Package 'xRing' reference manual

Title:	Identify and Measure Tree Rings on X-Ray Micro-Density Profiles
Description:	Contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface (GUI) to visualize density profiles and correct tree-ring borders. Campelo F, Mayer K, Grabner M. (2019) <doi:10.1016/j.dendro.2018.11.002>.
Authors:	Filipe Campelo [aut, cre, cph] , Konrad Mayer [ctb]
Maintainer:	Filipe Campelo <[email protected]>
License:	GPL (>= 2)
Version:	0.1.1
Built:	2025-01-23 03:08:56 UTC
Source:	https://github.com/cran/xRing

Add Tree-Ring Border(s)

Description

Add a tree-ring border by defining the position of the new border

Usage

addRing(object, x, series = NULL)
addRing(object, x, series = NULL)

Arguments

`object`	an object of class "xRingList" or "xRing"
`x`	the position (number of the resp. pixel(s)) to set the new tree-ring border
`series`	the name of the series to be changed when the `object` is "xRingList", by default is `NULL`

Value

a "xRing" or "xRingList" object with a tree-ring border added at the position x for the series given by series argument

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
plot(PaPi$"AFO1001a")
PaPi$AFO1001a <- removeRing(PaPi$AFO1001a, 47)
plot(PaPi$"AFO1001a")
PaPi <- addRing(PaPi, series = "AFO1001a", x = 47)
plot(PaPi$"AFO1001a")

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
plot(PaPi$"AFO1001a")
PaPi$AFO1001a <- removeRing(PaPi$AFO1001a, 47)
plot(PaPi$"AFO1001a")
PaPi <- addRing(PaPi, series = "AFO1001a", x = 47)
plot(PaPi$"AFO1001a")

Calibrate Film

Description

Convenience function to do the whole calibration of a densitometry image in one function call internally calling getSteps and fitCalibrationModel

Usage

calibrateFilm(
  im,
  thickness = stepIncrease(0.24, 7),
  density = 1.2922,
  plot = TRUE,
  auto = FALSE,
  nPixel = 50,
  plotAuto = FALSE,
  ...
)
calibrateFilm(
  im,
  thickness = stepIncrease(0.24, 7),
  density = 1.2922,
  plot = TRUE,
  auto = FALSE,
  nPixel = 50,
  plotAuto = FALSE,
  ...
)

Arguments

`im`	a grayscale image
`thickness`	a vector specifying the thickness of the calibration wedge at each step
`density`	the density of the reference material (i.e. the calibration wedge)
`plot`	if TRUE the calibration model is displayed
`auto`	logical. If TRUE, automatic detection of the steps given a line is carried out. Use with care
`nPixel`	if 'auto = TRUE': number of pixels gives the line width
`plotAuto`	if TRUE the automatic detection of the grayscale values is displayed
`...`	further arguments to be passed to loess

Value

an object of class 'loess' representing the film calibration

Examples

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # display the image
  imDisplay(im)

  # calibrate the film:
  calibration <- calibrateFilm(im,
    thickness = stepIncrease(0.24, 7),
    density = 1.2922,
    plot = TRUE
  )
}

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # display the image
  imDisplay(im)

  # calibrate the film:
  calibration <- calibrateFilm(im,
    thickness = stepIncrease(0.24, 7),
    density = 1.2922,
    plot = TRUE
  )
}

Combine Fragments

Description

This function combines fragments by series

Usage

combineFrag(x, frag = NULL)
combineFrag(x, frag = NULL)

Arguments

`x`	an "xRingList" object
`frag`	integer, defines the character position within the series name that identifies fragments. If `NULL` the function considers series with names having one more character as fragments

Value

an object of class "xRingList" with merged fragments

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi.merge <- combineFrag(PaPi, frag = 9)

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi.merge <- combineFrag(PaPi, frag = 9)

Correct Tree-Ring Borders Interactively

Description

A Graphical User Interface (GUI) to correct tree-ring borders

Usage

correctRings(x, chrono = NULL)
correctRings(x, chrono = NULL)

Arguments

`x`	an `xRingList` object
`chrono`	a data.frame with a reference chronology, if `NULL` a reference chronology is calculated using tree-ring width series from `x`

Details

This function uses the tkRplot function (tkRplotR package) to interact with X-ray microdensity profiles.

