Package 'geoelectrics'

Adjust Profile Height

Description

Adjusts the height of a single profile (adds a delta value to ALL data points). This is necessary if GPS measurement heights of two profiles differ systematically.

Usage

adjustHeight(object, delta)

## S4 method for signature 'Profile'
adjustHeight(object, delta)

Arguments

object	a single Profile.
delta	positive or negative value.

Value

adjusted profile

See Also

GpsCoordinates-class, Profile-class

Examples

p3 <- new(
  "Profile",
  title = "Profile 3",
  processedData =
    new("ProcessedData",
        address = system.file("extdata/processed/p3_DipolDipol_S-N.xyz",
                  package='geoelectrics')),
  rawData =
    new("RawData",
        address = system.file("extdata/raw/p3_DipolDipol_S-N.dat",
                  package='geoelectrics')),
  measurementType = "DipolDipol",
  gpsCoordinates =
    new("GpsCoordinates",
        address = system.file("extdata/gps/p3.txt",
                  package='geoelectrics'))
)

p3 <- adjustHeight(p3, -10)

---

Calculate Relative Coordinates

Description

Calculates relative coordinates (unity: meters) from GPS coordinates (either given in UTM or Gauss Krueger). This method is used when a profile set of many profiles is instantiated.

Usage

calcRelativeCoords(coords, minLat, minLon)

Arguments

coords	exact coordinates of a single Profile.
minLat	starting point (latititude).
minLon	starting point (longitude).

Value

data frame that contains the relative coordinates (latitude and longitude).

See Also

ProfileSet-class, GpsCoordinates-class

---

Graphical User Interface of the Geoelectrics R Package

Description

This method starts a simple TclTk graphical user interface (GUI) provided by this package.

Usage

geoelectricsGui()

Examples

# geoelectricsGui()

---

Gets the Height Information for a Profile

Description

Returns the heights for certain distances along the profile (topography information).

Usage

getHeightInformation(object)

## S4 method for signature 'ProcessedData'
getHeightInformation(object)

Arguments

object

a single Profile.

Value

data frame containing distances and heights along the profile

See Also

GpsCoordinates-class, Profile-class, ProcessedData-class

Examples

data(sinkhole)

getHeightInformation(sinkhole@profiles[[1]]@processedData)

---

GPS Coordinates Class

Description

A class to handle gps coordinates.

Slots

address

address of the gps ascii file

exact

data frame that contains measured gps coordinates

relative

relative coordinates, normalized to (0,0)

lm

linear model of the measured gps coordinates

lmRelative

linear model of relative coordinates

See Also

Profile-class, ProfileSet-class, adjustHeight, calcRelativeCoords

Examples

gpsCoordinates = new('GpsCoordinates', address = system.file('extdata/gps/p1.txt',
                 package='geoelectrics'))

data(sinkhole)
sinkhole@profiles[[1]]@gpsCoordinates
sinkhole@profiles[[1]]@gpsCoordinates@address
sinkhole@profiles[[1]]@gpsCoordinates@exact
sinkhole@profiles[[1]]@gpsCoordinates@lm
sinkhole@profiles[[1]]@gpsCoordinates@relative
sinkhole@profiles[[1]]@gpsCoordinates@lmRelative

---

Levelplot of Geoelectrics Data

Description

Plots the interpolated resistance values of the geoelectrics data.

Usage

levelplot(x, data, ...)

## S4 method for signature 'Profile'
levelplot(x, dataType = "processed",
  withTopo = FALSE, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title), col = colors, breaks = 18, trafo = log,
  backtrafo = exp, aspect = "iso", ...)

## S4 method for signature 'ProfileSet'
levelplot(x, dataType = "processed",
  withTopo = FALSE, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title), col = colors, breaks = 18, trafo = log,
  backtrafo = exp, aspect = "iso", ...)

levelplotProcessedData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography"), col = colors,
  breaks = 18, trafo = log, backtrafo = exp, aspect = "iso", ...)

levelplotProcessedDataWithTopo(x, xlab = "Length [m]",
  ylab = "Height [m]", main = paste(x@title, "with topography"),
  col = colors, breaks = 18, trafo = log, backtrafo = exp,
  aspect = "iso", ...)

levelplotRawData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography (raw data)"), col = colors,
  trafo = log, aspect = "iso", ...)

Arguments

x	profile object.
data	is always NULL
...	lattice levelplot arguments.
dataType	specify whether 'processed' (default) or 'raw' data should be plotted
withTopo	TRUE if topography information is plotted
xlab	label for x-axes.
ylab	label for y-axes.
main	title to be plotted.
col	vector of colors.
breaks	number of color breaks.
trafo	transformation to be done on data (default: log).
backtrafo	back transformation to plot correct labels (default: exp).
aspect	the y/x aspect ratio (default: iso).

