Calibrate ring-width series

This function can calibrate the ring-width series using arcs of inner rings.

Usage

pith_measure(ring.data, inner.arc = TRUE, last.yr = NULL,
  color = "black", border.type = 16, label.cex = 1.5)

Arguments

ring.data

A magick image object produced by ring_read.

inner.arc

A logical value indicating whether to calibrate the ring-width series using the arcs of inner rings. See details below.

last.yr

NULL or an integer giving the year of formation of the left-most ring. If NULL, border numbers (starting from 1) are used instead of years.

color

Color for labels.

border.type

Symbol for ring borders. See pch in points for possible values and shapes.

label.cex

The magnification to be used for years or border numbers.

Value

A data frame of the calibrated ring-width series. The measurements units are millimeters (mm)

Details

This function allows the user to create a path, and manually mark ring borders by clicking on the graphical window.

An example demonstrated with pictures can be found in the package vignette. Type vignette('pith-MtreeRing') to see this example.

• If inner.arc = TRUE, the ring-width series is calibrated using arcs of inner rings (Duncan, 1989).

  Step1. You can click the left mouse button to add a horizontal path. The path should traverse an appropriate arc (read the reference below for more details).

  Step2. You can add three points to the selected arc by left-clicking. The first point should be placed on the left endpoint of the arc, and the second point is placed on the right endpoint.

  After adding these two points, a vertical dashed line will be plotted automatically according to the (x,y) positions of endpoints you just added. The third points should be placed on the intersection of the vertical dashed line and the selected arc.

  Step3. you are prompted to mark tree rings along the path by left-clicking on the image. Every click draws a point. Note that the left endpoint of the arc will be considered as the last ring border without the need to mark it.

  After marking tree rings, the identification process does not automatically stop by itself. On the Windows platform, the identification process can be terminated by clicking the second button and selecting Stop from the menu. On the MacOS system, you can press the Escape key to terminate this process.

  The ring-width series are corrected using formulas proposed by Duncan (1989).

• If inner.arc = FALSE, the user can create a path which matches the direction of wood growth.

  Step1. You can add two points by left-clicking on the image. Every click draws a point. A path passing through these two points will be plotted. The path should follow the rays from bark to pith.

  Step2. You can mark tree rings along the path by left-clicking on the image. The termination of identification process is similar.

References

Duncan R. (1989) An evaluation of errors in tree age estimates based on increment cores in Kahikatea (Dacrycarpus dacrydiodes). New Zealand Natural Sciences 16(4), 1-37.

Author

Jingning Shi

Examples

img.path <- system.file("missing_pith.png", package = "MtreeRing")

## Read the image:
t1 <- ring_read(img = img.path, dpi = 1200, plot = FALSE)

## Use the arcs of inner rings to calibrate ring-width series:
t2 <- pith_measure(t1, inner.arc = TRUE, last.yr = 2016)
#> Error in round(step1$y): non-numeric argument to mathematical function

## Try another method to measure ring widths:
t3 <- pith_measure(t1, inner.arc = FALSE, last.yr = 2016)
#> Error in model.frame.default(formula = path.position$y ~ path.position$x +     1, drop.unused.levels = TRUE): invalid type (NULL) for variable 'path.position$y'