Value

an xRingList object

Examples

if (interactive()) {
  data(PaPiRaw)
  data(PaPiSpan)
  PaPi <- detectRings(PaPiRaw, PaPiSpan)
  PaPiCorrect <- correctRings(PaPi)
}

if (interactive()) {
  data(PaPiRaw)
  data(PaPiSpan)
  PaPi <- detectRings(PaPiRaw, PaPiSpan)
  PaPiCorrect <- correctRings(PaPi)
}

Detect the Transition from Earlywood to Latewood

Description

This function detects the end of earlywood and the start of latewood

Usage

detectEwLw(x, ew = 0.5, lw = NULL)
detectEwLw(x, ew = 0.5, lw = NULL)

Arguments

`x`	an "xRingList" object
`ew`	defines the end of earlywood as the ratio of the density range. The default value is 0.5, which means that the end of earlywood is placed at the point where the density is half the range between the minimum and maximum density values within an annual ring
`lw`	defines the start of latewood, the default value is `NULL`. When ew is 0.5 and lw is `NULL` the boundary between earlywood and latewood is placed where the density is half the range between the minimum and maximum density values within an annual ring

Value

an "xRingList" object with limits.ew and limits.lw added.

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi.merge <- combineFrag(PaPi, frag = 9)
PaPiRings <- detectEwLw(PaPi.merge, ew = 0.5)

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi.merge <- combineFrag(PaPi, frag = 9)
PaPiRings <- detectEwLw(PaPi.merge, ew = 0.5)

Detect Tree-Ring Borders

Description

This function identifies tree-ring borders on X-ray microdensity profiles.

Usage

detectRings(x, y = NULL, k = 3, minTrw = 3, threshold = 0.215)
detectRings(x, y = NULL, k = 3, minTrw = 3, threshold = 0.215)

Arguments

`x`	a dataframe with X-ray microdensity profiles or an "xRingList" object
`y`	a dataframe with the first and last year in columns and the series in rows, is `NULL` by default
`k`	width of the rolling window to find the local maximum and minimum (for more details please see the help of `getBorders` function)
`minTrw`	integer width of the narrowest tree-ring, rings narrower than this value will not be considered
`threshold`	the minimum difference between local maximum and minimum density to identify a tree-ring border

Details

This function uses the getBorders function to identify tree-ring borders based on the difference between local maximum and minimum density.

Value

detectRings returns an "xRingList" object, an S3 class with "xRing" lists as members, with the following elements:

span first and last year

trw gives the tree-ring width

name a string giving the series name

limits a vector with the position of the tree-ring borders

years a vector with the calendar year

profile.raw a vector with the input

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- toxRingList(PaPiRaw, PaPiSpan)
PaPi <- detectRings(PaPi)
# give the same
PaPi <- detectRings(PaPiRaw, PaPiSpan)
# Because the last year is not supplied the last year for all series is the last calendar year
# as.numeric(format(Sys.time(), "%Y"))-1
PaPi <- detectRings(PaPiRaw)

data(PaPiRaw)
data(PaPiSpan)
PaPi <- toxRingList(PaPiRaw, PaPiSpan)
PaPi <- detectRings(PaPi)
# give the same
PaPi <- detectRings(PaPiRaw, PaPiSpan)
# Because the last year is not supplied the last year for all series is the last calendar year
# as.numeric(format(Sys.time(), "%Y"))-1
PaPi <- detectRings(PaPiRaw)

Fit a Calibration Curve

Description

Fit a model to calibrate a film from X-ray densitometry.

Usage

fitCalibrationModel(
  grayvalues,
  thickness = stepIncrease(0.24, 7),
  density = 1.2922,
  plot = TRUE,
  ...
)
fitCalibrationModel(
  grayvalues,
  thickness = stepIncrease(0.24, 7),
  density = 1.2922,
  plot = TRUE,
  ...
)

Arguments

`grayvalues`	a numeric vector containing the gray values of the steps of the calibration wedge at various thicknesses given by the argument 'thickness'
`thickness`	a vector specifying the thickness of the calibration wedge at each step.
`density`	the density of the reference material
`plot`	if TRUE the calibration model is displayed
`...`	further arguments to be passed to loess

Value

an object of class 'loess' representing the film calibration

Examples

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # display the image
  imDisplay(im)

  # get the grayvalues from the calibration wedge on the film
  grayvalues <- getSteps(im, 7)

  # calibrate the film by fitting a model:
  calibration <- fitCalibrationModel(grayvalues,
    thickness = stepIncrease(0.24, 7),
    density = 1.2922,
    plot = TRUE
  )
}

