Package ‘geophys’

January 21, 2018

Type Package
Title Geophysics, Continuum Mechanics, Gravity Modeling
Version 1.4-1
Date 2018-01-18
Depends R (>= 2.15)
Imports RPMG, RSEIS, RFOC, GEOmap, cluster
Suggests stats
Author Jonathan M. Lees [aut, cre],
Jake Anderson [ctb],
Francois Beauducel [ctb],
Dmitry Nicolsky [ctb]
Maintainer Jonathan M. Lees <[email protected]>
Description
Codes for analyzing various problems of geophysics, continuum mechanics and gravity models.
License GPL (>= 2)
Copyright see inst/COPYRIGHTS
NeedsCompilation no
Repository CRAN
Date/Publication 2018-01-21 19:39:01 UTC

R topics documented:
geophys-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
annotatebox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
annotateplane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
AXB.prod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
BMOD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
centroid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
desh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
DGzx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
dircheck . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1
2 R topics documented:

DO.DYKE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
DO.HALFSPACE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
dofry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
DoMohr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
DoMohrFig1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
draw.brachiopod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
elipfit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
erf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
flipZEE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
get.brachiopod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
get.heat2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Glines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
heat.sol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
labelLine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
lipper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Maxstress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
ModelG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
mogi1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
mogiM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
mohrleg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
NinePointCircle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
NORMvec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
okada85 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
perpproj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
PLOTbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
plotfry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
PLOTplane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
points2line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
PolarDecomp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
PPoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
pstart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
PXY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
randFRY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
randpoles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
REplane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
rev2RH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
rot2Zplane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Sect2vex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
setSTRESS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Showfry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
stress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
stressSETUP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
tauline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
TriangleCenter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
TriangleInfo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
vecproj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
vlength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
xtractlip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
geophys-package 3

Index 76

geophys-package Geophysics

Description
Geophysics, Continuum Mechanics, Mogi Models, Mohr’s Circles, Okada Model

Details

Package: geophys
Type: Package
Version: 1.2-0
Date: 2010-05-12
License: GPL
LazyLoad: yes

Author(s)
Jonathan M. Lees
Maintainer: Jonathan M. Lees <[email protected]>

References
Mogi

See Also
RSEIS, RFOC, GEOmap, zoeppritz

Examples

## Not run:

stress()

## End(Not run)
4 annotateplane

annotatebox Annotate Box

Description
Show a box with corner points annotated

Usage
annotatebox(Rbox = matrix(ncol = 4, nrow = 8), add = TRUE)

Arguments
Rbox Box matrix
add logical, TRUE= add to existing plot

Value
Graphical Side effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
stress, stressSETUP, annotateplane

Examples

annotatebox()

annotateplane Annotate Plane

Description
Show a box and plane with the three points annotated

Usage
annotateplane(Rp = matrix(ncol = 4, nrow = 3), add = TRUE)
AXB.prod 5

Arguments
Rp Points matrix
add logical, TRUE= add to existing plot

Value
Graphical Side effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
stress, stressSETUP, annotatebox

Examples
annotateplane()

AXB.prod Vector Cross Product

Description
Vector Cross Product

Usage
AXB.prod(A, B)

Arguments
A vector, 2 or 3 elements
B vector, 2 or 3 elements

Details
Can be 2D or 3D vectors. If lists are input they are converted to vectors.

Value
vector
6 BMOD

Author(s)
Jonathan M. Lees<[email protected]>

Examples
AXB.prod(c(1,0,0), c(0,1,0)) ### = c(0, 0 , 1)
AXB.prod(c(0,1,0), c(1,0,0)) ### = c(0, 0 ,-1)

BMOD Plot block model for gravity

Description
Plot block model with several polygonal structures for gravity modeling.

Usage
BMOD(bill, nstn = 100, PLOT = TRUE, obs=NULL)

Arguments
bill Polygon data from ModelG
nstn number of stations
PLOT logical, TRUE=plot
obs Observed Profile Gravity (x,g)

Details
Used internally in interactive modeling.

Value
graphical Side effects.

Author(s)
Jonathan M. Lees<[email protected]>

See Also
ModelG
centroid 7

centroid centroid

Description

calculate the centroid of a polygon

Usage

centroid(p)

Arguments

p list: x,y

Details

same code as centroid.polygon

Value

vector x, y

Author(s)

Jonathan M. Lees<[email protected]>

Examples

L=list()
L$x=c( 0.2188,-0.6668,-1.0992,-0.5105, 0.5106)
L$y=c( 0.76822, 0.75292,-0.01741,-0.74692,-0.48165)
centroid(L)
8 desh

desh Display Mesh

Description
Display Mesh

Usage
desh(M, add = TRUE, PTS = TRUE, colmesh = grey(0.8), colpts = grey(0.5),
...)

Arguments
M Mesh output of meshgrid
add logical, add to plot
PTS logical, add points
colmesh color for mesh
colpts color for points
... graphical parameters from par

Details
Used for showing strain mesh plots.

Value
graphical side effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
meshgrid

Examples

### warping of the ground from a Mogi source

P=1e5
a = 0.01
f = .1
nu=0.25
E = 10e13
mu = E/(2*(1+nu));
DGzx 9

EX = seq(from=-3, by=.4, to= 3)

mm = RPMG::meshgrid(EX, EX)
rho = sqrt(mm$x^2 + mm$y^2)

cen = list(x=mean(EX), y=mean(EX))

are = sqrt( (mm$x-cen$x)^2 + (mm$y-cen$y)^2 )

o1 = mogi1(a, P, rho, mu, f)

shiftx = o1$ur*(mm$x-cen$x)/are
shifty = o1$ur*(mm$y-cen$y)/are

newmesh = list(x=mm$x+shiftx , y=mm$y+shifty)

desh(mm, add=FALSE, PTS=FALSE, colmesh=grey(.8) )

desh(newmesh, add=TRUE, PTS=FALSE, colmesh=rgb(.6,.8, .6) )

DGzx Gravity anomaly in 2.5D

Description
Gravity anomaly in 2.5-Dimensions from an arbitrary polynomial at many stations.

Usage
DGzx(xs, zs, xv, zv, den)

Arguments
xs station locations in X
zs station locations in Z
xv x-vertices
zv z-vertices
den density contrast
10 DGzx

Details

calculate the 2.5D solution to gravity. Orientation of the vertices should be right handed.

Value

vector of Delta-Gz and Delta-Gx at each station

Author(s)

Jonathan M. Lees<[email protected]>

References

Won and Bevis (1987) Computing the gravitational and magnetic anomalies due to a polygon:
Algorithms and Fortran subroutines <doi:https://doi.org/10.1190/1.1442298>

Examples

nstn = 10
xstart = -10000
xend = 10000
xcen = 0
zcen = 5000
RAD = 2000

xs = seq(from=xstart, by=(xend-xstart)/nstn , length=nstn)

zs = rep(0, length=length(xs))

den = 0.2

Np = 6
theta = seq(from=0, to=2*pi, length=Np)
KZ = list(x=NA, y=NA)
KZ$x = xcen+RAD*cos(theta)
KZ$y = zcen+RAD*sin(theta)

Ngrav = DGzx(xs, zs, KZ$x, KZ$y, den)

dircheck 11

dircheck Check direction of polygon

Description
Check direction of polygon for Right Handed orietnation

Usage
dircheck(pol)

Arguments
pol list of x,y

Details
Gets cross product of consecutive points in polygon and returns the sign of each. If most are
positive, should try to reverse.

Value
vector of signs

Note
Co-linear values should return zero.

Author(s)
Jonathan M. Lees<[email protected]>

See Also
rev2RH, flipZEE

Examples

L=list()
L$x=c( 0.2188,-0.6668,-1.0992,-0.5105, 0.5106)
L$y=c( 0.76822, 0.75292,-0.01741,-0.74692,-0.48165)
dircheck(L)

K = rev2RH(L)
### after reversing,
dircheck(K)
12 DO.DYKE

DO.DYKE Heat for Dyke Intrusion

Description
Solve heat equation for dyke intrusion.

Usage
DO.DYKE(a = a, x = x, t = t, k = k, T0 = T0, NDIM = TRUE)

Arguments
a Thickness of dyke (meters)
x vector of distances across dyke (m)
t time in seconds
k diffusion constant
T0 Temperature at infinity
NDIM logical, TRUE=use nondimensional temperature for text labels

Value
graphical side effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
get.heat2, DO.HALFSPACE

Examples

a = 10;
k=10^6

DO.DYKE(NDIM=TRUE)

#### dimensional variable plot

DO.DYKE(NDIM=FALSE)
DO.HALFSPACE 13

DO.HALFSPACE Heat Equation in Halfspace

Description
Heat Equation in Halfspace

Usage
DO.HALFSPACE()

Details
Several solution for different times are displayed in succession.

Value
Graphical Side effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
DO.DYKE

Examples

DO.HALFSPACE()

dofry Fry Estimation

Description
Calculate the Fry diagram for estimating shear on random point patterns

Usage
dofry(x, y, PLOT = FALSE)
14 dofry

Arguments
x x-coordinates
y y-coordinates
PLOT logical, TRUE=plot

Details
The number of points returned can be large and plotting can take a long time, so when plotting can
restrict the points by using plotfry.

