The software described here will be updated occasionally. For the description of the program you have, type:
% program_name -h
for a help message.
Here follows hints for the use of all the programs referred to in the excercises in this book as well as some supplemental programs that are helpful.
The programs described here are part of the package pmag1.0. They are designed to take advantage of the power of UNIX in that they all take command line arguments. The common features are:
1) All programs repond with a help message if the [-h] switch is used:
% program_name -h
2) Programs that produce pictures use the freeware program plotxy (see section on getting and installing plotxy. Pmag1.0 programs output plotxy commands which can be piped directly to plotxy:
% program_name | plotxy
This causes plotxy to create a postscript file, which can be viewed with a postscript viewer such as pageview, ghostscript or ghostview, or it can be printed to a postscript compatible printer. The plotxy commands generated by the pmag1.0 programs can also be saved to a file and modified as needed:
% program_name > myfile.com
A text editor can be used to modify the commands to taste (see also plotxy documentation plotxy.doc in the Plotxy directory:
/usr/local/pmag1.0/Plotxy).
3) Programs read from standard input and write to standard output unless otherwise noted. This means that the typical syntax will be:
% program_name < input_file > output_file
The output from one program can be piped as input to another program.
Here follows a brief manual for using the programs in the pmag1.0 package. Refer to the examples in the book for further hints about how to use them.
Usage: arai [-sf][min max field][Standard I/O]
Description: makes an Arai plot from input data.
Options:
-s sets fit from [min] to [max]
-f sets lab field to [field] (in Tesla)
-d uses .dat file as input if [ta] = 0 (default) uses geographic (Dg,Ig)
if [ta] = 1 uses tilt adjusted ( Dta,Ita)
-m uses .mag file as input
Defaults:
finds optimum interval - beware
uses lab field of 40 microT
Input options:
Default input:
Sample_name treatment intensity D I
[-m] option: .mag file
Sample_name treatment CSD intensity D I
.dat file
[-d] option:
Sample_name position treatment CSD intensity Dg
Ig Dta Ita
treatment steps are coded as follows:
XXX.YY where XXX is the temperature and YY is as follows:
NRM data: .00
pTRM: .11
pTRM check: .12
Output: plotxy commands.
Usage: bootams [-pP] [Standard I/O]
Description: calculates bootstrap eigenparameters from input file.
Options:
-p option specifies parametric (by sample) bootstrapInput:
-P option specifies parametric (by site) bootstrap
s_1 s_2 s_3 s_4 s_5 s_6 sigma
Output: bootstrap error statistics:
tau_1 sigma D I eta D I zeta D I
tau_2 sigma D I eta D I zeta D I
tau_3 sigma D I eta D I zeta D I
Usage: bootdi [-pPv] [Standard I/O]
Description: calculates bootstrap statistics for input file.
Options:
-p option selects parametric bootstrap
-P works on principal eigenvectors
-v spits out bootstrapped eigenvectors
Defaults:
simple bootstrap works on Fisher meansInput:D I [kappa N]
Output:
Fisher statistics if Fisherian, otherwise bootstrap ellipses:
tau_1 D I eta D I zeta D I
tau_2 D I eta D I zeta D I
tau_3 D I eta D I zeta D I
or if -v selected, bootstrapped eigenvectors D I
Usage: bootstrap [-pb] [Nb] [Standard I/O]
Description: calcluates bootstrap statistics from input data.
Options:
-p plot a histogram
-b sets number of bootstraps [Nb](<10000)
Input: single column of numbers
Output:
if no plot, then: N, Nb, mean, bounds containing 95% of means if plot,
then output is series of plotxy commands
Defaults:
no plot and nb=1000
Usage: cart_dir [Standard I/O]
Description: converts cartesian data to geomagnetic elements
Input: x1 x2 x3
Output: D I magnitude
Usage: cart_hist [-dcbpr][dec inc][file1 file2][Standard I/O]
Description: makes histograms of cartesian coordinates of input.