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # display the image
  imDisplay(im)

  # get the grayvalues from the calibration wedge on the film
  grayvalues <- getSteps(im, 7)

  # calibrate the film by fitting a model:
  calibration <- fitCalibrationModel(grayvalues,
    thickness = stepIncrease(0.24, 7),
    density = 1.2922,
    plot = TRUE
  )
}

Get Tree-Ring Borders

Description

Identify tree-ring borders

Usage

getBorders(x, k = 3, minTrw = 3, threshold = 0.215, addLastBorder = FALSE)
getBorders(x, k = 3, minTrw = 3, threshold = 0.215, addLastBorder = FALSE)

Arguments

`x`	an object of class "xRing"
`k`	integer; width of the rolling window
`minTrw`	integer; width of the narrowest tree-ring, rings narrower than this value will not be considered
`threshold`	the minimum difference between the local maximum and minimum density to detect tree-ring borders
`addLastBorder`	logical; if `FALSE` the last border is not added. If `TRUE` the last border is placed at the position of the last value.

Details

This function uses local maximum and minimum densities in order to detect tree-ring borders.

Value

The getBorders function returns an object of lass "xRing" including the following elements:

names a string giving the series name

span the first and last year

trw a data.frame with tree-ring width

limits a vector with the position of the tree-ring borders

years a vector with the calendar year

profile.raw a vector with the raw X-ray values

profile a vector with the the smoothed X-ray values (if is supplied in the input)

Examples


data("PaPiRaw")
data("PaPiSpan")
AFO1001a <- toxRing(PaPiRaw, PaPiSpan, "AFO1001a")
AFO1001a <- getBorders(AFO1001a)

AFO1001a <- toxRing(PaPiRaw, seriesName = "AFO1001a")
AFO1001a <- getBorders(AFO1001a)

data("PaPiRaw")
data("PaPiSpan")
AFO1001a <- toxRing(PaPiRaw, PaPiSpan, "AFO1001a")
AFO1001a <- getBorders(AFO1001a)

AFO1001a <- toxRing(PaPiRaw, seriesName = "AFO1001a")
AFO1001a <- getBorders(AFO1001a)

Get Density Values

Description

Get wood density parameters by tree-ring.

Usage

getDensity(x)
getDensity(x)

Arguments

`x`	a "xRingList" or "xRing" object

Value

a "xRingList" or "xRing" object with density values c("Dmean", "Dmin", "Dmax", "Dew", "Dlw") for each ring

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi.merge <- combineFrag(PaPi, frag = 9)
PaPiRings <- detectEwLw(PaPi.merge, ew = 0.5)

PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPiRings <- detectEwLw(PaPi, ew = 0.5)

# xRingList object
PaPiDen <- getDensity(PaPiRings)

PaPiDen$AFO1001a[]
PaPiDen$AFO1001a$density

# xRing object
PaPi_AFO1001a <- getDensity(PaPi$AFO1001a)
# the same
PaPi_1 <- getDensity(PaPi[[1]])
identical(PaPi_AFO1001a, PaPi_1)

# do not work for PaPi[1]
# class(PaPi[1])
# getDensity(PaPi[1]) # 'list' class

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi.merge <- combineFrag(PaPi, frag = 9)
PaPiRings <- detectEwLw(PaPi.merge, ew = 0.5)

PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPiRings <- detectEwLw(PaPi, ew = 0.5)

# xRingList object
PaPiDen <- getDensity(PaPiRings)

PaPiDen$AFO1001a[]
PaPiDen$AFO1001a$density

# xRing object
PaPi_AFO1001a <- getDensity(PaPi$AFO1001a)
# the same
PaPi_1 <- getDensity(PaPi[[1]])
identical(PaPi_AFO1001a, PaPi_1)

# do not work for PaPi[1]
# class(PaPi[1])
# getDensity(PaPi[1]) # 'list' class

Get Data-Frames With Ring Width and Density Values

Description

Produce a list with 8 data.frames (trw, ew, lw, Dmean, Dew, Dlw, Dmin, Dmax ) that can be used by other packages (dplR, detrendeR)

Usage

getRwls(x)
getRwls(x)