Value
List:

X x-coordinates
Y y
mx mean X
my mean Y

Author(s)
Jonathan M. Lees<[email protected]>

References
Fry, N., (1979) <http://dx.doi.org/10.1016/0040-1951(79)90135-5> Random point distributions and
strain measurement in rocks Tectonophysics, 60:89-105.

See Also
Showfry, plotfry, xtractlip

Examples

RDAT = randFRY(400, LIM=c(0,0, 200, 200) , rlen=5 )

length(RDAT$x)
plot(RDAT$x, RDAT$y, asp=1, pch=".", cex=2)
flag = sqrt( (RDAT$x-mean(RDAT$x))^2 + (RDAT$y-mean(RDAT$y))^2)<75

DAT = list(x=RDAT$x[flag], y=RDAT$y[flag])

x = DAT$x
y = DAT$y
plot(x,y, asp=1, pch=21, col='red', bg='gold', ann=FALSE, axes=FALSE)

FF = dofry(DAT$x, DAT$y )
AF = plotfry(FF, dis=30)

Z = xtractlip(AF)
DoMohr 15

lines(cluster::predict.ellipsoid(Z$hull), col='red')

DoMohr Mohr’s Circle

Description

Mohr’s Circle

Usage

DoMohr(Stensor=diag(c(3,2,1)), axis=NULL)

Arguments

Stensor Stress tensor

axis vector of axes to plot, c(1,2,3,4)

Details

Stress tensor is a 2 by 2 or 3 by 3 symmetric matrix

Value

Graphical Side effects

Author(s)

Jonathan M. Lees<[email protected]>

References

W.D. Means, Stress and Strain: Basic Concepts of Continuum Mechanics for Geologists, Springer;
1976. 4th ed., 339 p. (ISBN-10:0387075569).

See Also

DoMohrFig1, stress
16 DoMohrFig1

Examples
Stensor = matrix(c(2,.3, .3, 1), ncol=2)

Stensor = matrix(c(50, 40, 40, 10), ncol=2)

DoMohr(Stensor)

Stensor = matrix(c(
-50, 40, 20,
40, 10, 10,
20, 10, 5), ncol=3)

DoMohr(Stensor)

DoMohrFig1 Annotated Stress Tensor

Description

Annotated plot of a 2D stress tensor

Usage

DoMohrFig1(Stensor=matrix(c(5,1, 1, 3), ncol=2), rot1=NULL)

Arguments

Stensor stress tensor

rot1 rotation matrix

Value

Graphical Side effects

Author(s)

Jonathan M. Lees<[email protected]>

See Also

DoMohr
draw.brachiopod 17

Examples

Stensor =matrix(
c(50, 40,
40, 10), ncol=2)

DoMohrFig1(Stensor)

draw.brachiopod Draw Brachiopod

Description
Draw Brachiopod at a particular location

Usage
draw.brachiopod(BK = matrix(), x = 0, y = 0, col = "black", fill = NULL, ...)

Arguments
BK brachiopod matrix
x x-coordinate location on plot
y y-coordinate location on plot
col col for outline
fill color for fill
... other par parameters for plotting

Details
Used for strain illustrations

Value
side effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
get.brachiopod
18 draw.brachiopod

Examples

gb = get.brachiopod()

draw.brachiopod(gb)

BB = get.brachiopod()
phi0=0
phi = rep(phi0, 6)
shears = seq(from=0, to=1.5, length=6)
shearmats = list()
for(i in 1:length(shears))
{
shr = shears[i]
shearmats[[i]] = matrix(c(1, shr, 0, 1), ncol=2)
}

phi0=0
phi = rep(phi0, 6)
phi=runif(6, 0, 90)
shears = rep(0, 6)

for(i in 1:length(phi))
{
shr = shears[i]
shearmats[[i]] = matrix(c(1, shr, 0, 1), ncol=2)
}

x = rep(c(25,75), times=3)

y = as.vector( t(matrix( rep(c( 75, 50,25 ), times=2) , ncol=2)) )

siz = rep(30, 6)

plot(c(0, 100), c(0, 100), asp=1, type='n', ann=FALSE, axes=FALSE)

for(i in 1:length(x))
{
cosp=cos(phi[i]*pi/180)
sinp=sin(phi[i]*pi/180)
####### make a rotation matrix
#### rmat=matrix(c(cosp,-sinp, x, sinp, cosp, y), ncol=2)

####
rmat1=matrix(c(cosp,-sinp, sinp, cosp), ncol=2)
elipfit 19

total = rmat1

rmat= rbind( total, c(x[i],y[i]) )

n = length(BB[,1])

RACK1 = cbind(siz[i]*BB[,1:2], rep(1,n))

draw.brachiopod(RACK1)

elipfit Least Squares Ellipse

Description
Fit best Ellipse to a set of points using least squares.

Usage
elipfit(ex, ey, PLOT = FALSE, add = TRUE, ...)

Arguments
ex x-coordinates
ey y-coordinates
PLOT Logical, TRUE plots lines
add logical, add=TRUE adds to existing plot, FALSE starts new plot
... graphical parameters from par

Details
Program removes mean values from x-y points prior to fitting

Value
Vector of semi major axes and angle (radians)

Author(s)
Jonathan M. Lees<[email protected]>
20 erf

See Also
ellipsoidhull, xtractlip

Examples

EL=list()
EL$x=c(-9.478057124959,-8.887247178079,-7.679217676939,-5.843342603491,
-4.827065854640,-4.524213862912,-3.640069016562,-3.181663570301,
-2.830460290732,-2.276944364728,-0.258719497667, 5.987620544313,
5.262029128773, 4.233925281717, 3.463189680754, 3.295838697506,
1.127493106453, 0.611037858455, 0.308185866727,-1.034364425884,
-1.385567705454,-1.939083631457,-3.957308498518)
EL$y=c(-7.379108143633,-8.077163749968,-8.353322965687,-8.375311165710,
-8.133874868636,-8.988274156710,-7.715168397536,-7.629855105316,
-7.978224323725,-7.658390735870,-5.981004273181, 0.550983019511,
0.717119185592, 1.901196979324, 1.691334007646, 2.938457310537,
1.506850181485, 1.471885910595, 2.326285198669, 0.967866147275,
1.316235365684, 0.996401777829,-0.680984684860)

plot(EL, asp=1)

LL = elipfit(EL$x,EL$y, PLOT=TRUE, add=TRUE, col='purple')

erf Error Function

Description
Error Function

Usage
erf(x)
philpotts.erf(x)
erfc(x)
erfinv(x)

Arguments
x

Details
Uses pnorm to calculate the error function. erfinv returns the inverse of the erf function.
flipZEE 21

Value
error function

Author(s)
Jonathan M. Lees<[email protected]>

See Also
philpotts.erf

Examples

j = seq(from=0, to=5.5, by=0.01)

y = erf(j)
phil = philpotts.erf(j)

plot(j,y)
points( j, phil, pch=3, col='red' )

#### plot the difference

plot(j, y-phil)
lines(j, y-phil)

##### inverse of erf function:

j = seq(from=0, to=5.5, by=0.1)

y = erf(j)

for(i in 1:length(j))
{

z = erfinv(y[i])
print(paste(i, y[i], j[i], z, sep=" "))
}

flipZEE Flip Z direction

Description
Flip the zee direction so negative is down.
22 get.brachiopod

Usage
flipZEE(pol)

Arguments
pol list of x,y

Details
Reverse the sign of the y-direction to achieve negative down Z values.

Value
same as input with -y

Note
Uses the y component as if it were Z.

Author(s)
Jonathan M. Lees<[email protected]>

See Also
rev2RH, dircheck

Examples
L=list()
L$x=c( 0.2188,-0.6668,-1.0992,-0.5105, 0.5106)
L$y=c( 0.76822, 0.75292,-0.01741,-0.74692,-0.48165)
flipZEE(L)

get.brachiopod Brachiopod icon

Description
set Brachiopod icon

Usage
get.brachiopod()
get.heat2 23

Details
Program returns the outline of a brachiopod for strain analysis.

Value
2D Matrix of coordinates.

Note
Used in conjunction with draw.brachiopod

Author(s)
Jonathan M. Lees<[email protected]>

See Also
draw.brachiopod

Examples

gb = get.brachiopod()

draw.brachiopod(gb)

get.heat2 Heat Equation Solution

Description
Solution of the diffusion equyation when contact is made instananeously with an infinite half space.
Used for sudden exposure of magma at the surface, as in an oceanic ridge.

Usage
get.heat2(x, T0, k, t)

Arguments
x numeric vector, distance
T0 Temperature at infinity
k diffusion constant
t time
24 Glines

Details
get.heat2 is used when temperature at the boundary (atmosphere) remains constant for all time.
get.heat is used when temperature in half space changes (warms up).