Options:
-d compares with direction [dec inc]
-c compares two files [file1 file2]
-b plots confidence bounds
-p specifies parametric bootstrap
-r flips second mode for reversals test
Input:D I [\kappa N]
Output is plotxy command file
Defaults:
standard input of single file no confidence bounds simple bootstrap
no reversals test
Usage: curie -[lspt] [smooth] [low hi step] [Tmin Tmax] [Standard I/O]
Description: analyzes curie temperature data.
Options:
-l smooth over [smooth] data points
NB: [smooth] must be an odd number
-s scan range of smoothing intervals [low] to [hi] using a spacing
of [step] [low],[hi] and [step] must be odd
-p plot option on to generate Plotxy command file can be piped directly
to plotxy and viewed:
curie -p < filename | plotxy; ghostview mypost
printed:
curie -p < filename | plotxy; lpr mypost
or saved to a file for modification:
curie -p < filename > eqarea.com
-t truncates to interval between [Tmin] and [Tmax] input: temperature,magnetization
Defaults: no smoothing plot option off uses entire record
Usage: di_geo [Standard I/O]
Description: rotates directions from specimen to geographic coordinates.
Input: D I azimuth plunge
Output: D I (in geographic coordinates)
Notes: the azimuth and plunge are the declination and inclination of the arrow used for reference during the measurements.
Usage: dir_cart [-m] [Standard I/O]
Description: converts geomagnetic elements to cartesian coordinates.
Option: -m read magnitude field
Input: D I [ magnitude]
Output:x1 x2,x3
Notes: longitude, latitude can be substituted for D,I.
Usage: di_tilt [Standard I/O]
Description: rotates directions from geographic to tilt adjusted coordinates.
Input: D I strike dip
Output: D I (in adjusted coordinates)
Notes: convention is that dip is to the ``right'' of strike.
Usage: di_vgp [Standard I/O]
Description: transforms declination/inclination to VGP.
Input: D I site latitude (N), longitude (E)
Output: Pole Longitude Latitude
Notes: convention is positive: North, negative: South and positive: East, negative: West
Usage: eigs_s [Standard I/O]
Description: converts eigenparameters to .s format.
Input:
tau1 DV1 IV1
tau2 DV2 IV2
tau3 DV3 IV3
Output:I>s1 s2 s3 s4 s5 s6
Notes: tau1 is the largest eigenvalue and V1 is the associated eigenvector
Usage: eqarea [Standard I/O]
Description: makes an equal area projection of input data.
Input: D I
Output: plotxy commands
Usage: fishdmag [-f] [beg end ta] [Standard I/O]
Description: calculates Fisher mean from specified portion of demagnetization data.
Options:
-f Fisher mean from [beg] to [end] steps
-d uses .dat file as input
if [ta] = 0 (default), uses geographic (Dg Ig)
if [ta] = 1 uses tilt adjusted ( Dta Ita)
-m uses .mag file as input where [beg] and [end] are the number of the treatment (i.e. 1st, 2nd, 3rd).
Input:
default:
sample_name treatment intensity D I
-m .mag file option:
sample_name treatment CSD intensity D I
-d dat file option:
sample_name treatment CSD intensity Dg
Ig Dta Ita)
Output: sample_name f n beg end a95 D I
Usage: fisher -kns [kappa] [N] [seed] [Standard I/O]
Description: generates set of Fisher distribed data from specified distribution.
Options:
-k specifies \kappa as [kappa]
-n specifies number as [N]
-s specifies random seed (non-zero integer) as [seed]
Defaults:
k = 30
N = 100
seed = 1200
Usage: fishqq [Standard I/O]
Description: plots Q-Q diagram for input against Fisher distribution.
Input: D I
Output: plotxy commands
Usage: fishrot -kndis [kappa] [N][dec][inc][seed] [Standard I/O]
Description: draws a Fisher distribution with mean of [dec] [inc] and [kappa], [N], using random seed [seed].
Options:
-k specifies kappa as [kappa]
-n specifies number as [N]
-d specifies D as [dec]
-i specifies I as [inc]
-s specifies [seed] for random number generator (non-zero)
Defaults:
kappa= 30
N = 100
D = 0
I = 90
Usage: foldtest [-p] [Standard I/O]
Description: performs bootstrap fold test.