Arguments

`x`	an "xRingList" object

Value

a list with 8 elements:

trw: a data.frame with tree-ring widths
ew: a data.frame with earlywood widths
lw: a data.frame with latewood widths
Dmean: a data.frame with mean tree-ring density
Dew: a data.frame with mean earlywood density
Dlw: a data.frame with mean latewood density
Dmin: a data.frame with the minimum ring density
Dmax: a data.frame with the maximum ring density

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi <- combineFrag(PaPi)
PaPi <- detectEwLw(PaPi)
rwls <- getRwls(PaPi)
names(rwls)
library(dplR)
rwl.report(rwls$trw)
library(detrendeR)
RwlInfo(rwls$trw)

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
PaPi <- combineFrag(PaPi)
PaPi <- detectEwLw(PaPi)
rwls <- getRwls(PaPi)
names(rwls)
library(dplR)
rwl.report(rwls$trw)
library(detrendeR)
RwlInfo(rwls$trw)

Select the Steps of a Calibration Wedge Interactively

Description

Obtain the Grayvalue of Each Step of a Calibration Wedge

Usage

getSteps(im, nSteps = NULL, auto = FALSE, nPixel = 50)
getSteps(im, nSteps = NULL, auto = FALSE, nPixel = 50)

Arguments

`im`	an image.
`nSteps`	number of steps of the calibration wedge to obtain grayvalues from.
`auto`	logical. If TRUE, automatic detection of the steps given a line is carried out. Use with care.
`nPixel`	gives the line width when 'auto = TRUE'

Value

a numeric vector

Examples

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # display the image
  imDisplay(im)

  # get the grayvalues from the calibration wedge on the film
  steps <- grayvalues <- getSteps(im, 7) # select 7 ROIs
  steps1 <- grayvalues <- getSteps(im, 7, auto = TRUE) # select a single ROI
  cor(steps, steps1)
}

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # display the image
  imDisplay(im)

  # get the grayvalues from the calibration wedge on the film
  steps <- grayvalues <- getSteps(im, 7) # select 7 ROIs
  steps1 <- grayvalues <- getSteps(im, 7, auto = TRUE) # select a single ROI
  cor(steps, steps1)
}

Crop Image Interactively

Description

A GUI for cropping an image

Usage

imCrop(im)
imCrop(im)

Arguments

`im`	a cimg object

Value

a cropped image

Examples


if (interactive()) {
  file_path <-
    system.file("img", "AFO1046.1200dpi.png", package = "xRing")
  im <- imRead(file_path)
  print(dim(im))
  im_crop <- imCrop(im)
  print(dim(im_crop))
}

if (interactive()) {
  file_path <-
    system.file("img", "AFO1046.1200dpi.png", package = "xRing")
  im <- imRead(file_path)
  print(dim(im))
  im_crop <- imCrop(im)
  print(dim(im_crop))
}

Display Image Using tcltk Package

Description

xRing

Usage

imDisplay(im, zoom = NULL, title = NULL)
imDisplay(im, zoom = NULL, title = NULL)

Arguments

`im`	an image (an object of class "cimg")
`zoom`	the zoom factor (ratio), for zoom = 1 the image is shown with no zoom (original size), when zoom is less than 1 the image is zoomed out. The default value of zoom is NULL.
`title`	the window title

Value

a tcltk object

Examples

if (interactive()) {
  file_path <- system.file("img", "AFO1046.1200dpi.png", package = "xRing")
  im <- imRead(file_path)
  tkWin <- imDisplay(im, zoom = .25)
  tkWin$env$ZOOM # 4 means 25% zoom
}

if (interactive()) {
  file_path <- system.file("img", "AFO1046.1200dpi.png", package = "xRing")
  im <- imRead(file_path)
  tkWin <- imDisplay(im, zoom = .25)
  tkWin$env$ZOOM # 4 means 25% zoom
}

Load Image From a File

Description

Load an image using the load.image function from imager package

Usage

imRead(file)
imRead(file)

Arguments

file

path to file

Value

an object of class "cimg"

Examples

if (interactive()) {
  file_path <- system.file("img", "AFO1046.1200dpi.png", package = "xRing")
  im <- imRead(file_path)
  imDisplay(im)
}

if (interactive()) {
  file_path <- system.file("img", "AFO1046.1200dpi.png", package = "xRing")
  im <- imRead(file_path)
  imDisplay(im)
}

Measure Profiles Interactively

Description

Several profiles can be selected in an image and a calibration for that image is used to convert pixels into wood density

