first.cell: Detection of the first cells

In RAPTOR: Row and Position Tracheid Organizer

Description

This function uses an is.raptor file (preferably obtained from align) and adds a column with the first cells detected within radial files (i.e. first cell formed in the growing season). The value indicates to which radial file the first cell belongs to (counting from left to right). All cells with NA are not considered as first row cells and are excluded in further analyses.

Usage

first.cell(input, frac.small, yrs, make.plot = TRUE)

Arguments

input	an is.raptor file.
frac.small	a numeric value (between 0 and 1) that is multiplied by the average cell lumen size of the ring, determining the minimum threshold used to exclude cells in the first row that are too small (default = 0.5).
yrs	either a numeric vector providing the year(s) of interest or FALSE to select all years included in input (default = FALSE).
make.plot	logical flag indicating whether to make a plot (default = FALSE).

Details

The first row of cells is detected by using a local search algorithm, where the first cell is indicated by a green box when make.plot = TRUE, and the last by a red box. Values within the graph indicate the row numbers that have been detected. The output adds a column to the input data which indicates the first row of cells. The frac.small argument allows the user to filter out unrealistically small cells.

Value

An is.raptor file with an added column describing the first cells.

Examples

## Not run: 
#first row detection example
input<-is.raptor(example.data(species="LOT_PICEA"), str = FALSE)
input<-input[which(input[,"YEAR"]>2006 & input[,"YEAR"]<2011),]
aligned<-align(input,list=c(0.04,0.04,0,0))
first<-first.cell(aligned, frac.small = 0.5, yrs = FALSE, make.plot = TRUE)

## End(Not run)

RAPTOR documentation built on March 13, 2020, 3:02 a.m.