Package 'GrimR'

Title: Calculate Optical Parameters from Spindle Stage Measurements
Description: Calculates optical parameters of crystals like the optical axes, the axis angle 2V, and the direction of the principal axes of the indicatrix from extinction angles measured on a spindle stage mounted on a polarisation microscope stage. Details of the method can be found in Dufey (2017) <arXiv:1703.00070>.
Authors: Florian Dufey [aut, cre]
Maintainer: Florian Dufey <[email protected]>
License: GPL-3
Version: 0.5
Built: 2024-12-01 08:41:47 UTC
Source: CRAN

Help Index

Bloss73

Description

Adularia data from: Bloss, F. D., and D. Riess. "Computer determination of 2V and indicatrix orientation from extinction data." American Mineralogist 58 (1973): 1052-1061.

Usage

data("Bloss73")

Format

A data frame with 19 observations on the following 2 variables.

S

a numeric vector

MS

a numeric vector

Examples

res<-fit.joel(Bloss73,MR=180.95,cw="ccw",optimMR=FALSE)

Data for Topaz by Carman

Description

Data from F. Donald Bloss, "The spindle stage, principles and practice", Cambridge UP, Cambridge, 1981, p. 226, for Topaz provided by Prof. Carman.

Usage

data("Carman")

Format

A data frame with 36 observations of the following 2 variables.

S

a numeric vector

MS

a numeric vector

Examples

res<-fit.joel(Carman,cw="ccw",optimMR=TRUE)

excalibrII

Description

Example data for Tiburon Albite from Bartelmehs, K. L., et al. "Excalibr II." Zeitschrift fuer Kristallographie 199.3-4 (1992): 185-196.

Usage

data("excalibrII")

Format

A data frame with 19 observations on the following 2 variables.

S

a numeric vector

MS

a numeric vector

Examples

res<-fit.joel(excalibrII,MR=180.15,cw="ccw",optimMR=FALSE)

Function fit.joel

Description

Calculate the angle between the optical axes 2V, the optical axes in cartesian and polar coordinates and the principal axes of the dielectric tensor in cartesian and polar coordinates.

Usage

fit.joel(Data, MR = NULL, cw = c("ccw", "cw"),optimMR=FALSE)

Arguments

Data

(data frame) containing the spindle angles S and the extinction angles ES
MR

(numeric) The reference azimuth; If numeric and optimMR==TRUE, this value will be used as a starting value for further optimization. If NULL, a starting value will be guessed.

cw

(character) string "cw" for a clockwise graduated table, "ccw" for a counter-clockwise graduated table (default)
optimMR

(logical) If FALSE, the provided MR will be used without further refinement, if TRUE, the MR will be refined so as to minimize the deviance

Value

(list) with elements:

coeffs

list of the fitted parameters
covmat

matrix of covariances of the parameters
delta2V

list of estimate of 2V, its standard deviation and upper and lower confidence limits
kart

data frame with cartesian coordinates of the axes, sd, and confidence intervals
sphaer

data frame with S and ES values of the axes, sd, and confidence intervals
principal

data frame with S and MS angles to bring axes into extinction
Extinctions

data frame with S, MS, ES, calculated ES and ES-ES calculated
Wulffdat

data necessary to create a plot on the Wulff stereonet

Author(s)

Florian Dufey <[email protected]>

Examples

# With 360 deg. data:
res<-fit.joel(Carman,MR=NULL,cw="ccw",optimMR=TRUE)
Wulffplot(res) #Plot data on a Wulff net
#with 180 degree data:
res<-fit.joel(Gunter,MR=-0.89,cw="cw",optimMR=FALSE)
Wulffplot(res) #Plot data on a Wulff net

Data from Gunter et al.

Description

Gunter, Mickey E., et al. "Results from a McCrone spindle stage short course, a new version of EXCALIBR, and how to build a spindle stage." MICROSCOPE-LONDON THEN CHICAGO-. 52.1 (2004): 23-39.

Usage

data("Gunter")

Format

A data frame with 19 observations on the following 2 variables.

S

a numeric vector

MS

a numeric vector

Examples

res<-fit.joel(Gunter,MR=-0.89,cw="cw",optimMR=FALSE)

Circle Plot

Description

Add a circle to a plot, with cross-hairs

Usage

pcirc(gcol = "black", border = "black", ndiv = 36)

Arguments

gcol

color of crosshairs
border

border color

ndiv

number of divisions for the circle

Value

no return values, used for side effects

Author(s)

Jonathan M. Lees <[email protected]>

Examples

plot(c(-1,1),c(-1,1))
pcirc(gcol = "black", border = "black", ndiv = 36)

Function Wulffnet

Description

Function Wulffnet Plot a Wulffnet modified from RFOC package; Wulff net rotated

Usage

Wulffnet(add = FALSE, col = gray(0.7), border = "black", lwd = 1)

Arguments

add

Logical, TRUE=add to existing plot
col

color
border

border color
lwd

line width

Details

Plots equal-angle stereonet as opposed to equal-area. In comparison to the original Wnet function from RFOC package, Wulff net is rotated by 90 degrees so as to conform with custom in mineralogy.

Value

graphical side effects

Author(s)

Jonathan M. Lees <[email protected]>, Florian Dufey <[email protected]>

Examples

Wulffnet(add = FALSE, col = gray(0.7), border = "black", lwd = 1)

Function Wulffplot

Description

Function Wulffplot Plot the S and ES values of measured points calculated points and of all axes on a Wulff stereonet

Usage

Wulffplot(x)

Arguments

x

(list) Output list from the fit.joel function

Author(s)

Florian Dufey <[email protected]>

Examples

res<-fit.joel(Gunter,MR=-0.89,cw="cw",optimMR=FALSE)
Wulffplot(res)

Function Wulffpoint Plots Points in the Wulffnet given S and ES

Description

Function Wulffpoint Plots Points in the Wulffnet given S and ES

Usage

Wulffpoint(ES, S, col = 2, pch = 5, bg="white" , lab = "")

Arguments

ES

(numeric) azimuth (extinction angle) in degrees
S

(numeric) spindle angle in degrees
col

color
pch

symbol type
lab

label
bg

background colour of symbol

Author(s)

Florian Dufey <[email protected]>

See Also

Wnet

Examples

Wulffnet()
Wulffpoint(23, 34)