Options:
-p option selects parametric bootstrap
Input: D I strike dip [kappa N]
Output: plotxy commands
Notes: unfolding curve of data is solid line, pseudo samples are dashed histogram is fraction of \tau maxima. Also, dip is to the ``right'' of strike.
Usage: gauss -msni [mean] [sigma] [N] [seed] [Standard I/O]
Description: draws a set of Gaussian distributed data from specified distribution.
Options:
-m sets the mean to [mean]
-s sets the standard deviation to [sigma]
-n sets the number of points to [N]
-i sets integer random seed to [seed]
Defaults:
[mean] is 1
[sigma] is .5
[N] is 100
Usage: gofish [Standard I/O]
Description: calculates Fisher statistics from input file.
Example
4.2
Input: D I
Output:
mean D mean I N R k a95
Usage: goprinc [Standard I/O]
Description: calculates principal component from input data.
Example: 4.2
Input: D I
Output: D I N tau_1 of the principal component
gtcirc
Usage gtcirc [-g] [beg end ta] [Standard I/O]
Description: calculates best-fit plane through specified input data.
Options:
-g best-fit great circle (plane) from [beg] to [end] steps [beg] and
[end] are the numbers of the treatment step. For example the NRM step is
[1], the second step is [2], etc.
-d uses .dat file as input if [ta]=0 (default), uses geographic (Dg,
Ig) if [ta] = 1 uses tilt adjusted ( Dta,
Ita)
-m uses .mag file as input
Input options:
Default input: Sample_name treatment intensity D I
-m .mag file option:
Sample_name treatment CSD intensity D I
-d .dat file option:
Sample_name treatment CSD intensity Dg,
Ig, Dta, Ita
Default is to do whole file
Output:
sample_name g N beg end MAD D I
where D and I are for the pole to the best-fit plane and [beg] and [end] are the numbers of the treatment step.
Usage: histplot [-lb] [bin] [Standard I/O]
Description: creates a histogram of input data.
Example
4.6
Options:
-l plots the distributions of logs
-b sets bin size to [bin]
Input: single column of data
Output: Plotxy commands
Defaults:
not logs auto binning
hystcrunch
Usage: hystcrunch -[mptl] [trunc_deg] [label] [Standard I/O]
Description: plots hysteresis loop data and massages them.
Options:
-m Micromag data file
-p do not plot
-a do not adjust slope
-t truncate to trunc_deg harmonics
-l label plot with label
Defaults:
- xy data file
- retain 99 terms of FFT
- adjust for high field slope
- no plot label
- generate plotxy commands
Usage: igrf [Standard I/O]
Description: calculates reference field vector at specified location and time uses appropriate IGRF or DGRF for date > 1945.
Example: 1.4
Input: decimal year, altitude (km), latitude (13 N), longitude (13 E)
Output: D I B (nT)
Usage: incfish [Standard I/O]
Description: calculates an estimated inclination, assuming a Fisher distribution, for data with only inclinations. Uses the method of McFadden and Reid [1982].
Input: inclinations
Output: <I>, upper and lower bounds, N, estimated and a95.
Usage: jackstrat Standard I/O
Description: calculates magnetostratigraphic jackknife parameter J.
Example
6.1
Input: VGP latitudes or inclinations in stratigraphic order
Output: plotxy commands
Usage: k15_hext [-tga] [Standard I/O]
Description: calculates Hext statistics from 15 measurements uses Jelinek's 15 measurement scheme.
Example
5.5 and Example
5.6
-a average whole file
-g geographic coordinates
-t geographic tilt coordinates
Default: average by sample
Input: 1 line with sample_name [azimuth plunge strike dip] followed
by 3 rows of 5 measurements for each specimen in the following order (see
Chapter 5):
K1,K2,K3,K4,K5 K6,K7,K8,K9,K10 K11,K12,K13,K14,K15
Output: Hext statistics
[if individual samples, id and bulk chi]
F, F12,
F23
tau1 D I epsilon12 D I epsilon13 D
I
tau2 D I epsilon21 D I epsilon23 D
I
tau3 D I epsilon32 D I epsilon31 D
I
Usage: k15_s [-gt] [Standard I/O]
Description: calculates s from 15 measurements scheme (Ki) (see Chapter 5).