See Also

Profile-class

Examples

data(sinkhole)

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE)
levelplotLegendLabel()

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)
levelplotLegendLabel()

levelplot(sinkhole@profiles[[1]], dataType = 'raw')
levelplotLegendLabel()

---

Levelplot Legend Label

Description

Plots the label of the levelplot.

Usage

levelplotLegendLabel(legend.lab = "Resistivity",
  unit = expression(paste("[", Omega, "m]")))

Arguments

legend.lab	label (default: 'Resistivity').
unit	unit (default: 'Ohm*m').

See Also

levelplot

Examples

data(sinkhole)

levelplot(sinkhole@profiles[[1]])
levelplotLegendLabel()

levelplot(sinkhole@profiles[[2]])
levelplotLegendLabel()

levelplot(sinkhole@profiles[[3]])
levelplotLegendLabel()

---

Maps color to resistivity value

Description

Maps color to (resistivity) values. A minimum and maximum value can be specified.

Usage

myColorRamp(col, values, minData = min(values), maxData = max(values))

Arguments

col	Character vector of colors.
values	Numeric vector of values.
minData	Minimum value (default min(values)). All smaller values will assigned to the first color in vector col.
maxData	Maximum value (default max(values)). All higher values will assigned to the last color in vector col.

---

Parses a Processed Data File

Description

Parses .xyz files produced by the software Res2DInv. Needs to be overwritten if another processed data format is used.

Usage

parseProcessedDataFile(address, skip = 0)

Arguments

address	address of the raw data ascii file.
skip	the number of lines of the data file to skip before beginning to read data.

Value

list of two data frames: The first data frame contains points without topography (distance, depth and resistivity values). The second data frame contains points with topography (distance, height and resistivity values).

See Also

ProcessedData-class, Profile-class

Examples

fileAddress <- system.file('extdata/processed/p1_DipolDipol_SW-NE.xyz',
                   package = 'geoelectrics')

processedData = new('ProcessedData')
processedData@address = fileAddress
processedData@points <- parseProcessedDataFile(address = fileAddress)[[1]]
processedData@pointsWithTopo <- parseProcessedDataFile(address = fileAddress)[[2]]

---

Parses a Raw Data File

Description

Parses a geoelectrics raw data file created by the GeoTest software by Dr. Rauen. Needs to be overwritten if another raw data format is used.

Usage

parseRawDataFile(address, skip = 9)

Arguments

address	address of the raw data ascii file.
skip	the number of lines of the data file to skip before beginning to read data.

Value

data frame containing distance, depth and resistivity values

See Also

RawData-class, Profile-class

Examples

fileAddress <- system.file('extdata/raw/p1_DipolDipol_SW-NE.dat',
                   package = 'geoelectrics')
                   
rawData = new('RawData')
rawData@address = fileAddress
rawData@points <- parseRawDataFile(address = fileAddress)

---

Plot Geoelectrics Data Points

Description

Plots the geoelectrics data points of a profile.

Usage

## S4 method for signature 'Profile,ANY'
plot(x, dataType = "processed", withTopo = T,
  xlab = "Length [m]", ylab = "Height [m]", main = paste(x@title,
  "with topography"), asp = 1, ...)

## S4 method for signature 'ProfileSet,ANY'
plot(x, dataType = "processed",
  withTopo = T, xlab = "Length [m]", ylab = "Height [m]",
  main = paste(x@title, "with topography"), asp = 1, ...)

plotProcessedData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography"), ...)

plotProcessedDataWithTopo(x, xlab = "Length [m]", ylab = "Height [m]",
  main = paste(x@title, "with topography"), ...)

plotRawData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography"), ...)

plotRawDataWithTopo(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "with topography"),
  height = x@processedData@height, spline = TRUE, ...)

Arguments

x	profile object.
dataType	specify whether 'processed' (default) or 'raw' data should be plotted
withTopo	TRUE if topography information is plotted
xlab	label for x-axes.
ylab	label for y-axes.
main	title to be plotted.
asp	the y/x aspect ratio (default: 1).
...	plot parameters (such as pch, cex, col, ...).
height	topo data frame of distances and height.
spline	if TRUE spline interpolation is conducted.

See Also

Profile-class, plot3d, levelplot

Examples

data(sinkhole)

plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE)
plotProcessedData(sinkhole@profiles[[1]])

plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)
plotProcessedDataWithTopo(sinkhole@profiles[[1]])

plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = FALSE)
plotRawData(sinkhole@profiles[[1]])

plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = TRUE)
plotRawDataWithTopo(sinkhole@profiles[[1]])

---

3D Scatterplot of Geoelectrics Profiles

Description

Plots the interpolated resistance values of the processed data for a single profile or a set of profiles.