Author(s)
Jonathan M. Lees<[email protected]>

Examples
k = 1*10^(-6)
dt = 3600
dz = 20*10^(-2)

T0=25

T1 = 1200

x = seq(from=0, to=80, by=0.5)/100

i = 1
Tx = get.heat2(x, T1-T0, k, i*dt)

plot(Tx, max(x)-x, type='n', xlim=c(700, 1200) , axes=FALSE, xlab="Temp", ylab="Depth, cm")

axis(3)
axis(2, at=pretty(x), labels=100*(max(x)-pretty(x)))

for(j in 1:5)
{
Tx = get.heat2(x, T1-T0, k, j*dt)
Tx = Tx+T0
lines(Tx, max(x)-x, lty=2, col=j)
}

Glines Igneous Petrology Lines

Description
Scanned lines from igneous petrology

Usage
data(Glines)
Glines 25

Format

The format is: List of 10 $ :List of 2 ..$ x: num [1:77] 55.2 56.1 57.2 58.5 59.5 ... ..$ y: num [1:77]
1.62 1.67 1.82 2.15 2.35 ... $ :List of 2 ..$ x: num [1:6] 50.7 51.7 53.1 54.4 56.3 ... ..$ y: num [1:6]
9.21 9.16 9.24 9.21 9.09 ... $ :List of 2 ..$ x: num [1:14] 41.7 41.9 42.8 44.9 48.4 ... ..$ y: num
[1:14] 3.35 3.55 4.22 5.82 8.49 ... $ :List of 2 ..$ x: num [1:13] 52.1 52.2 52.2 52.2 52.3 ... ..$ y:
num [1:13] 1.72 2.7 3.77 5.27 5.67 ... $ :List of 2 ..$ x: num [1:20] 45.5 46.8 47.8 48.8 49.7 ... ..$
y: num [1:20] 5.74 5.69 5.69 5.69 5.64 ... $ :List of 2 ..$ x: num [1:2] 63.2 63.4 ..$ y: num [1:2]
6.64 3.45 $ :List of 2 ..$ x: num [1:2] 55.2 55.2 ..$ y: num [1:2] 5.34 1.75 $ :List of 2 ..$ x: num
[1:2] 46.7 53.2 ..$ y: num [1:2] 7.04 7.07 $ :List of 2 ..$ x: num [1:2] 49.7 55.1 ..$ y: num [1:2]
14.7 11.2 $ :List of 2 ..$ x: num [1:5] 58.8 60 61.8 62.3 62.5 ..$ y: num [1:5] 11.5 12.3 13.4 13.8
13.9

Details

Can click on here with a mixture to get a location on the plot.

Source

scanned figure

References

Principles of Igneous and Metamorphic Petrology, A. R. Philpotts, 1990, Prentice Hall (ISBN-
13:978-0521880060)

Examples

data(Glines)
data(PPoints)

plot(Glines[[1]], type='n', xlab="SiO2", ylab="NA2O+K2O")

for(i in 1:length(Glines))
{

lines(Glines[[i]]$x, Glines[[i]]$y)

for(i in 1:length(PPoints$x))
{
text(PPoints$x[i],PPoints$y[i], label=PPoints$lab[i], srt=PPoints$rots[i])
}
26 heat.sol

heat.sol Heat Equation Solution

Description
Heat Equation Solution

Usage
heat.sol(x, T0, k, t)

Arguments
x distance
T0 temperature
k diffusion constant
t time vector

Details
INteractive code to see evolution

Value
Graphical Side Effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
get.heat, get.heat2,DO.HALFSPACE

Examples

## Not run:
k = 1e-6
t = 1*365*24*60*60
T0 = 1000
x = seq(0,20, length=1000)
T = heat.sol(x, T0, k, t)

## End(Not run)
labelLine 27

labelLine Label a Line Segment

Description
Label a Line Segment

Usage
labelLine(P1, P2, above = TRUE, dinch = 0.2, lab = "text",
acode = 3, alength = 0.06, aty = 1, acol = "black", bty = 1,
bcol = "black", tcol = "black", font = 1, cex = 1)

Arguments
P1 Point 1 c(x,y)
P2 Point 2 c(x,y)
above logical, TRUE=label above the line, else below
dinch length the legs
lab character, text label
acode code for arrows, see arrows
alength length for arrows
aty lty for arrows
acol color for arrows
bty style for legs
bcol color for legs
tcol color for text
font font for text
cex character expansion for text, see par

Details
Two short lines are drawn perpendicular to the line between the points, the length of this line is
dinch. The arrow is drawn between the legs, using the parameters provided.

Value
graphical side effects

Author(s)
Jonathan M. Lees<[email protected]>
28 lipper

See Also
par, arrows, text

Examples

V1 = c(runif(1) , runif(1),runif(1) , runif(1))

P1 = c(V1[1], V1[3])
P2 = c(V1[2], V1[4])
plot(c(P1[1], P2[1]), c(P1[2], P2[2] ), asp=1, type='n' )
arrows(P1[1], P1[2], P2[1], P2[2], length=.04, col='red')

labelLine( P1, P2 , lab="ABOVE", dinch = .5,

aty=2, acol='blue' )
labelLine( P1, P2 , above=FALSE, lab="below",
dinch = .5, aty=2, acol='green', tcol="magenta" )

lipper Ellipse calculator

Description
Return parametric version of ellipse from equation of an ellipse.

Usage
lipper(a, b, c, d = 0, f = 0, g = -1)

Arguments
a numeric
b numeric
c numeric
d numeric
f numeric
g numeric

Details
General quadratic equation is, ax2 + 2bxy + cy 2 + 2dx + 2f y + g = 0
Maxstress 29

Value
vector=c(ap, bp, phi)

Author(s)
Jonathan M. Lees<[email protected]>

References
<http://mathworld.wolfram.com/Ellipse.html>

Examples

LIP = lipper(10, 3, 9)

theta = seq(from=0, to=2*pi, length=360)

phi = LIP[3]
px = LIP[1]*cos(theta)*cos(phi)- LIP[2]*sin(theta)*sin(phi)
py = LIP[1]*cos(theta)*sin(phi) + LIP[2]*sin(theta)*cos(phi)

plot(px, py, type='p', asp=1)

lines(px, py)

Maxstress Maximum Stress

Description
Maximum Normal and Shear stress in a plane

Usage
Maxstress(NN, Stensor)

Arguments
NN Normal Vector
Stensor Stress tensor

Details
Stress tensor can be entered as a vector of 3 or six values or as a 3 by 3 matrix. If three values are
provided provided they are assumed to be the principal stresses. If six values are provided, they are
c(x11, x12, x13, x22, x33). In either case eigen values and eigen vectors are calculated and used in
the following analysis.
30 Maxstress

Value
NN Normal vector to plane is returned
sigNORMmax maximum normal stress
tauSHEARmax maximum shear stress in the plane

Author(s)
Jonathan M. Lees<[email protected]>

See Also
stress

Examples

S = stressSETUP( )

Nvec = NORMvec(S$PPs, S$xscale, S$Rview, S$aglyph , add = FALSE)

Stensor = matrix(c(
15, 0, 0,
0, 8, 0,
0, 0, 5), ncol=3)

Mstress = Maxstress(Nvec, Stensor)

DoMohr(Stensor)
axis(1)
axis(2)

points(Mstress$sigNORMmax , Mstress$tauSHEARmax, pch=21, col='blue' , bg='gold' )

u=par('usr')

segments(0, Mstress$tauSHEARmax, Mstress$sigNORMmax ,

Mstress$tauSHEARmax, lty=2, col='green' )

text(mean(c(0, Mstress$tauSHEARmax)), Mstress$tauSHEARmax,

"MaxShear in Plane", pos=3)

segments(Mstress$sigNORMmax , u[3] , Mstress$sigNORMmax ,

Mstress$tauSHEARmax, lty=2, col='purple' )

text(Mstress$sigNORMmax , u[3], "MaxNormal stress", adj=c(0,-1) )

ModelG 31

ModelG Interactive 2.5D Gravity Modeling

Description
Interactive 2.5D Gravity Modeling

Usage
ModelG(Data, labs = c("Done"), obs=NULL, ZCOLS=RPMG::pastel.colors(24, seed=2 ))

Arguments
Data list: xmin, xmax, zmin, zmax
labs Labels
obs Observed Profile Gravity (x,g)
ZCOLS Color Palette for plotting blocks

Details
Forward modeling using the code of Won and Bevis.
For input, at a minimum, one must provide the boundary of the model region, xmin, xmax, ymin,
ymax (or depth). more comprehensive input, i.e. with a starting model, will provide a model in
addition: xmin, xmax, zmin, zmax, mod, cens, n. The mod is a list of polygons, each with xy
coordinates and a delta-rho value.

Value
Model

Note
You type in the polygons interactively and execute the gravity forward modeling.