Options:
-g geographic rotation
-t geographic AND tectonic rotation
Input: (see k15_hext)
Output:
s1 s2 s3 s4 s5
s6
Usage: lnp [-f] [infile] [Standard I/O]
Description: calculates Fisher mean from combined directed lines and great circles using the method of McFadden and McElhinny [1988].
Example
4.3
Options:
-f calculates mean from data in [infile], one site at a time
Input: output file from pca, gtcirc, fishdmag programs,
i.e.
sample_name [fpg] n beg end [a95 mad] dec inc
sample_ name convention:
ABC123D[1] where ABC is a study designator of letters (any length)
123 is the site number (any length) D is a (single) letter for each separately
oriented sample [1] is an optional (single digit) specimen number
Default: assumes whole file is one site.
Output:
site NL NG a95 D I
where NL is the number of directed lines where NG is
the number of great circles
Usage: mag_dat -n nfofile [Standard I/O]
Description: converts magnetometer data file to format with geographic and tilt adjusted coordinates. Also pastes in stratigraphic position data. Uses .nfo files made by mk_nfo.
Input:
magnetometer data (.mag file format):
sample[optional specimen_number] treatment CSD intensity D I
(.nfofile format):
sample_name position sampling_convention NBaz NBpl LABaz LABpl NBstr
strike dip
Output:
(.dat file foramt)
sample_name position treatment CSD intensity Dg, Ig, Dta, Ita
where Dg and Ig are D,I in geographic coordinates and Dta and Ita are D,I in tilt adjusted coordinates.
Usage: mk_nfo [-HbBDstfk][strike dip][magdec][lat. long. delta T][cpsdu][az_add az_mult pl_add pl_mult][basename][keyboard input]
Description: makes a information file(s) for conversion of data into geographic, tectonic and stratigraphic references.
Options:
-H stratigraphic position data
-b structural strike/dip for each sample
-B structural for entire suite read as [strike dip]
-D add [magdec] to all declination/strike info
-s sun compass data using [lat. long. dT] lat/long of study area and
dT is time difference from GMT
-t type of conversion from notebook azimuth (= NBaz)/ notebook plunge
(= NBpl) to lab azimuth (= LABaz)/ lab plunge (= LABpl) [c]ube: NBaz/NBpl
are strike and dip on face perpendicular to face with lab arrow LABaz=NBaz-90,
LABpl=NBpl-90 [p]omeroy orientation device: NBaz/NBpl are direction of
drill and angle from vertical LABaz=NBaz, LABpl=-NBpl [s]trike/dip: NBaz/NBpl
are strike and dip on face with lab arrow LABaz=NBaz+90, LABpl=NBpl [d]rill
direction/dip: NBaz/NBpl are direction of drill (az/pl) in plane perpendicular
to face with lab arrow LABaz=NBaz, LABpl=NBpl-90 [u]ser defined conversion
input [az_add az_mult pl_add pl_mult] to specify affine for NBaz/NBpl to
LABaz/LABpl e.g. for [p] above, az_add=0, az_mult=1 pl_add=-90, az_mult=-1
-f output file specified as [basename] ouput file will be appended
to basename.nfo and if sun compass data calculated, basename.snfo too
-k input from keyboard with prompts <cntl-D>. to quit. Input: sample,NBaz,NBpl
[pos][strike dip][yyyymmdd hhmm shadow] Output: sample, pos, type, NBaz,NBpl,LABaz,LABpl,NBstr,strike,dip
Defaults: read/write from Standard I/O input only: sample, NBaz,NBpl no declination adjustment LABaz=NBaz; LABpl=NBpl
Usage: pca [-pmd] [beg end][ta] [Standard I/O]
Description: calculates best-fit line through specified input data.