Usage

## S4 method for signature 'ProfileSet'
plot3d(x, title = x@title, sub = "",
  xlab = "", ylab = "", zlab = "", minData = x@minData,
  maxData = x@maxData, col = colors, trafo = log,
  psize = pointsize, ...)

## S4 method for signature 'Profile'
plot3d(x, title = "", sub = "", xlab = "",
  ylab = "", zlab = "", minData = x@processedData@minData,
  maxData = x@processedData@maxData, col = colors, trafo = log,
  psize = pointsize, ...)

Arguments

x	either an object of a single Profile or a ProfileSet.
title	title to be plotted.
sub	subtitle to be plotted.
xlab	label of the x-axes, e.g. length [m].
ylab	label of the y-axes, e.g. height above sea level [m].
zlab	label of the z-axes, e.g. length [m].
minData	mimimum value to adjust color bar.
maxData	maximum value to adjust color bar.
col	vector of colors.
trafo	transformation to be done on data (default: log).
psize	size of value points (default: 10).
...	parameters passed to points3d method of rgl package

See Also

Profile-class, ProfileSet-class, plot, levelplot

Examples

data(sinkhole)

plot3d(sinkhole@profiles[[1]])
plot3d(sinkhole)

---

Plot Profile Intersection

Description

Plots resistivity against height on and next to the intersection line between two profiles.

Usage

plotIntersect(.Object1, .Object2 = NULL,
  xlab = "Height above sea level [m]",
  ylab = expression(paste("Resistivity [", Omega, "m]")), main = "",
  trafo = log, backtrafo = exp, col = colors, pch = c(20, 20),
  type = "p", legendLoc = "bottomleft")

## S4 method for signature 'ProfileSet,ANY'
plotIntersect(.Object1, xlab, ylab, main, trafo,
  backtrafo, col, pch, type, legendLoc)

## S4 method for signature 'Profile,Profile'
plotIntersect(.Object1, .Object2 = NULL,
  xlab = "Height above sea level [m]",
  ylab = expression(paste("Resistivity [", Omega, "m]")), main = "",
  trafo = log, backtrafo = exp, col = colors, pch = c(20, 20),
  type = "p", legendLoc = "bottomleft")

Arguments

.Object1	either a single Profile or a ProfileSet.
.Object2	either a second single Profile or NULL if .Object1 is of type ProfileSet.
xlab	label of the x-axes, e.g. length [m].
ylab	label of the y-axes, e.g. height above sea level [m].
main	title to be plotted.
trafo	transformation to be done on data (default: log).
backtrafo	back transformation to plot correct labels (default: exp).
col	character vector of colors.
pch	numeric vector of plotting symbols.
type	plot type (default "p" for points). "b" for both points and lines, "c" for empty points joined by lines, "o" for overplotted points and lines, "s" and "S" for stair steps and "h" for histogram-like vertical lines. Finally, "n" does not produce any points or lines.
legendLoc	legendLocation (default "bottomleft").

See Also

ProfileSet-class

Examples

data(sinkhole)

plotIntersect(sinkhole)
plotIntersect(sinkhole@profiles[[1]], sinkhole@profiles[[2]])

---

Plots Legend

Description

Plots the legend for resistivity values.

Usage

plotLegend(.Object, legend.lab = expression(paste("Resistivity [", Omega,
  " m]")), minData = 0, maxData = 999999, breaks = NULL,
  legend.line = 2.2, nlevel = 18, lab.breaks = c(), horizontal = T,
  col = colors, trafo = log, backtrafo = exp, ...)

## S4 method for signature 'ProfileSet'
plotLegend(.Object, legend.lab,
  minData = .Object@minData, maxData = .Object@maxData)

## S4 method for signature 'Profile'
plotLegend(.Object, legend.lab,
  minData = .Object@processedData@minData,
  maxData = .Object@processedData@maxData)

Arguments

.Object	either a single Profile or a ProfileSet.
legend.lab	label of legend (default: expression(paste("Resistivity [", Omega, "]"))).
minData	minimum value.
maxData	maximum value.
breaks	Break points in sorted order to indicate the intervals for assigning the colors. Note that if there are nlevel colors there should be (nlevel+1) breakpoints. If breaks is not specified (nlevel+1) equally spaced breaks are created where the first and last bin have their midpoints at the minimum and maximum values in z or at zlim.
legend.line	distance in units of character height (as in mtext) of the legend label from the color bar. Make this larger if the label collides with the color axis labels.
nlevel	number of color levels.
lab.breaks	number of breaks.
horizontal	If false legend will be a vertical strip on the right side. If true (default) the legend strip will be along the bottom.
col	vector of colors.
trafo	transformation to be done on data (default: log). For linear scale: function(x) x.
backtrafo	back transformation to plot correct labels (default: exp). For linear scale: function(x) x.
...	image.plot arguments.