Usage

measureProfiles(im, nPixel = 50, cal = NULL)
measureProfiles(im, nPixel = 50, cal = NULL)

Arguments

`im`	an image
`nPixel`	the line width
`cal`	calibration

Value

an xRingList object with all xRing objects

Examples

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # to display the image
  imDisplay(im)

  cal1 <- calibrateFilm(im, thickness = stepIncrease(0.24, 7), density = 1.2922, plot = TRUE)
  profiles <- measureProfiles(im, cal = cal1)
}

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # to display the image
  imDisplay(im)

  cal1 <- calibrateFilm(im, thickness = stepIncrease(0.24, 7), density = 1.2922, plot = TRUE)
  profiles <- measureProfiles(im, cal = cal1)
}

PaPiRaw

Description

A dataframe with 44 series of wood density (g/m³).

Usage

data("PaPiRaw")data("PaPiRaw")

Format

A data.frame containing 44 series in columns and 3111 values of wood density in rows.

Examples

data(PaPiRaw)
plot(na.omit(PaPiRaw[,1]), type="l", ann = FALSE)
data(PaPiRaw)
plot(na.omit(PaPiRaw[,1]), type="l", ann = FALSE)

PaPiSpan

Description

A dataframe giving the first and the last year of 44 series. The row names give the name of series.

Usage

data("PaPiSpan")data("PaPiSpan")

Format

A data frame with 44 observations on the following 2 variables.

first: a numeric vector giving the first year
last: a numeric vector giving the last year

Examples

data(PaPiSpan)
head(PaPiSpan)
data(PaPiSpan)
head(PaPiSpan)

Plot xRing and xRingList Objects

Description

Plot method for objects of class "xRing" and "xRingList".

Usage

## S3 method for class 'xRing'
plot(x, years = NULL, EwLw = TRUE,  xlim = NULL, ylim = NULL, ...)

## S3 method for class 'xRingList'
plot(x, series = 1, years = NULL, EwLw = TRUE,  xlim = NULL, ylim = NULL, ...)
## S3 method for class 'xRing'
plot(x, years = NULL, EwLw = TRUE,  xlim = NULL, ylim = NULL, ...)

## S3 method for class 'xRingList'
plot(x, series = 1, years = NULL, EwLw = TRUE,  xlim = NULL, ylim = NULL, ...)

Arguments

`x`	an object of class "xRing" or "xRingList".
`years`	the years to be plotted, if `NULL` the whole time span is plotted.
`EwLw`	logical. If `TRUE` the earlywood and latewood boundaries and width is plotted.
`xlim`	vector of length 2 giving the x limits for the plot.
`ylim`	the y limits of the plot.
`...`	other arguments to be passed to plotRings function
`series`	gives the name (or the index) of the series to be plotted, by default is 1 (i.e., the first series)

Value

None.

Examples


data(PaPiRaw)
data(PaPiSpan)

PaPi <- detectRings(PaPiRaw, PaPiSpan)
class(PaPi)

PaPiRings <- detectEwLw(PaPi, ew = 0.5)
plot(PaPiRings, series = "AFO1001a")

PaPiRings1 <- detectEwLw(PaPi, ew = 0.35, lw = 0.55)
plot(PaPiRings1, series = "AFO1001a")

plot(PaPiRings, series = "AFO1001a", years = c(1990, 2000))
plot(PaPiRings$AFO1001a)

data(PaPiRaw)
data(PaPiSpan)

PaPi <- detectRings(PaPiRaw, PaPiSpan)
class(PaPi)

PaPiRings <- detectEwLw(PaPi, ew = 0.5)
plot(PaPiRings, series = "AFO1001a")

PaPiRings1 <- detectEwLw(PaPi, ew = 0.35, lw = 0.55)
plot(PaPiRings1, series = "AFO1001a")

plot(PaPiRings, series = "AFO1001a", years = c(1990, 2000))
plot(PaPiRings$AFO1001a)

Plot xRing Objects

Description

Plot "xRing" objects.

Usage

plotRings(x, xlim = NULL, ylim = NULL, id = NULL, corr = NULL, EwLw = TRUE)
plotRings(x, xlim = NULL, ylim = NULL, id = NULL, corr = NULL, EwLw = TRUE)

Arguments

`x`	an object of class "xRing"
`xlim`	the x limits of the plot. The default value, NULL, indicates that the whole profile will be plotted.
`ylim`	the y limits of the plot.
`id`	a sufix to be added to the name of the series (<series_name> [id])
`corr`	value to be print at the top of the graph
`EwLw`	logical. If `TRUE` the earlywood and latewood assignments are plotted, by default is `TRUE`

Value

None. A plot is produced.

