write.output {RAPTOR}

Output generation and visualization

Description

Generating final output graphs and files for the row and position detection. Input data should be provided as produced by pos.det.

Usage

write.output(input, location, flip = FALSE)

Arguments

input

a data.frame produced by pos.det.

location

an optional character string containing the location where the output .pdf and .txt file should be stored. If not supplied, the function returns the computed output, which can be stored in an object.

flip

logical flag indicating in which direction to plot the cells, i.e. with earlywood at the bottom (default; flip = FALSE) or at the top (flip = TRUE).

Details

Function that aids in graphing the output and writing output tables. The generated plot provides an overview of the detected cells, rows, and the position of the cells within each radial file. The output table provides the standard output table with three additional columns containing; the "ROW" number and "POSITION" within the row and the "MARKER" column (cf. pos.det. This output can provide crucial information that can be used with other packages to generate tracheidograms (cf. de la Cruz & DeSoto, 2015) and link the output to xylogenesis data (cf. Rathgeber et al., 2011).

Value

Plots the detected radial files and writes output according to the is.raptor format.

References

de la Cruz, M., & DeSoto, L. (2015) tgram: Functions to compute and plot tracheidograms. CRAN: https://cran.r-project.org/web/packages/tgram/tgram.pdf.

Rathgeber, C.B.K., Longuetaud, F., Mothe, F., Cuny, H., & Le Moguedec, G. (2011) Phenology of wood formation: Data processing, analysis and visualisation using R (package CAVIAR). Dendrochronologia 29, 139-149.

Examples

## Not run: 
#example to write output
input<-is.raptor(example.data(species="SIB_LARIX"), str = FALSE)
aligned<-align(input)
first<-first.cell(aligned, frac.small = 0.5, yrs = FALSE, make.plot = FALSE)
output<-pos.det(first, swe = 0.3, sle = 3, ec = 1.5, swl = 0.5, sll = 5, lc = 15,
                prof.co = 4, max.cells = 0.5, yrs = FALSE, aligning = FALSE, make.plot = FALSE)
sib_larix<-write.output(output)

#removing rows which are unsuitable
corrections<-data.frame(year=c(2010,2010,2010,2009,2009,2009,2009,2008,2008,
                        2008,2008,2008,2008,2007,2007,2007),
                        row=c(19,15,9,6,11,14,17,5,6,14,17,24,15,2,8,14))
for(i in c(1:nrow(corrections))){
sib_larix[which(sib_larix[,"YEAR"]==corrections[i,1]  &
          sib_larix[,"ROW"]==corrections[i,2] ),"POSITION"]<-rep(NA,length(sib_larix[
          which(sib_larix[,"YEAR"]==corrections[i,1]& sib_larix[,"ROW"]==corrections[i,2] ),
          "POSITION"]))
sib_larix[which(sib_larix[,"YEAR"]==corrections[i,1]  &
          sib_larix[,"ROW"]==corrections[i,2] ),"ROW"]<-rep(NA,length(sib_larix[
          which(sib_larix[,"YEAR"]==corrections[i,1]&sib_larix[,"ROW"]==corrections[i,2] ),
          "POSITION"]))}
SIB_LARIX<-write.output(sib_larix)
for(i in c(1:length(unique(SIB_LARIX[,"YEAR"])))){
row_id<-unique(SIB_LARIX[which(SIB_LARIX[,"YEAR"]==unique(SIB_LARIX[,"YEAR"])[i]),"ROW"],
               na.rm=TRUE)
row_id<-na.omit(row_id[order(row_id)])
for(j in c(1:length(row_id))){
SIB_LARIX[which(SIB_LARIX[,"YEAR"]==unique(SIB_LARIX[,"YEAR"])[i] &
          SIB_LARIX[,"ROW"]==row_id[j]), "ROW"]<-j
}}

## End(Not run)