See Also

Profile-class, ProfileSet-class, plot3d,

Examples

data(sinkhole)

plotLegend(sinkhole)

# for linear scale:
plotLegend(sinkhole@profiles[[1]],
           trafo=function(x) x,
           backtrafo=function(x) x,
           minData=100, maxData=50000)

---

Processed Data Class

Description

A class to handle processed geoelectrics data in ascii format. The processed data class parses .xyz files produced by the software Res2DInv. If you want to use another format, overwrite the parseProcessedDataFile method.

Slots

address

address of the processed ascii file

points

data frame that contains positions and values withouth topography information

pointsWithTopo

data frame that contains positions and values with topography information

height

data frame that contains topography information (distances and heights). It is reconstructed from .xyz-file.

minData

minimum value

maxData

maximum value

See Also

parseProcessedDataFile, Profile-class, ProfileSet-class

Examples

processedData = new('ProcessedData',
                     address = system.file('extdata/processed/p1_DipolDipol_SW-NE.xyz',
                     package='geoelectrics'))

data(sinkhole)
sinkhole@profiles[[1]]@processedData
sinkhole@profiles[[1]]@processedData@points
sinkhole@profiles[[1]]@processedData@pointsWithTopo
sinkhole@profiles[[1]]@processedData@height
sinkhole@profiles[[1]]@processedData@minData
sinkhole@profiles[[1]]@processedData@maxData

---

Profile Class

Description

A class to handle a single profile.

Slots

title

title of the profile (e.g. Profile 1).

number

index of the profile.

processedData

object of Processed Data Class (ProcessedData-class).

rawData

object of Raw Data Class (RawData-class).

measurementType

type of measurement (e.g. Dipole Dipole, Wenner, ...).

gpsCoordinates

object of GpsCoordinates Class (GpsCoordinates-class).

See Also

ProcessedData-class, RawData-class, GpsCoordinates-class, plot3d, plot

Examples

p1 <- new('Profile',
           title = 'Profile 1',
           processedData =
             new('ProcessedData', address = system.file('extdata/processed/p1_DipolDipol_SW-NE.xyz',
                                      package='geoelectrics')),
           rawData =
             new('RawData', address = system.file('extdata/raw/p1_DipolDipol_SW-NE.dat',
                                      package='geoelectrics')),
           measurementType = 'DipoleDipole',
           gpsCoordinates =
             new('GpsCoordinates', address = system.file('extdata/gps/p1.txt',
                                             package='geoelectrics')))

p1@title
p1@processedData
p1@rawData
p1@measurementType
p1@gpsCoordinates

plot3d(p1)

---

Profile Set Class

Description

A class to handle a collection of many profiles.

Slots

title

title to plot

profiles

list that contains objects of class Profile (Profile-class)

minLat

minimum latitude value of all profiles

minLon

minimum longitude value of all profiles

minData

minimum data value of all profiles

maxData

maximum data value of all profiles

See Also

Profile-class, plot3d

Examples

# sinkhole <- new('ProfileSet',
#                profiles = list(p1, p2, p3),
#                title='Sinkhole')

data(sinkhole)
plot3d(sinkhole)

---

Raw Data Class

Description

A class to handle geoelectrics raw data. The raw data class parses .dat files provided by the GeoTest software by Dr. Rauen. If you want to use another format, overwrite the parseRawDataFile method.

Slots

address

address of the raw data ascii file.

points

data frame that contains raw data resistance values and their positions (distance and depth).

See Also

parseRawDataFile, Profile-class, ProfileSet-class

Examples

rawData = new('RawData', address = system.file('extdata/raw/p1_DipolDipol_SW-NE.dat',
          package='geoelectrics'))

data(sinkhole)
sinkhole@profiles[[2]]@rawData
sinkhole@profiles[[2]]@rawData@address
sinkhole@profiles[[2]]@rawData@points

---

Filled Sinkhole

Description

Geoelectrics profiles measured at a filled sinkhole. This data set contains an object of the ProfileSet class.

Format

Object of Profile Set class including three Profiles.

See Also

ProfileSet-class, Profile-class, plot3d, plot, levelplot, plotLegend, plotIntersect

Examples

data(sinkhole)

# Plot the processed data in three dimensions
plot3d(sinkhole)

# Plot legend for the profile set
plot.new()
plotLegend(sinkhole)

# Plot raw data of profile 1
plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = FALSE, 
     main = 'Profile 1', ylab = 'Depth [m]')

plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = TRUE)

levelplot(sinkhole@profiles[[1]], dataType = 'raw')
levelplotLegendLabel()

# Plot processed data of profile 1
plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE,
     main = 'Profile 1', ylab = 'Depth [m]')

plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE)
levelplotLegendLabel()

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)
levelplotLegendLabel()

# Compare processed data values on the intersection line between two profiles
plotIntersect(sinkhole)

---