Author(s)
Jonathan M. Lees<[email protected]>

References
Won and Bevis (1987) Computing the gravitational and magnetic anomalies due to a polygon:
Algorithms and Fortran subroutines <doi:https://doi.org/10.1190/1.1442298>

See Also
DGzx
32 mogi1

Examples

## Not run:
blum = list(xmin=0, xmax=26000, zmin=0, zmax=-1000)
gill = ModelG(blum)

## End(Not run)

mogi1 Mogi’s model

Description
Mogi’s model (point source in elastic half-space)

Usage
mogi1(d = 1, f = 1, a = 0.1, P = 1e+05, mu = 4e+09, nu = 0.25)

Arguments
d distance along surface, m
f depth to source, m
a radius of sphere injected, m
P hydrostatic pressure of injection, Pa
mu shear modulus
nu Poisson’s ratio

Details
Units should be constistent, e.g.: R, F, A, Ur and Uz in m imply V in m3; E, mu and P in Pa; Dt in
rad, Er, Et and nu dimensionless.

Value
list

ur radial displacement
uz vertical displacement

Author(s)
Jonathan M. Lees<[email protected]>
mogi1 33

References
Mogi, K., Relations between the eruptions of various volcanoes and the deformations of the ground
surfaces around them, Bull. Earthquake Res. Inst. Univ. Tokyo, 36, 99-134, 1958.

Examples

P=1e5
a = 0.1
f = 1

nu=0.25
E = 10e9

mu = E/(2*(1+nu));

#############
rho = seq(from=-3, to=3, by=0.1)
o1 = mogi1(a, P, rho, mu, f)
plot(rho, o1$uz)

plot(rho, o1$ud)

EX = seq(from=-3, by=.1, to= 3)

mm = RPMG::meshgrid(EX, EX)

rho = sqrt(mm$x^2 + mm$y^2)

o1 = mogi1(a, P, rho, mu, f)

#############
image(EX, EX, o1$uz, asp=1)

contour( EX, EX, o1$uz, add=TRUE)

#############
image(EX, EX, o1$ur, asp=1)

contour( EX, EX, o1$ur, add=TRUE)

#############
image(EX, EX, o1$uz, asp=1)
contour( EX, EX, o1$ur, add=TRUE)
34 mogiM

mogiM Mogi Model

Description
Mogi model deformation returns the deformation from a point source presurized inflation in an
elastic medium.
Mogi’s model (point source in elastic half-space). computes radial and vertical displacements Ur
and Uz, ground tilt Dt, radial and tangential strain Er and Et on surface, at a radial distance R
from the top of the source due to a hydrostatic pressure inside a sphere of radius A at depth F,
in a homogeneous, semi-infinite elastic body and approximation for A « F (center of dilatation).
Formula by Anderson [1936] and Mogi [1958].

Usage
mogiM(R = 1, F = 1, A = 0.1, P = 1e+05, E = 1e+10, nu = 0.25)

Arguments
R Hoirizontal Distance frm source, m
F Depth below surface, m, positive down
A radius of magma chamber
P hydrostatic pressure change in the sphere
E elasticity (Young’s modulus)
nu Poisson’s ratio

Details
Original paper by Mogi used poisson’s ratio equale to 0.25, i.e. lame parameters lambda and nu
were equal.

Value
list:

ur radial displacements Ur
uz vertical displacements Uz, Uz > 0 = UP
dt ground tilt Dt
er radial strain Er
et tangential strain Et on surface

Author(s)
Jonathan M. Lees<[email protected]>
mogiM 35

References

Anderson, E.M., Dynamics of the formation of cone-sheets, ring-dikes, and cauldron-subsidences,

Proc. R. Soc. Edinburgh, 56, 128-157, 1936.
Mogi, K., Relations between the eruptions of various volcanoes and the deformations of the ground
surfaces around them, Bull. Earthquake Res. Inst. Univ. Tokyo, 36, 99-134, 1958.

Examples

data(PXY)

delV = 2.3E13/(100^3) ##### (convert to meter^3 from cm^3)

F = 2.8E5/100 ##### (convert to meter from cm )

EX = seq(from=0, by=100, to= 9000)

Atest = mogiM(R=EX,F=F,A=delV)

plot(PXY, pch=6, col='purple', xlim=c(0,9), ylim=c(0, 1) )

### model
lines(EX/1000, Atest$uz/max(Atest$uz))

############ best fit optimization

library(stats)

fr<-function(x)
{

Atest = mogiM(R=PXY$x*1000 ,F=x[1],A=x[2])

rms = sum ( (PXY$y - Atest$uz/max(Atest$uz))^2 )

return(rms)
}
xin = c(2600, 2.0e+07)

FOUT = stats::optim(xin , fr)

Btest = mogiM(R=EX,F=FOUT$par[1] ,A=FOUT$par[2])

plot(PXY, pch=6, col='purple', xlim=c(0,9), ylim=c(0, 1) )

lines(EX/1000, Btest$uz/max(Btest$uz))
36 mohrleg

mohrleg Legend for Mohr

Description
Legend for Mohr

Usage
mohrleg(ES)

Arguments
ES Eigen Value Decomposition, output of function eigen

Details
Add notes to plots of Mohr’s circles. Uses the eigenvalues of the decomposition.

Value
Graphical Side Effects

Author(s)
Jonathan M. Lees<[email protected]>

See Also
DoMohr

Examples
Stensor = matrix(c(50, 40, 40, 10), ncol=2)

DoMohr(Stensor)
NinePointCircle 37

NinePointCircle Nine Point Circle

Description
Nine Point cirlce of a triangle

Usage
NinePointCircle(P1, P2 = c(0, 1), P3 = c(1, 0), add = FALSE, SHOW = TRUE)

Arguments
P1 vector, Point 1
P2 vector, Point 1
P3 vector, Point 1
add add to existing plot
SHOW create a new plot and add

Details
circle passes through nine points that can be calculated for any triangle. Also known as Feuerbach’s
circle, Euler’s circle, Terquem’s circle, the six-point circle, the twelve-point circle, the n-point
circle, the medioscribed circle, the mid circle, the circum-midcircle.

Value
list of essential points:
A 2-vector, vertex point 1
B 2-vector, vertex point 2
C 2-vector, vertex point 3
D 2-vector, mid-point opposite A
E 2-vector, mid-point opposite B
F 2-vector, mid-point opposite C
G 2-vector, foot altitude point opposite A
H 2-vector, foot altitude point opposite B
I 2-vector, foot altitude point opposite C
J 2-vector, mid point from S-A
K 2-vector, mid point from S-B
L 2-vector, mid point from S-C
S 2-vector, Intersection point of altitudes
CEN 2-vector, center of nine point circle
R radius of nine point circle
38 NORMvec

Author(s)
Jonathan M. Lees<[email protected]>

References
<http://en.wikipedia.org/wiki/Nine-point_circle>

See Also
TriangleInfo, TriangleCenter

Examples

P1 = 10*runif(2)
P2 = 10*runif(2)
P3 = 10*runif(2)

TRI = NinePointCircle(P1, P2, P3, add=TRUE, SHOW=TRUE)

NORMvec Plot Normal Vector

Description
Calculate and plot a normal vecotor to a plane

Usage
NORMvec(PPs, xscale, Rview, aglyph = list(), add = TRUE)

Arguments
PPs Points for plotting, these define the plane
xscale scale for the figure
Rview viewing matrix
aglyph glyph for plotting the normal vector in 3D
add logical, whether to add to current plot

Value
Graphical Side effects
NORMvec 39

Note
Used internally

Author(s)
Jonathan M. Lees<[email protected]>

See Also
pstart, PLOTbox, PLOTplane, stress

Examples

####### set colors

axcol = 'black'
boxcol = 'blue'
planecol = 'brown'

#### view angle

Rview = RFOC::ROTZ(-130)

### set arbitrary scale

xscale = 100

### set glphy for plotting 3D vectors

headlen =xscale* .3/6
len =xscale* .7/6
basethick =xscale* 0.05/2
headlip =xscale* .02/2
aglyph = RFOC::Z3Darrow(len = len , basethick =basethick ,
headlen =headlen , headlip=headlip )

#### set three points and combine them with rbind

P1 = xscale*c(.2, 1,1,0)
P2 = xscale*c(1, .1,1,0)
P3 = xscale*c(1, 1,.4,0)

PPs = rbind(P1, P2, P3)

### convert points for view

Rp = PPs

### create box and scale it

BOX <-matrix(c(0,0,0,0,
0, 1, 0,0,
0, 1, 1,0,
0, 0, 1,0,
1,0,0,0,
1, 1, 0,0,
1, 1, 1,0,
1, 0, 1,0), ncol=4, byrow=TRUE)
40 okada85

BOX = xscale*BOX

############## create axes and scale them

AX = matrix(c(0,0,0,0,
1, 0, 0,0,
0, 0, 0,0,
0, 1, 0,0,
0,0,0,0,
0, 0, 1,0), ncol=4, byrow=TRUE)

AX = 1.5*xscale*AX

############## rotate axes and box

Rax = AX

Rbox = BOX

############## start the figure

pstart(xscale=xscale)
###### plot the box
PLOTbox(Rax, Rbox, axcol= 'black', boxcol= 'blue')
############## plot the plane
PLOTplane(Rp)

####### plot the normal

NN = NORMvec(PPs, xscale, Rview,aglyph=aglyph, add=TRUE)

okada85 Okada Fault Deformation Model

Description
Calculate the deformation due to a fault based on Okada 1985 code.