Options:
-p PCA from [beg] to [end] steps [beg] and [end] are the numbers of
the treatment step. For example the NRM step is [1], the second step is
[2], etc.
-d uses .dat file as input if[ta]=0 (default), uses geographic (Dg,
Ig) if [ta] = 1 uses tilt adjusted ( Dta,
Ita)
-m uses .mag file as input:
Input options:
Default: Sample_name treatment D I
-m .mag file option:
Sample_name treatment CSD D I
-d .dat file option:
Sample_name position treatment CSD, Dg,
Ig, Dta, Ita
Output:
sample_name p N beg end MAD D I
where D and I are for the princinpal component.
Usage: plotams [-BpPvxjn] [name] [Standard I/O]
Description: plots AMS data from s data
Options:
-B do not plot simple bootstrap ellipses
-p plot parametric (sample) bootstrap ellipses
-P plot parametric (site) bootstrap ellipses
-v plot bootstrap eigenvectors - not ellipses
-x plot Hext [1963] ellipses
-j plot Jelinek [1978] ellipses
-n use [name] as plot label
Default: plot only the simple bootstrap
Input: s1 s2s3s4s5s6 [sigma]
Output: plotxy commands
Usage: plotdi [-pPv] [Standard I/O]
Description: makes equal area plot of input data, with uncertainties.
Options:
-p parametric bootstrap
-P works on principal eigenvector
-v plots bootstrapped eigenvectors
Defaults: simple bootstrap works on Fisher means plots estimated 95% conf. ellipses
Input: D,I, [,k, N]
Output: plotxy commands
Usage: plotdike [-BpPvn] [name] [Standard I/O]
Description: plots AMS data in a sepate directory for a particular dike.
-B DONT plot simple bootstrap ellipses
-p plot parametric (sample) ellipses
-P plot parametric (site) ellipses
-v plot bootstrap eigenvectors
-n use [name] as plot label
Input: -one or both files called: e.s and w.s containing:
s1 s2 s3 s4 s5 s6 [ sigma] for the nominal east and west margins respectively
- a file called dike.dd containing one or more measurements of the
dip direction and dip of the dike
-optional files:
struct.dat: contains first and second tectonic corrections as strike
and dips
lin.di: contains dec,inc of lineation data
Output:
plotxy commands and a files:
fort.20 is summary file
Default: plot only the simple bootstrap confidence ellipses
Usage: plotdmag [-pgfrmd] [beg end][D][ta][Standard I/O]
Description: makes orthogonal and equal area projections of input demagnetization data.
Options:
-p PCA from [beg] to [end] steps
-g gtcirc from [beg] to [end] steps
-f fisher mean from [beg] to [end] steps
-r plot horizontal axis = [D] degrees
Defaults:
North on horizontal ([D] = 0) no PCA, gtcircle, or fisher calculations
Input options:
Default:
Sample_name treatment D I
-m .mag file option:
Sample_name treatment CSD D I
-d dat file option:
Sample_name position treatment CSD Dg
Ig Dta Ita
Output: plotxy commands
Notes: select either p, f OR g
Usage: qqplot [Standard I/O]
Description: plots data against Normal Quantile
Input: single column of data
Output: plotxy commands
Notes: On the plot, there are these parameters:
N: the number of data points mean: the Gaussian mean sigma: the standard
deviation D: the Kolmogorov-Smirnov D-statistic Dc:
the critical value given N at 95% confidence (if D>Dc,
distribution not Gaussian at 95% confidence)
Usage: s_eigs [Standard I/O]
Description: converts s format data to eigenparameters.
Input: s1,s2,s3,s4,s5,s6
Output:
tau1 DV1 IV1
tau2 DV2 IV2
tau3 DV3 IV3
Notes:DV, IV are the directions of the eigenvectors
corresponding to the eigenvalues, tau.
Usage: s_flinn [-pl] [Standard I/O]
Description: plots Flinn diagram of input s data.
