TreeRingShape

This package is designed for efficiently recording the shape of all annual rings in a tree trunk cross-section. It interpolates the annual rings (L2) between representative annual ring lines (L) from the annual ring points (P) and representative annual ring lines inputted on radii measured in GIS software (‘Qgis’). A “representative annual ring” refers to the annual rings that characterize the shape of the outer circumference and the cross-section of the disc, requiring fewer rings the closer their shape is to a perfect circle. Although annual rings grow concentrically around the pith, their shape is not perfectly circular. Traditionally, dendrochronology and tree-ring analysis have evaluated tree growth based on the width of the annual rings. However, with the advancement of image analysis technologies, there has been an increasing number of studies evaluating growth based on the area of the annual rings. Most of these studies have focused on conifer plantation samples, where the annual rings are clearly defined. However, this package also enables the recording of annual ring shapes in trees from natural forests, where the ring shapes are more complex. It should be noted, however, that currently, information regarding the shape of the annual rings needs to be manually inputted, which can be labor-intensive.

Execute

The TreeRingShape() function establishes the S4 class classTreeRingShape and executes the interpolation of annual rings to complete the annual ring shape data.

Table 1. classTreeRingShape : TR <- TreeRingShape()

Slot	R	Qgis
*Input*
P	data frame of Tree Ring Points	Points shape, field(id,ring)
P_filename	shape file name of tree ring points	*.shp
P_id.tag	column name of id in shape file (P)	default ‘id’
P_ring.tag	column name of ring no.(ordinaly year,outermost=0)	default ‘ring’
L	list of Representative Tree Ring Lines	Lines shape, field(ring)
L_filename	shape file name for representative tree ring lines (L)	*.shp
L_ring.tag	column name of ring no.(ordinaly year,outermost=0) in shape file (L)	default ‘ring’
*Append*
L2	list of All Tree Ring Lines including interpolated lines	Lines shape, field(ring)
L2_filename	file name of shape file (L2) for tree ring lines interpolated	*.shp
etc.	see classTreeRingShape for details

Flow of making whole tree ring shapes
TreeRingShape() includs the prosedure from new_classTreeRingShape() to TreeRingInterpolation()

Procedures

I. Processing the Disc

Harvest the tree disc, avoiding areas with branches, rot, or cracks as much as possible.
Polish the disc until the annual rings are clearly visible.
Draw lines from the pith in generally eight directions with a pencil. These lines are referred to as radii measurement lines.
Starting from the cambium layer (the outermost layer of wood touching the bark) as zero, count the annual rings towards the inside and mark them.
Ensure that the number of annual rings matches across all radii measurement lines.
Trace the lines of representative annual rings with a pencil. This improves work efficiency, especially in areas where there are many rings or the rings are unclear.

II. Scanning the Entire Disc Image

Scan the entire disc image at 1200 dpi or higher using a flatbed scanner or a high-resolution digital camera capable of geometric correction.

III. Inputting Annual Ring Coordinates Using Qgis

Project Properties

Set the project’s CRS to ‘none’. Leave the default CRS blank.
Adding Layers
1. Import the annual rings raster image (TreeRing***.tif).
2. Create a new shapefile layer for annual ring points (TreeRingPoints***.shp) with integer attributes for id and ring.
3. Create a new shapefile layer for annual ring lines (TreeRingLines***.shp) with an integer attribute for ring.
Manually Inputting Annual Ring Coordinates
1. Annual Ring Points ** id ** is the number of the radii measurement line or the correction point group number, and ring is typically the count of the annual rings from the cambium layer inward. Mark all annual rings along the radii measurement lines. After completing the annual ring interpolation, if there is any discrepancy in the rings, add correction points where the rings must pass.
2. Representative Annual Ring Lines Input the coordinates while tracing the lines of annual rings that characterize the shape of the outer circumference and the disc. The count starts from the cambium layer as zero and goes inward.

Usage

Tree ring interpolation

library(TreeRingShape)

setwd(system.file("shp",package = "TreeRingShape"))

TR<-TreeRingShape(
P_filename='Abies_277_h400_TreeRing_Points.shp',
L_filename='Abies_277_h400_TreeRing_Representative.shp',
L2_filename='Abies_277_h400_TreeRing.shp',
P_id.tag='id',P_ring.tag='ring',
L_ring.tag='ring')
#> 'data.frame':    3776 obs. of  4 variables:
#>  $ x : num  0 -7117 -7100 -7068 -7047 ...
#>  $ y : num  0 -4837 -4828 -4802 -4786 ...
#>  $ id: num  0 1 1 1 1 1 1 1 1 1 ...
#>  $ yr: num  186 0 1 2 3 4 5 6 7 8 ...

Plots for tree ring area and index

 ya <- plot_year_RingArea(TR@L2, 2018)$Year_TreeRingArea

 # Figure of relationships year and tree ring area
  plot(ya,type='b')
  tri. <- TreeRingIndex(ya)
  lines(tri.$spline,col='red',lw=2)

 # Figure of relationships year and tree ring index
  plot(tri.$idx,type='b')
  abline(h=1,col='red')

https://github.com/ishidamgm/TreeRingShape

Reference

Pebesma, E., & Bivand, R. (2023). Spatial Data Science: With Applications in R. Chapman and Hall/CRC.

QGIS Development Team. (2024). QGIS Geographic Information System. QGIS Association. https://www.qgis.org/en/site/