Usage
okada85(e = 0, n = 0, depth = 0, strike = 20,
dip = 20, L = 5, W = 3, rake = 20, slip = 1, U3 = 1, nu = 0.25)

Arguments
e vector or matrix, Easting Observation, km
n vector or matrix, Northing Observation, km
depth depth of fault
strike degrees, strike of fault, measured from north
okada85 41

dip degrees, strike of fault, measured from horizontal

L Length, km
W Width, km
rake rake (degrees)
slip slip
U3 dilitation (m)
nu Poisson’s ration, default=0.25

Details
Computes displacements, tilts and strains at the surface of an elastic half-space, due to a dislocation
defined by RAKE, SLIP, and OPEN on a rectangular fault defined by orientation STRIKE and DIP,
and size LENGTH and WIDTH. The fault centroid is located (0,0,-DEPTH).
R-Code is a translation of original Matlab code by Francois Beauducel. UNC student Lan Ngo
worked on the first version and J. M. Lees tested, verified and finalized the package.

Value
list:

uE East deformation
uN North deformation
uZ Vertical deformation
uZE tilt vertical east
uZN tilt vertical north
uNN horizontal strains North-North
uNE horizontal strains North-East
uEN horizontal strains East-North
uEE horizontal strains East-East

Note
Units should be in km.
Note that vertical strain components can be obtained with following equations: uNZ = -uZN; uEZ
= -uZE; uZZ = -(uEE + uNN)*NU/(1-NU);
Be careful about the definition of strike: seems that here the strike may be measured positive north
of east, not east of north as stated in the documentation above.

Author(s)
Jonathan M. Lees<[email protected]>
42 perpproj

References
Aki K., and P. G. Richards (1980) (ISBN-13: 978-1891389634) Quantitative seismology, Freemann
& Co, New York.
Okada Y., Surface deformation due to shear and tensile faults in a half-space, Bull. Seismol. Soc.
Am., 75:4, 1135-1154, 1985.
Acknowledgments: Francois Beauducel, Dmitry Nicolsky, University of Alaska

See Also
mogi1, mogiM

Examples

library(RPMG)

EX = seq(from=-10, to=10, length=50)

WHY = seq(from=-10, to=10, length=50)
M = RPMG::meshgrid(EX, WHY )

OKout = okada85(M$x, M$y,2,30,70,5,3,-45,1,1)

old.par <- par(no.readonly = TRUE)

par(mfrow=c(2, 2))

image(EX, WHY, OKout$uN, col=terrain.colors(100) ,

asp=1, main="uN" );contour(EX, WHY, OKout$uN, add=TRUE)

image(EX, WHY, OKout$uE, col=terrain.colors(100) ,

asp=1 , main="uE" );contour(EX, WHY, OKout$uE, add=TRUE)

image(EX, WHY, OKout$uZ, col=terrain.colors(100) ,

asp=1, main="uZ" );contour(EX, WHY, OKout$uZ, add=TRUE)

plot(EX, OKout$uZ[, 25 ])

par(old.par)

perpproj Perpendicular Projection

Description
Perpendicular Projection in two-dimensions
perpproj 43

Usage
perpproj(V1, V2, add = FALSE)
pointproj(P1, VEC )

Arguments
V1 vector 1
V2 vector 1
add logical, TRUE add to plot
P1 point coordinates,
VEC vector coordinates,

Details
V1 and V2 are arrays with, for example, V1=c(x1 , x2 , y1, y2) or lists with V2=list(x=c(x1, x2),
y-c(y1, y2)) which gets converted into the first format.
The points are from the head of each vector projected onto the the line formed by the other vector.
If the the x1 y1 of each vector do not coincide, the interesections of two lines is determined and the
tail of each vector is moved to that point for determining the projection positions.
for the pointproj the input can be a 2-element vector or a list with (x,y) elements. The VEC should
be organized, as (x1,x2, y1, y2) or as an (x,y) list. The P1 vector can include many points, so a large
number of projections are doable.

Value
list:

P1 x, y
P2 x, y

Author(s)
Jonathan M. Lees<[email protected]>

See Also
vecproj

Examples

V1 = c( 2, 6, 1, 9)
V2 = c( 0, 5, 1, 2)

PP = perpproj( V1, V2, add=FALSE )

44 PLOTbox

R = range(c(V1, V2, unlist(PP) ))

plot(R, R, type='n', asp=1)

arrows(V1[1], V1[3], V1[2], V1[4], length=.08 )

arrows(V2[1], V2[3], V2[2], V2[4], length=.08 )

points(PP$P1[1],PP$P1[2], col='red')
points(PP$P2[1],PP$P2[2], col='blue')

arrows(V2[2], V2[4],PP$P1[1],PP$P1[2] , length=.08, col='red' )

arrows(V1[2], V1[4], PP$P2[1],PP$P2[2], length=.08, col='blue' )

PLOTbox Plot 3D box

Description
Plot 3D box

Usage
PLOTbox(Rax, Rbox, axcol = "black", boxcol = "blue")

Arguments
Rax rotated axes
Rbox rotated box
axcol axes color
boxcol box color

Value
Graphical Side effects

Author(s)
Jonathan M. Lees<[email protected]>
PLOTbox 45

See Also
pstart, PLOTplane, stress, NORMvec

Examples

####### set colors

axcol = 'black'
boxcol = 'blue'
planecol = 'brown'

#### view angle

Rview = RFOC::ROTZ(-130)

### set arbitrary scale

xscale = 100

### create box and scale it

BOX <-matrix(c(0,0,0,0,
0, 1, 0,0,
0, 1, 1,0,
0, 0, 1,0,
1,0,0,0,
1, 1, 0,0,
1, 1, 1,0,
1, 0, 1,0), ncol=4, byrow=TRUE)

BOX = xscale*BOX

############## create axes and scale them

AX = matrix(c(0,0,0,0,
1, 0, 0,0,
0, 0, 0,0,
0, 1, 0,0,
0,0,0,0,
0, 0, 1,0), ncol=4, byrow=TRUE)

AX = 1.5*xscale*AX

############## rotate axes and box

Rax = AX

Rbox = BOX

############## start the figure

pstart(xscale=xscale)
###### plot the box
PLOTbox(Rax, Rbox, axcol= 'black', boxcol= 'blue')
46 plotfry

plotfry Plot Fry Output

Description
Plot Fry Output limited by a specified distance.

Usage
plotfry(fry, dis, col = grey(0.7), ann = FALSE, axes = FALSE)

Arguments
fry list output of dofry
dis distance to limit plotting to the center
col color for points
ann logical, annotation of axes, see par
axes logical, whether to plot the axes, see par

Details
Used for plotting the points attained through the fry method

Value
x x-coordinates
y y-coordinates
mx x center of plot
my y center of plot
dis distance for limiting plot

Author(s)
Jonathan M. Lees<[email protected]>

References
Fry, N., (1979) <http://dx.doi.org/10.1016/0040-1951(79)90135-5> Random point distributions and
strain measurement in rocks Tectonophysics, 60:89-105.
PLOTplane 47

See Also
dofry, Showfry

Examples

RDAT = randFRY(400, LIM=c(0,0, 200, 200) , rlen=5 )

length(RDAT$x)
plot(RDAT$x, RDAT$y, asp=1, pch=".", cex=2)
flag = sqrt( (RDAT$x-mean(RDAT$x))^2 + (RDAT$y-mean(RDAT$y))^2)<75

DAT = list(x=RDAT$x[flag], y=RDAT$y[flag])

x = DAT$x
y = DAT$y
plot(x,y, asp=1, pch=21, col='red', bg='gold', ann=FALSE, axes=FALSE)

FF = dofry(DAT$x, DAT$y )
AF = plotfry(FF, dis=30)

Z = xtractlip(AF)

lines(cluster::predict.ellipsoid(Z$hull), col='red')

PLOTplane Plot Plane on box

Description
Plot Plane on box

Usage
PLOTplane(Rp, planecol = "brown")

Arguments
Rp Rotated points
planecol color for plotting plane

Author(s)
Jonathan M. Lees<[email protected]>
48 PLOTplane

See Also
pstart, PLOTbox, stress

Examples

####### set colors

axcol = 'black'
boxcol = 'blue'
planecol = 'brown'

#### view angle

Rview = RFOC::ROTZ(-130)

### set arbitrary scale

xscale = 100

#### set three points and combine them with rbind

P1 = xscale*c(.2, 1,1,0)
P2 = xscale*c(1, .1,1,0)
P3 = xscale*c(1, 1,.4,0)

PPs = rbind(P1, P2, P3)

### convert points for view

Rp = PPs

### create box and scale it

BOX <-matrix(c(0,0,0,0,
0, 1, 0,0,
0, 1, 1,0,
0, 0, 1,0,
1,0,0,0,
1, 1, 0,0,
1, 1, 1,0,
1, 0, 1,0), ncol=4, byrow=TRUE)

BOX = xscale*BOX

############## create axes and scale them

AX = matrix(c(0,0,0,0,
1, 0, 0,0,
0, 0, 0,0,
0, 1, 0,0,
0,0,0,0,
0, 0, 1,0), ncol=4, byrow=TRUE)

AX = 1.5*xscale*AX

############## rotate axes and box

points2line 49

Rax = AX

Rbox = BOX

############## start the figure

pstart(xscale=xscale)
###### plot the box
PLOTbox(Rax, Rbox, axcol= 'black', boxcol= 'blue')
############## plot the plane
PLOTplane(Rp)

P1 = xscale*c(0, 0,.4,0)
P2 = xscale*c(0.8, 0,0,0)
P3 = xscale*c(0, .7, 0 ,0)

PPs = rbind(P1, P2, P3)

### convert points for view

Rp = PPs

PLOTplane(Rp, planecol = "gold" )

points2line Points to Line

Description

Given a point and a matrix of lines, calculate the projection of the vector of the point to the first
coordinate of each line and the perpendicular distance.