Examples

if (interactive()) {
  data(PaPiRaw)
  data(PaPiSpan)

  PaPi <- detectRings(PaPiRaw[, 1, drop = FALSE], PaPiSpan)
  plotRings(PaPi$AFO1001a)
  plotRings(PaPi, series = "AFO1001a")
  plotRings(PaPi, series = "AFO1001a", xlim = c(120, 450))

  PaPi1 <- detectEwLw(PaPi, ew = 0.5)
  plotRings(PaPi1, series = "AFO1001a", EwLw = FALSE)
  plotRings(PaPi1, series = "AFO1001a")
}

if (interactive()) {
  data(PaPiRaw)
  data(PaPiSpan)

  PaPi <- detectRings(PaPiRaw[, 1, drop = FALSE], PaPiSpan)
  plotRings(PaPi$AFO1001a)
  plotRings(PaPi, series = "AFO1001a")
  plotRings(PaPi, series = "AFO1001a", xlim = c(120, 450))

  PaPi1 <- detectEwLw(PaPi, ew = 0.5)
  plotRings(PaPi1, series = "AFO1001a", EwLw = FALSE)
  plotRings(PaPi1, series = "AFO1001a")
}

Print xRing and xRingList Objects

Description

Print method for objects of class "xRing" and "xRingList".

Usage

## S3 method for class 'xRing'
print(x, ...)

## S3 method for class 'xRingList'
print(x, ...)
## S3 method for class 'xRing'
print(x, ...)

## S3 method for class 'xRingList'
print(x, ...)

Arguments

`x`	the object of class "xRing" or "xRingList" to print
`...`	additional parameters

Value

None

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
class(PaPi)
print(PaPi$AFO1001a)
PaPi$AFO1001a
PaPi$AFO1001a[]
print(PaPi)
PaPi

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
class(PaPi)
print(PaPi$AFO1001a)
PaPi$AFO1001a
PaPi$AFO1001a[]
print(PaPi)
PaPi

Remove Tree-Ring Border(s)

Description

Remove the closest tree-ring border

Usage

removeRing(object, x, series = NULL)
removeRing(object, x, series = NULL)

Arguments

`object`	an object of class "xRing" or "xRingList"
`x`	the position to delete the closest tree-ring border
`series`	the name of the series to be changed when the object is a "xRingList", by default is NULL

Value

an object of class "xRing" or "xRingList" without the tree-ring border at the position x for the series given by series argument

Examples

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
plotRings(PaPi$AFO1001a)
abline(v = 60, lty = 2, col = 2)
PaPi$AFO1001a <- removeRing(PaPi$AFO1001a, x = 60)
# PaPi$AFO1001a <- removeRing(PaPi$AFO1001a, x = locator(1)$x)
plotRings(PaPi$AFO1001a)

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
plotRings(PaPi$AFO1001a)
abline(v = 60, lty = 2, col = 2)
PaPi$AFO1001a <- removeRing(PaPi$AFO1001a, x = 60)
# PaPi$AFO1001a <- removeRing(PaPi$AFO1001a, x = locator(1)$x)
plotRings(PaPi$AFO1001a)

Select Profile(s)

Description

Uses a line to select a profile (or a region of interest), when selecting a radius the line should start at the pith side and end at the bark side of the sample.

Usage

selectProfiles(im, nPixel = 50, cal = NULL, multiple = TRUE)
selectProfiles(im, nPixel = 50, cal = NULL, multiple = TRUE)

Arguments

`im`	an image
`nPixel`	the width of the line
`cal`	calibration
`multiple`	a single or several profiles

Value

a vector with the average grayvalue along the selected line when a multiple is TRUE and a list when multiple is FALSE

Examples

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # to display the image
  imDisplay(im)

  # select a profile
  profile <- selectProfile(im)

  # to display the profile
  plot(profile, type = "l")
}

if (interactive()) {
  # read a sample file
  im <- imRead(file = system.file("img", "AFO1046.1200dpi.png", package = "xRing"))

  # to display the image
  imDisplay(im)

  # select a profile
  profile <- selectProfile(im)

  # to display the profile
  plot(profile, type = "l")
}

Set Last Year

Description

Changes the calendar year of the last ring for a specific series.

