Nothing
#'@method summary plant3dlist
#'@S3method summary plant3dlist
#'@rdname summary.plant3d
summary.plant3dlist <- function(object, writefile=FALSE, ...){
plants <- object
nplants <- attributes(plants)$nplants
sums <- list()
message("Summarizing ",nplants," plants.\n")
message("Overall progress:")
wp <- txtProgressBar(title = "Summarizing plants.", label = "",
min = 0, max = nplants, initial = 0, width = 50, style=3)
for(i in 1:nplants){
sums[[i]] <- try(summary(plants[[i]], quiet=TRUE, progressbar=FALSE, ...))
if(inherits(sums[[i]], "try-error")){close(wp);stop("Problem with plant number ",i)}
setTxtProgressBar(wp, i)
}
close(wp)
sums2 <- lapply(1:length(sums[[1]]), function(x)sapply(sums, "[[", x))
sumsdfr <- as.data.frame(sums2)
names(sumsdfr) <- names(sums[[1]])
sumsdfr$nsignif <- NULL
if(!writefile)return(sumsdfr)
if(writefile){
filen <- paste0("PlantSummaries-",as.Date(Sys.time()),".txt")
unlink(filen)
sumsdfr$ALAC <- with(sumsdfr, LA / crownsurf)
sumsdfr$stemsurf <- sumsdfr$stemsurf * 10^4
sumsdfr$stemvol <- sumsdfr$stemvol * 10^6
r <- c()
r[1] <- " LA - Total leaf area (m2)"
r[2] <- " meanleafsize - Mean leaf size (cm2)"
r[3] <- " nleavesp - Number of leaves"
r[4] <- " leaflen - Mean leaf length (cm)"
r[5] <- " meanleafang - Mean leaf angle (deg)"
r[6] <- " wmeanleafang - Mean leaf angle weighted by leaf area (deg)"
r[7] <- " Xellipsoid - Ellipsoidal leaf angle dist. par."
r[8] <- " crownvol - Crown volume (convex hull) (m3)"
r[9] <- " crownsurf - Crown surface area (convex hull) (m2)"
r[10] <- " ALAC - Crown density (AL/AC) (m2 m-2)"
r[11] <- " cw - Crown width (m)"
r[12] <- " cl - Crown length (m)"
r[13] <- " htot - Total height (m)"
r[14] <- " cshape - Crown shape index (-)"
r[15] <- " stemsurf - Stem + branch surface area (cm2)"
r[16] <- " stemvol - Stem + branch volume (cm3)"
r[17] <- " stemdiam - Stem base diameter (mm)"
r[18] <- " meanpath - Mean pipe length (mm)"
r[19] <- " sdpath - Standard deviation of pipe length (mm)"
r[20] <- " totlen - Total woody segment length (mm)"
r[21] <- " Ek - Expected distance to 5 nearest leaves (no edge corr.)"
r[22] <- " Ek2 - Expected distance to 5 nearest leaves (with edge corr.)"
r[23] <- " Ok - Observed distance to 5 nearest leaves"
r[24] <- " disp - Dispersion parameter (no edge corr.)"
r[25] <- " disp2 - Dispersion parameter (with edge corr.)"
if(!is.na(sums[[1]]$STARbar))
r[26] <- " STARbar - Spherically averaged STAR (m2 m-2)"
r <- c("Plant summary results - produced with YplantQMC.\n", r)
r <- c(r, "\n\n\n")
writeLines(r, filen)
options(warn=-1)
write.table(sumsdfr, filen, append=TRUE, sep="\t", quote=FALSE, row.names=FALSE)
options(warn=0)
message("\nSummary written to file:\n ", filen)
return(invisible(sumsdfr))
}
}
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