Usage

points2line(Lp, VL)

Arguments

Lp Point list (x,y)

VL Matrix of points, N by 4 as X1, Y1, X2, Y2

Details

The first point in the matrix is considered the base.

50 PolarDecomp

Value
list:
rat cosine projection
srat sine projection

Author(s)
Jonathan M. Lees<[email protected]>

See Also
REplane

Examples

S= stressSETUP()
pstart()
PLOTbox(S$Rax, S$Rbox, axcol= 'green', boxcol= 'purple')
PLOTplane(S$Rp, planecol="brown")

basepoint = 3

legpoints = c(7,4,2)

VL = cbind( rep(S$Rbox[basepoint,1] , length(legpoints)),

rep(S$Rbox[basepoint,2] , length(legpoints)),
S$Rbox[legpoints,1], S$Rbox[legpoints,2])

Lp=list()
Lp$x=c(40.0180732557)
Lp$y=c(40.4847345741)

G = points2line(Lp, VL )

PolarDecomp Polar Decomposition

Description
Polar Decomposition for Strain

Usage
PolarDecomp(A)
PolarDecomp 51

Arguments
A Strain Matrix

Details
Polar decomposition uses the svd to extract 2 matrices that represent the stretch and rotation of a
strain: A = UP. U is orthogonal rotation matrix and P is the stretch tensor. These are extracted from
the singular value decomposition.

Value
P matrix, stretch tensor
U matrix, orthogonal rotation matrix

Author(s)
Jonathan M. Lees<[email protected]>

References
<http://en.wikipedia.org/wiki/Finite_strain_theory>

See Also
svd

Examples

A = matrix(runif(4, -1, 1), ncol=2)

PD = PolarDecomp(A)

E = svd(A)

### W S V
E$u

###t(E$v) %*% diag(E$d)%*% (E$u)

P = E$v
U = E$u

U
52 PPoints

PPoints Igneous Petrology Points

Description
Scanned points from igneous petrology

Usage
data(PPoints)

Format
The format is: List of 4 $ x : num [1:16] 45.4 56.4 64.1 71.1 66.3 ... $ y : num [1:16] 9.39 13.56
11.36 8.36 5.84 ... $ lab : chr [1:16] "minor varieties" "phonolites" "trachytes" "rhyolites" ... $ rots:
num [1:16] 45 0 0 0 0 0 0 -90 0 0 ...

Details
Can click on here with a mixture to get a location on the plot.

Source
scanned figure

References
Principles of Igneous and Metamorphic Petrology, A. R. Philpotts, 1990, Prentice Hall <ISBN-
13:978-0521880060>.

Examples

data(Glines)
data(PPoints)

plot(Glines[[1]], type='n', xlab="SiO2", ylab="NA2O+K2O")

for(i in 1:length(Glines))
{

lines(Glines[[i]]$x, Glines[[i]]$y)

for(i in 1:length(PPoints$x))
{
text(PPoints$x[i],PPoints$y[i], label=PPoints$lab[i], srt=PPoints$rots[i])
}
pstart 53

pstart Start an empty plot

Description

Start an empty plot

Usage

pstart(xscale = 30, expand=1.2)

Arguments

xscale Arbitray scale for plot

expand factor to expand the plotting region, default=1.2

Details

Creates a plotting region with no drawing. Default region is defined by: xlim= c(-expand*xscale,
expand*xscale) and ylim= c(-expand*xscale, expand*xscale).

Value

Graphical Side effects

Author(s)

Jonathan M. Lees<[email protected]>

Examples

pstart()

axis(1)
axis(2)
54 PXY

PXY Deformation of a volcano

Description

Deformation of Pozzuoli Italy 1982

Usage

data(PXY)

Format

The format is: List of 2 $ x: num [1:75] 0.0237 0.3478 0.5252 0.8689 0.8387 ... $ y: num [1:75] 1
0.991 0.975 0.928 0.962 ...

Details

Used as example data for Mogi Source inversion.

Source

Digitized from publication listed in reference.

References

publication
Berrino, G., Corrado, G., Luongo, G., and Toro, B., Ground deformation and gravity changes ac-
companying the 1982 Pozzuoli Uplift, in Monograph:On the 1982-1984 bradyseismic crisis at Phle-
graean Fields (Italy) eds: Barberi, F., Hill, D P., Innocenti, F., Luongo, G., Treuil, M., Bulletin Vol-
canologique, vol.47, no.2, special issue, pp.187-200, 1984 <doi:https://doi.org/10.1007/BF01961548>.

Examples

data(PXY)

plot(PXY)
randFRY 55

randFRY Random data for Fry analysis

Description

Random distribution of points that have a specified radial spacing.

Usage

randFRY(N = 200, LIM = c(0, 0, 100, 100), rlen = 5, PLOT=FALSE)

Arguments

N integer, number of points

LIM Limit in x-y direction
rlen distance length. points are selected if they are greater than this distance from
each other.
PLOT logical, TRUE=make a plot of data

Details

A spatial data set is generated that has random distribution with points no closer than a specified
distance apart.

Value

x x-coordinate
y y-coordinate

Author(s)

Jonathan M. Lees<[email protected]>

References

Fry, N., (1979) <http://dx.doi.org/10.1016/0040-1951(79)90135-5> Random point distributions and

strain measurement in rocks Tectonophysics, 60:89-105.

See Also

dofry
56 randpoles

Examples

RDAT = randFRY(100, LIM=c(0,0, 100, 100) , rlen=5 )

length(RDAT$x)
plot(RDAT$x, RDAT$y, asp=1, pch=".", cex=2)

randpoles Random Poles

Description
Create a set of random poles distributed around a given pole.

Usage
randpoles(az, iang, alphadeg, opt = "unif", BALL.radius = 1, N = 10, add = TRUE, ...)

Arguments
az azimuth of given direction
iang inclination angle of given direction
alphadeg standard error for distribution
opt Optional distribution, "unif" or "norm"
BALL.radius radius of small circle to draw
N Number of points to create
add logical, TRUE=add points to net plot
... graphical parameters for plotting

Details
A given geographic pole is supplied and N normally or uniformly distributed poles are created.

Value
az azimuths of new poles
dip dips of new poles
x x position on plot
y y position on plot

Author(s)
Jonathan M. Lees<[email protected]>
REplane 57

See Also
net

Examples

RFOC::net();
GG = randpoles(30, 40, 10, opt="norm", N=20)

RFOC::addsmallcirc(30, 40, 10)

REplane Replot plane

Description
Replot the plane after points have moved

Usage
REplane(m1, Lp, PPs, Rbox, Rview, xscale)

Arguments
m1 axis chosen
Lp x,y location to move to.
PPs Points matrix
Rbox Box matrix
Rview Viewing matrix
xscale arbitrary scale

Details
Used internally in stress program. The new locations are constrained to lie on associated axis.

Value
graphical side effects

Author(s)
Jonathan M. Lees<[email protected]>
58 rev2RH

See Also

stress

rev2RH Reverse to Right Hand

Description

Reverse orientation of the vectors to a right handed polygon.

Usage

rev2RH(pol)

Arguments

pol List with x and y components

Details

program reverses the order of the x and y components so they traverse in the oposite direction.

