tracheider: Compute standardized tracheidograms

In tracheideR: Standardize Tracheidograms

Description

This function computes standardized tracheidograms from raw tracheidograms.

Usage

tracheider(traq, method = c("nCells", "kCells", "relPos"), k = 20)

Arguments

traq	a raw tracheidogram (or a list of raw tracheidograms)
method	a string defining the method to be used. Possible values are c("nCells","kCells","relPos"). The default method is "nCells".
k	a integer to determine the number of cells of the standardized tracheidogram when method is "kCells"

Details

This function takes as input raw tracheidograms (obtained using the getTrac function) and standardizes them using 3 different methods. The first method ("nCells") standardizes rays of a given ring using the mean number of cells, allowing that different rings have different number of cells. The method "kCells" normalizes tracheidograms to a constant number of tracheids (k). The "relPos" method standardizes the tracheidogram based on the relative position of each tracheid inside the tree ring.

Value

the function tracheider returns a list with the following elements:

LD ordered sequence of lumen diameters.

CWT ordered sequence of radial cell wall thikness.

LWratio ordered sequence of LD/CWT ratio.

Examples

## Not run:
y2010 <- getTrac(tch$'y2010', scale=0.169)
y2013 <- getTrac(tch$'y2013', scale=0.169)

## nCells
y2010n <- tracheider(y2010, method = "nCells")
y2013n <- tracheider(y2013, method = "nCells")
plot(rowMeans(as.data.frame(y2010n$LD)), type="l", xlim=c(0,86),
     ylim=c(0,60), yaxs="i", xaxs="i", xlab="Number of tracheid",
     ylab=expression(paste("LD (", mu,"m)")), col=2, lwd=2)
lines(rowMeans(as.data.frame(y2013n$LD)), col="blue", lwd=2)
legend("topright",lty=1,lwd=2,col = c(2,4), legend=c("2010 ","2013 "),
        text.col = c(2,4), box.col = "#00000000", bg="#00000000")

## k = 53
TCH <- lapply(tch, getTrac, scale=0.169)
TCHn53 <- lapply(TCH, tracheider,method = "kCells", k=53)

plot(rowMeans(as.data.frame(TCHn53$'y2010'$LD)), type="l",
     xlab="Number of tracheid", ylab=expression(paste("LD (", mu,"m)")),
     xlim=c(0,54), ylim=c(0,60), col=2, lwd=2, yaxs="i", xaxs="i")
lines(rowMeans(as.data.frame(TCHn53$'y2013'$LD)), col="blue", lwd=2)
legend("topright",lty=1,lwd=2,col = c(2,4),legend=c("2010 ","2013 "),
     text.col = c(2,4), box.col = "#00000000", bg="#00000000")

## Relative position
TCH <- lapply(tch, getTrac, scale=0.169)
TCHrelPos <- lapply(TCH, tracheider, method ="relPos")
plot(rowMeans(as.data.frame(TCHrelPos$'y2010'$LD)),
     type="l", xlim=c(0,101), ylim=c(0,60), col=2, lwd=2,
     xlab="Number of tracheid", ylab=expression(paste("LD (", mu,"m)")),
     yaxs="i", xaxs="i")
lines(rowMeans(as.data.frame(TCHrelPos$'y2013'$LD)),
      col="blue", lwd=2)
legend("topright",lty=1,lwd=2,col = c(2,4), legend=c("2010 ","2013 "),
       text.col = c(2,4), box.col = "#00000000", bg="#00000000")
## End(not run)

tracheideR documentation built on May 2, 2019, 7:29 a.m.