+'/'+infile
critfile=dir_path+'/'+critfile
Accept=['site_k','site_alpha95','site_n','site_n_lines']
data,file_type=pmag.magic_read(infile)
if file_type!='pmag_sites':
print "Error opening file"
sys.exit()
# ordata,file_type=pmag.magic_read(orfile)
if '-exc' in sys.argv:
crits,file_type=pmag.magic_read(critfile)
for crit in crits:
if crit['pmag_criteria_code']=="DE-SITE":
SiteCrit=crit
for rec in data:
if rec['site_tilt_correction']==coord:
Dec=float(rec['site_dec'])
Inc=float(rec['site_inc'])
if '-exc' in sys.argv:
for key in Accept:
if SiteCrit[key]!="":
if float(rec[key])<=float(SiteCrit[key]):
D.append([Dec,Inc,1.])
else:
D.append([Dec,Inc,1.])
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
if len(D1) < 5 or len(D2) < 5:
print 'not enough data in two different modes for reversals test'
sys.exit()
print 'doing first mode, be patient'
BDI1=pmag.di_boot(D1)
print 'doing second mode, be patient'
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
pmagplotlib.drawFIGS(CDF)
ans= raw_input("s[a]ve plots, [q]uit: ")
if ans=='a':
files={}
for key in CDF.keys():
files[key]='REV'+'_'+key+'.'+fmt
pmagplotlib.saveP(CDF,files)
else:
print 'good bye'
sys.exit()
def main():
"""
NAME
revtest.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
revtest.py [-h] [command line options]
OPTION
-h prints help message and quits
-f FILE, sets input filename on command line
-fmt [svg,png,jpg], sets format for image output
-sav saves the figures silently and quits
"""
fmt,plot='svg',0
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
data=numpy.loadtxt(file).transpose()
D=numpy.array([data[0],data[1]]).transpose()
else:
print '-f is a required switch'
print main.__doc__
print sys.exit()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
print 'doing first mode, be patient'
BDI1=pmag.di_boot(D1)
print 'doing second mode, be patient'
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
files={}
for key in CDF.keys():
files[key]='REV'+'_'+key+'.'+fmt
if plot==0:
pmagplotlib.drawFIGS(CDF)
ans= raw_input("s[a]ve plots, [q]uit: ")
if ans=='a':
pmagplotlib.saveP(CDF,files)
print 'good bye'
sys.exit()
else:
pmagplotlib.saveP(CDF,files)
def main():
"""
NAME
common_mean.py
DESCRIPTION
calculates bootstrap statistics to test for common mean
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
common_mean.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, input file
-f2 FILE, optional second file to compare with first file
-dir D I, optional direction to compare with input file
NOTES
must have either F2 OR dir but not both
"""
d,i,file2="","",""
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file1=sys.argv[ind+1]
if '-f2' in sys.argv:
ind=sys.argv.index('-f2')
file2=sys.argv[ind+1]
if '-dir' in sys.argv:
ind=sys.argv.index('-dir')
d=float(sys.argv[ind+1])
i=float(sys.argv[ind+2])
D1=numpy.loadtxt(file1,dtype=numpy.float)
if file2!="": D2=numpy.loadtxt(file2,dtype=numpy.float)
#
counter,NumSims=0,1000
#
# get bootstrapped means for first data set
#
print "Doing first set of directions, please be patient.."
BDI1=pmag.di_boot(D1)
#
# convert to cartesian coordinates X1,X2, Y1,Y2 and Z1, Z2
#
if d=="": # repeat for second data set
print "Doing second set of directions, please be patient.."
BDI2=pmag.di_boot(D2)
else:
BDI2=[]
# set up plots
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],4,4)
pmagplotlib.plot_init(CDF['Y'],4,4)
pmagplotlib.plot_init(CDF['Z'],4,4)
# draw the cdfs
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[d,i])
pmagplotlib.drawFIGS(CDF)
try:
ans=raw_input("S[a]ve plots, <Return> to quit ")
except:
print "\n Good bye\n"
sys.exit()
if ans=="a":
files={}
files['X']='CD_X.svg'
files['Y']='CD_Y.svg'
files['Z']='CD_Z.svg'
pmagplotlib.saveP(CDF,files)