Value

list

Author(s)

Jonathan M. Lees<[email protected]>

See Also

dircheck, flipZEE

Examples
L=list()
L$x=c( 0.2188,-0.6668,-1.0992,-0.5105, 0.5106)
L$y=c( 0.76822, 0.75292,-0.01741,-0.74692,-0.48165)
rev2RH(L)
rot2Zplane 59

rot2Zplane Rotate to Z-plane

Description
Rotation matrix to project a set of 3D points to z-plane

Usage
rot2Zplane(vec, p)

Arguments
vec 3D normal vector
p translation from this point

Details
provides a matrix to rotate and translate a set of points to the X-Y plane. Used for internal calcula-
tions

Value
Matrix for projection

Author(s)
Jonathan M. Lees<[email protected]>

See Also
gmat

Examples

P1=runif(3)
P2=runif(3)
P3=runif(3)

PP = rbind(P1, P2, P3, rep(1, 3) )

g1 = PP[1, 1:3] - PP[3, 1:3]

g2 = PP[2, 1:3] - PP[3, 1:3]

B = unlist(AXB.prod(list(x = g1[1], y = g1[2], z = g1[3]),

list(x = g2[1], y = g2[2], z = g2[3])))
60 Sect2vex

B = B/sqrt(sum(B * B))

MF = rot2Zplane(B, P3)

UMAT = t(PP)

Sect2vex Intersect 2 Vectors

Description

Finder intersection point of two vectors in a plane

Usage

Sect2vex(V1, V2)

Arguments

V1 vector of 2 points
V2 vector of 2 points

Details

if vectors are parallel return NULL

Value

x-y location of intersection

Author(s)

Jonathan M. Lees<[email protected]>

See Also

AXB.prod
setSTRESS 61

Examples

v1 = matrix(runif(4), ncol=2)
v2 = matrix(runif(4), ncol=2)

pt = Sect2vex(v1, v2)

plot(c(v1[,1],v2[,1],pt[1] ) , c(v1[,2],v2[,2],pt[2]) , asp=1)

arrows(v1[1,1], v1[1,2], v1[2,1], v1[2,2])

arrows(v2[1,1], v2[1,2], v2[2,1], v2[2,2])

points(pt[1], pt[2], col='red', cex=2, pch=3)

setSTRESS Set Stress Tensor

Description
Set Stress Tensor: given either 3-vector, or 6-vector, create the symmetric stress tensor matrix.

Usage
setSTRESS(Stensor)

Arguments
Stensor stress tensor as a vector or a 3 by 3 matrix, a 3-vector (principal stresses) or a
6-vector (principal and off diagonal in row-order.

Details
Can be either three components of diagonal, or six components of the stress tensor. If the number
of elements is neither 3 nor 6, returns NULL and an error message.

Value
List: eigen value decomposition

Author(s)
Jonathan M. Lees<[email protected]>
62 Showfry

Examples

ES = setSTRESS(c(12, -6, 3) )

ES = setSTRESS(c(12, -6, 3, 3, 6, 1) )

Showfry Show Fry Diagrams

Description
Show Fry Diagrams with random data

Usage
Showfry(RDAT, shear = matrix(c(1, 1.2, 0, 1)), rad = 75)

Arguments
RDAT data list
shear 2D shearing matrix
rad radius of points from the center from which to select the points for analysis.

Details
The original data is deformed and a circular subset is extracted for analysis. This is to show that the
shape of the data does not affect the assessment of the fry ellipse. Plots input data and fry diagram,
side by side.

Value
graphical side effects

Author(s)
Jonathan M. Lees<[email protected]>

References
Fry, N., (1979) <http://dx.doi.org/10.1016/0040-1951(79)90135-5> Random point distributions and
strain measurement in rocks Tectonophysics, 60:89-105.
stress 63

See Also

dofry, plotfry, xtractlip

Examples

RDAT = randFRY(400, LIM=c(0,0, 200, 200) , rlen=5 )

length(RDAT$x)
plot(RDAT$x, RDAT$y, asp=1, pch=".", cex=2)

u = par( no.readonly = TRUE)

par(mfrow=c(3,2))
shr = 0.0
simpleshear = matrix(c(1, shr, 0, 1), ncol=2)

Showfry(RDAT, simpleshear, 75)

shr = 1.2
simpleshear = matrix(c(1, shr, 0, 1), ncol=2)

Showfry(RDAT, simpleshear, 75)

epsilon1 = 0.4
H = matrix(c(1+epsilon1, 0, 0, 1/(1+epsilon1) ), ncol=2)

Showfry(RDAT, H, 75)

par(u)

stress Stress Box

Description

Display interactive Stress Box illustrating normal and shear stress on an arbitrary plane given a
stress tensor.

Usage

stress(PPs = matrix(ncol = 4, nrow = 3), Rview = c(-130, -50),

xscale = 100, Stensor = matrix(ncol = 3, nrow = 3))
64 stress

Arguments
PPs 3Points in 3 by 4 matrix
Rview Viewing matrix
xscale arbitrary scale
Stensor stress tensor

Details
Interactive program to examine stress. To change the plane orientation, click on one of the points
and then on a new position along the axis selected.
If a stress tensor is provided, then a second graphics device is required to show the Mohr’s circle.

Value
Graphical Side effects

Note
Uses RPMG for interaction.

Author(s)
Jonathan M. Lees<[email protected]>

See Also
pstart, PLOTbox, PLOTplane, NORMvec

Examples

## Not run:
##### no stress tensor provided => no mohr's circle
stress()

######################### run program with a stress tensor

Stensor = matrix(c(
15, 0, 0,
0, 10, 0,
0, 0, 5), ncol=3)

stress(Stensor=Stensor)

P1 = c(0.2, 1, 1, 0)
P2 = c(1, 0.1, 1, 0)
P3 = c(1, 1, 0.4, 0)

S = stressSETUP(P1, P2, P3, xscale=30 )

stressSETUP 65

stress(PPs = S$PPs, Rview =S$Rview,

xscale = S$xscale, Stensor=Stensor )

## End(Not run)

stressSETUP Setup Stress Box

Description
Setup default stress box, plane information and normal vector 3d plotting glyph

Usage
stressSETUP(P1=c(.2, 1,1,0 ), P2=c(1, .1,1,0), P3=c(1, 1,.4,0), xscale=30)

Arguments
Arguments are optional
4-vector, point 1
P1
P2 4-vector,point 2
P3 4-vector,point 3
xscale scale factor for plotting

Details
Initialize the stress set up.

Value
List:
xscale arbitrary scale
Rview viewing rotation matrix
BOX Box coordinates, scaled
AX XYZ Axis coordinates
Rbox rotated box
Rax XYZ rotated axes
PPs Points along the Box axes
Rp rotated points
aglyph 3D glyph for plotted norm
66 tauline

Author(s)
Jonathan M. Lees<[email protected]>

See Also
stress, PLOTbox, PLOTplane, NORMvec

Examples

S = stressSETUP()
pstart()

PLOTbox(S$Rax, S$Rbox, axcol= 'green', boxcol= 'purple')

pstart()

PLOTplane(S$Rp, planecol="brown")
PLOTbox(S$Rax, S$Rbox, axcol= 'green', boxcol= 'purple')

NORMvec(S$PPs, S$xscale, S$Rview, S$aglyph, add=TRUE)

tauline Shear Stress along Line

Description
Calculate the shear stress along an arbitrary line in a plane with stress orientation

Usage
tauline(Rp, P1, P2, Rview, ES, NN)
tauplane(Rp, L, Rview, ES, NN)

Arguments
Rp rotated points describing plane
P1 point 1 extracted from screen (locator)
P2 point 2 extracted from screen
Rview rotation matrix for viewing
ES eigen value decomposition from eigen
NN normal vector to plan in unrotated coordinates
L list locations (x,y) in the figure, projected to the plane
tauline 67

Details
Used internally in stress. When the plan is plotted, if two points are located on the figure, the points
are positions on the plan and un-rotated using the Rview matrix. Then the shear stress in the plan
along that line is calculated and returned.

Value
shear stress along the line indicated

Author(s)
Jonathan M. Lees<[email protected]>

See Also
stress,NORMvec

Examples

S= stressSETUP()

pstart()

PLOTplane(S$Rp, planecol="brown")
PLOTbox(S$Rax, S$Rbox, axcol= 'green', boxcol= 'purple')

## L = locator(2)

L=list()
L$x=c(-13.6305297057, 52.6412739525)
L$y=c(26.2697350325,32.4501696158)

Stensor = matrix(c(
15, 0, 0,
0, 10, 0,
0, 0, 5), ncol=3)

P1 = list(x=L$x[1], y=L$y[1])
P2 = list(x=L$x[2], y=L$y[2])

ES = eigen(Stensor)
NN = NORMvec(S$PPs, S$xscale, S$Rview, aglyph=S$aglyph, add=FALSE)
68 TriangleCenter

tauline(S$Rp, P1, P2, S$Rview, ES, NN)

TriangleCenter Triangle Center

Description
Extract Triangle center in 3D

Usage
TriangleCenter(P1, P2, P3, A1= 0, A2= 360, KNum=10)

Arguments
P1 3-vector, point(x,y,z)
P2 3-vector, point(x,y,z)
P3 3-vector, point(x,y,z)
A1 degrees, initial angle in plane(default=0)
A2 degrees, final angle in plane(default=360)
KNum Divisor Number to divide range by (default=10)

Details
Program rotates the object to the X-Y plane and does calculations in 2D, then rotates back.