Usage

setLastYear(x, lastYear, series = NULL)
setLastYear(x, lastYear, series = NULL)

Arguments

`x`	an "xRing" or "xRingList" object
`lastYear`	the new calendar year for the last tree ring
`series`	individual series to be changed when the object is a "xRingList", by default is NULL

Value

the modified input object with new set last ring of the specified series.

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
plot(PaPi, series = "AFO1001b")
PaPi <- setLastYear(PaPi, 2005, series = "AFO1001b")
plot(PaPi, series = "AFO1001b")

data(PaPiRaw)
data(PaPiSpan)
PaPi <- detectRings(PaPiRaw, PaPiSpan)
plot(PaPi, series = "AFO1001b")
PaPi <- setLastYear(PaPi, 2005, series = "AFO1001b")
plot(PaPi, series = "AFO1001b")

Calculate the Steps Thickness of the Calibration Wedge

Description

convenience function to calculate the thickness of each steps of the calibration wedge for wedges with continous step increase.

Usage

stepIncrease(step.increase = 0.24, nsteps = 7)
stepIncrease(step.increase = 0.24, nsteps = 7)

Arguments

`step.increase`	height increase per wedge step
`nsteps`	total number of steps (the first step has the thickness of 0 - the area beside the wedge. Mention that when setting nsteps)

Value

a numeric vector

Create an "xRing" Object

Description

Converts a dataframe with X-ray microdensity profiles into an "xRing" object

Usage

toxRing(x, y = NULL, seriesName)
toxRing(x, y = NULL, seriesName)

Arguments

`x`	a dataframe with X-ray microdensity profiles
`y`	a dataframe with the numerical values of the first and last year in columns. The individual series are specified as row names.
`seriesName`	the name of series from x and y to be used to produce the "xRing" object.

Value

an "xRing" object, an S3 class with the following elements:

profile.raw a vector with the input density profile

span first and last year

name a string giving the series name

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi.AFO1001a <- toxRing(PaPiRaw, PaPiSpan, seriesName = "AFO1001a")
class(PaPi.AFO1001a)

data(PaPiRaw)
data(PaPiSpan)
PaPi.AFO1001a <- toxRing(PaPiRaw, PaPiSpan, seriesName = "AFO1001a")
class(PaPi.AFO1001a)

Create a "xRingList" Object

Description

Converts a dataframe with X-ray microdensity profiles in an "xRingList" object

Usage

toxRingList(x, y = NULL)
toxRingList(x, y = NULL)

Arguments

`x`	a dataframe with X-ray microdensity profiles
`y`	a dataframe with the numerical values of the first and last year in columns. The individual series are specified as row names. By default is NULL

Value

an "xRingList" object, an S3 class which list membera are "xRing" objects containing:

profile.raw a vector with the input density profile

span first and last year

name a string giving the series name

Examples


data(PaPiRaw)
data(PaPiSpan)
PaPi <- toxRingList(PaPiRaw, PaPiSpan)
class(PaPi)

data(PaPiRaw)
data(PaPiSpan)
PaPi <- toxRingList(PaPiRaw, PaPiSpan)
class(PaPi)

Package 'xRing'

Help Index

Add Tree-Ring Border(s)

Description

Usage

Arguments

Value

Examples

Calibrate Film

Description

Usage

Arguments

Value

See Also

Examples

Combine Fragments

Description

Usage

Arguments

Value

Examples

Correct Tree-Ring Borders Interactively

Description

Usage

Arguments

Details

Value

Examples

Detect the Transition from Earlywood to Latewood

Description

Usage

Arguments

Value

Examples

Detect Tree-Ring Borders

Description

Usage

Arguments

Details

Value

See Also

Examples

Fit a Calibration Curve

Description

Usage

Arguments

Value

See Also

Examples

Get Tree-Ring Borders

Description

Usage

Arguments

Details

Value

Examples

Get Density Values

Description

Usage

Arguments

Value

Examples

Get Data-Frames With Ring Width and Density Values

Description

Usage

Arguments

Value

Examples

Select the Steps of a Calibration Wedge Interactively

Description

Usage

Arguments

Value

Examples

Crop Image Interactively

Description

Usage

Arguments

Value

Examples