Options:
-p parametric bootstrap
-l plots L' versus F'
Input: s1 s2 s3 s4 s5 s6 [sigma]
Output: plotxy commands
Usage: s_geo [Standard I/O]
Description: rotates s data to geographic coordinates
Input: s1,s2,s3,s4,s5,s6, azimuth, plunge
Output: s1,s2,s3,s4,s5,s6 rotated to geographic coordinates
Usage: s_hext [Standard I/O]
Description: calculates Hext statistics from input s data.
Input: s1,s2,s3,s4,s5,s6
Output: Hext statistics
F F12 F23, sigma
tau1 D I epsilon12 D I epsilon13 D
I
tau2 D I epsilon22 D I epsilon23 D
I
tau3 D I epsilon32 D I epsilon33 D
I
Usage: s_hist [-cbpP123t][file1 file2][standard I/O]
Description: plots histograms of bootstrapped eigenparameters of s data.
Options:
-c compares [file1] and [file2]
-b plot 95% confidence bounds
-p sample parametric bootstrap
-P Site parametric bootstrap
-1 plots principal eigenvector
-2 plots major eigenvector
-3 plots minor eigenvector
-t plots eigenvalues
Defaults:
simple bootstrap all eigenparameters no confidence limits
Input: s1 s2 s3 s4 s5 s6 [sigma]
Output: plotxy command for histograms of eigenvalues and eigenvectors of bootstrap samples
Usage: s_jel78 [Standard I/O]
Description: calculates Jelinek (1978) statistics from s data.
Input: s1,s2,s3,s4,s5,s6
Output: Jelinek statistics
tau1 D I epsilon12 D I epsilon13 D
I
tau2 D I epsilon22 D I epsilon23 D
I
tau3 D I epsilon32 D I epsilon33 D
I
Usage: s_pt [-p] [Standard I/O]
Description: makes a Jelinek plot of input s data.
Options: -p parametric bootstrap
Input: s1 s2 s3 s4 s5 s6 [sigma]
Output: plotxy commands for P' versus T diagram
Usage: s_tern [-p][Standard I/O]
Description: makes a Ternary projection of input s data.
Example: See Chapter 5
Options: -p parametric bootstrap
Input: s1 s2 s3 s4 s5 s6
Output: plotxy command file of ternary diagram
Notes: triangles are data, dots are bootstrapped means
Usage: s_tilt [Standard I/O]
Description: rotates s data into tilt adjusted coordinates
Input:
s1,s2,s3,s4,s5,s6, strike, dip
Output:
s1,s2,s3,s4,s5,s6 [in tilt adjusted coordinates]
splint
Usage: splint [-i] [interval] [Standard I/O]
Description: calculates spline interpolation of input.
Option: -i uses interpolation interval [interval]
Default: [interval] = 1
Input: x,y, data with monotonic increasing x
Output: interpolated x,y
Usage: stats [standard I/O]
Description: calculates Gauss statistics for input data
Input: single column of numbers
Output: N, mean, sum, sigma, (%) , stderr, 95% conf.
Notes: sigma is the standard deviation % is sigma as percentage of the mean stderr is the standard error and 95% conf.= 1.96 43#43
Usage: sundec [-u] [delta T] [Standard I/O]
Description: calculates declination from sun compass measurements.
Options: -u sets the time difference [delta T] in hours from universal time (e.g. -5 for EST)
Input: latitude, longitude, year, month, day, hours, minutes, shadow angle
Output: D
Notes: positive: North, East; negative: South, West
Usage: vgp_di [Standard I/O]
Description: transforms VGP to equivalent D, I
Input: pole latitude, longitude, site latitude, longitude.
Output: D, I
Notes: convention is positive: North, negative: South and positive: East, negative: West
Usage: vspec [Standard I/O]
Description: calculates a vector average for multiple measurements of a single specimen at a single treatment step.
Input: (.mag file format)
sample_name treatment CSD intensity D I
Output: sample_name treatment CSD/R* intensity D I
Unique specimen/treatment data are simply copied. R* is the vector resultant (including intensity) over the sum of all intensities and ranges from 0 to 1.
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For content questions please contact: Lisa Tauxe |
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