Value
Center x-y of center of the inscribed circle
r radius of inscribed
Cinscribed inscribed circle points around center
CIRCUM x-y of center of the circumscribed circle

Author(s)
Jonathan M. Lees<[email protected]>

See Also
TriangleInfo
TriangleInfo 69

Examples

S = stressSETUP()
pstart()

PLOTbox(S$Rax, S$Rbox, axcol= 'green', boxcol= 'purple')

pstart()

PLOTplane(S$Rp, planecol="brown")
PLOTbox(S$Rax, S$Rbox, axcol= 'green', boxcol= 'purple')

NORMvec(S$PPs, S$xscale, S$Rview, S$aglyph, add=TRUE)

P1 = S$PPs[1, 1:3]
P2 = S$PPs[2, 1:3]
P3 = S$PPs[3, 1:3]

BV = TriangleCenter(S$PPs[1,1:3],S$PPs[2,1:3], S$PPs[3,1:3] )

CIRCview = BV$Cinscribed

lines(CIRCview[,1], CIRCview[,2], col='purple')

cview = BV$Center

points(cview[1,1], cview[1,2])

TriangleInfo Triangle Information

Description
Given a triangle (three non-colinear points, return info that is useful

Usage
TriangleInfo(P1, P2 = c(0, 1), P3 = c(1, 0), add = FALSE)

Arguments
P1 vector or list(x,y) of 2D point 1
P2 vector or list(x,y) of 2D point 2
P3 vector or list(x,y) of 2D point 3
add logical, if TRUE add a variety of lines to the plot
70 TriangleInfo

Details
If either P1 P2 or P3 are an x,y list, they are converted to vectors.
If P2 and P3 are missing, P1 contains all the points. Input can be list of 3 x,y values, a 3 by 2 matrix
.

Value
list
BI x,y location of center of inscribed circle
CIRCUM x,y location of center of circumscribed circle
IH x,y location of Intersection of bisectors
CEN centroid location
r radius of inscribed circle
R radius of circumscribed circle
AngBis loci of vectors bisecting each corner on opposite leg
H lengths of altitudes
M lengthsof medians
TEE lengths of perpendiculars
Area Area of triangle

Author(s)
Jonathan M. Lees<[email protected]>

References
<http://en.wikipedia.org/wiki/Triangle_center>
<http://en.wikipedia.org/wiki/Encyclopedia_of_Triangle_Centers>

See Also
Intersect2points, Sect2vex, AXB.prod, TriangleCenter, rot2Zplane

Examples

P1 = runif(2)
P2 = runif(2)
P3 = runif(2)

theX = c(P1[1],P2[1], P3[1])

theY = c(P1[2],P2[2], P3[2])
vecproj 71

plot(theX , theY, asp=1)

points(theX , theY)
text(theX , theY, labels=1:3, pos=3)
lines(c(theX, theX[1]), c(theY, theY[1]) )

TriangleInfo(P1, P2, P3, add=TRUE)

##### TriangleInfo(rbind(P1, P2, P3), add=TRUE)

vecproj Vector Projection

Description
Vector Projection information, such as angle and distances between points

Usage
vecproj(P1, P2)

Arguments
P1 Point 1
P2 Point 2

Details
The distances returned are the legs of right right triangles where the cosine of the angle is used to
get the projection distance of the opposite side on the specified direction. See the example for an
illustration.

Value
cang=cang, angrad=angrad, angdeg=angdeg, dis1=d1, dis2=d2

cang cosine of angle between points

angrad angle, radians
angdeg angle, degrees
dis1 distance
dis2 distance
72 vecproj

Author(s)
Jonathan M. Lees<[email protected]>

See Also
perpproj

Examples

P1 = c(2, 3)
P2 = c(5, 2)

I = vecproj(P1, P2)

plot(c(0, P1[1], P2[1]), c(0, P1[2], P2[2]), asp=1, ann=FALSE)

arrows(0, 0, P1[1], P1[2], length=.1)

arrows(0, 0, P2[1], P2[2], length=.1)

text(P1[1], P1[2], "Point 1", pos=3)

text(P2[1], P2[2], "Point 2", pos=3)

j1 = atan2(P1[2], P1[1])*180/pi
j2 = atan2(P2[2], P2[1])*180/pi

L1 = vlength(P1)
L2 = vlength(P2)

A = GEOmap::darc(L1*.2, j1, j2, 0, 0, n=1)

lines(A)
an = length(A$x)
arrows(A$x[an-1] , A$y[an-1] ,A$x[an] , A$y[an] , length=.08 )

text(A$x[an/2] , A$y[an/2], labels=format(I$angdeg, digits=4) , pos=4)

V1 = c( 0,P1[1], 0, P1[2])
V2 = c( 0,P2[1], 0, P2[2])

PP = perpproj( V1, V2, add=FALSE )

arrows(P1[1],P1[2],PP$P2[1], PP$P2[2], length=.07, lty=2, col='red')

arrows(P2[1],P2[2],PP$P1[1], PP$P1[2], length=.07, lty=2, col='blue')

labelLine( c(0, 0) , PP$P2 , lab="dis1", dinch = .25, aty=1,

acol='blue', above=FALSE )
vlength 73

labelLine( c(0, 0) , PP$P1 , lab="dis2", dinch = .25, aty=1,

acol='blue' )

vlength vector length

Description

calculate euclidian vector length

Usage

vlength(a)

Arguments

a vector

Value

Euclidian Length

Author(s)

Jonathan M. Lees<jonathan.lees.edu>

Examples

vlength(c(23, 43))
74 xtractlip

xtractlip Extract Convex Hull Ellipse from fry

Description
Extract Convex Hull Ellipse from fry-diagram

Usage
xtractlip(AF)

Arguments
AF x-y List out put of plotfry

Details
To get closest points to center, program cycles around in a circular manner pulling out the closest
points. These points are used to estimate the chull ellipse.

Value
List: see output of ellipsoidhull: an object of class ’"ellipsoid"’, basically a ’list’ with several
components

Author(s)
Jonathan M. Lees<[email protected]>

References
Fry, N., (1979) <http://dx.doi.org/10.1016/0040-1951(79)90135-5> Random point distributions and
strain measurement in rocks Tectonophysics, 60:89-105.

See Also
ellipsoidhull

Examples

RDAT = randFRY(400, LIM=c(0,0, 200, 200) , rlen=5 )

length(RDAT$x)
plot(RDAT$x, RDAT$y, asp=1, pch=".", cex=2)
flag = sqrt( (RDAT$x-mean(RDAT$x))^2 + (RDAT$y-mean(RDAT$y))^2)<75

DAT = list(x=RDAT$x[flag], y=RDAT$y[flag])

x = DAT$x
y = DAT$y
xtractlip 75

plot(x,y, asp=1, pch=21, col='red', bg='gold', ann=FALSE, axes=FALSE)

FF = dofry(DAT$x, DAT$y )
AF = plotfry(FF, dis=30)

Z = xtractlip(AF)

lines(cluster::predict.ellipsoid(Z$hull), col='red')
Index

∗Topic datasets points2line, 49

Glines, 24 PolarDecomp, 50
PPoints, 52 pstart, 53
PXY, 54 randFRY, 55
∗Topic misc randpoles, 56
annotatebox, 4 REplane, 57
annotateplane, 4 rev2RH, 58
AXB.prod, 5 rot2Zplane, 59
BMOD, 6 Sect2vex, 60
centroid, 7 setSTRESS, 61
desh, 8 Showfry, 62
DGzx, 9 stress, 63
dircheck, 11 stressSETUP, 65
DO.DYKE, 12 tauline, 66
DO.HALFSPACE, 13 TriangleCenter, 68
dofry, 13 TriangleInfo, 69
DoMohr, 15 vecproj, 71
DoMohrFig1, 16 vlength, 73
xtractlip, 74
draw.brachiopod, 17
∗Topic package
elipfit, 19
geophys-package, 3
erf, 20
flipZEE, 21 get.heat (get.heat2), 23
get.brachiopod, 22
get.heat2, 23 annotatebox, 4
heat.sol, 26 annotateplane, 4
labelLine, 27 AXB.prod, 5
lipper, 28
Maxstress, 29 BMOD, 6
ModelG, 31
centroid, 7
mogi1, 32
mogiM, 34 desh, 8
mohrleg, 36 DGzx, 9
NinePointCircle, 37 dircheck, 11
NORMvec, 38 DO.DYKE, 12
okada85, 40 DO.HALFSPACE, 13
perpproj, 42 dofry, 13
PLOTbox, 44 DoMohr, 15
plotfry, 46 DoMohrFig1, 16
PLOTplane, 47 draw.brachiopod, 17

76
INDEX 77

elipfit, 19 stress, 63
erf, 20 stressSETUP, 65
erfc (erf), 20
erfinv (erf), 20 tauline, 66
tauplane (tauline), 66
flipZEE, 21 TriangleCenter, 68
TriangleInfo, 69
geophys (geophys-package), 3
geophys-package, 3 vecproj, 71
get.brachiopod, 22 vlength, 73
get.heat2, 23
Glines, 24 xtractlip, 74

heat.sol, 26

labelLine, 27
lipper, 28

Maxstress, 29
ModelG, 31
mogi1, 32
mogiM, 34
mohrleg, 36

NinePointCircle, 37
NORMvec, 38

okada85, 40

perpproj, 42
philpotts.erf (erf), 20
PLOTbox, 44
plotfry, 46
PLOTplane, 47
pointproj (perpproj), 42
points2line, 49
PolarDecomp, 50
PPoints, 52
pstart, 53
PXY, 54

randFRY, 55
randpoles, 56
REplane, 57
rev2RH, 58
rot2Zplane, 59

Sect2vex, 60
setSTRESS, 61
Showfry, 62