getTrac: Compute tracheidograms
In tracheideR: Standardize Tracheidograms

Description Usage Arguments Details Value References See Also Examples

View source: R/getTrac.R

This function computes a tracheidogram from microscope light measurements in gray (0-255).

1	getTrac(x, val50 = 120, mw = 5, scale = 1)

`x`	a vector with the light measurements (pixel gray-level values)
`val50`	the value giving the "intensity" of the light measurements at which the measurments should be made (for more details please see the help of `tgram` function).
`mw`	width of the rolling window to smooth the original data (for more details please see the help of `tgram` function)
`scale`	distance per pixel, default = 1

This function uses the tgram function (tgram package) to convert gray pixel values (0-255) into a raw tracheidogram (keeping the original number of cells).

getTrac returns a list with following elements:

n number of cells

pos pos$RingWidth gives the tree-ring width and pos$x gives the "position" of each tracheid.

LD a vector with the lumen diameter (LD).

CWT a vector with the radial cell wall thikness (CWT).

LWratio a vector with the LD/CWT ratio.

DeSoto, L., De la Cruz, M., Fonti, P. (2011). Intra-annual patterns of tracheid size in the Mediterranean tree Juniperus thurifera as an indicator of seasonal water stress. Canadian Journal of Forest Research 41: 1280-1294. Vaganov, E., 1989. The tracheidogram method in tree-ring analysis and its application, in: Cook, E., Kairiukstis, L. (Eds.), Methods of Dendrochronology: Applications in the Environmental Sciences. Kluwer Academic Publishers, Dordrecht, The Netherlands.

tgram

## Not run:
y2010ray1 <- getTrac(tch$y2010$ray1, scale = 0.169)
y2010 <- getTrac(tch$y2010, scale = 0.169)
TCH <- lapply(tch,getTrac, scale = 0.169)
TCH$y2010$ray1$n #number of tracheids in ray1 in the year 2010
TCH$y2010$ray1$pos$RingWidth #number of tracheids in ray1 in the year 2010
#getTrac(tch$y2010$ray2, scale = 0.169)
#getTrac(data.frame(tch$y2010$ray2), scale=0.169)
## End(Not run)