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#'
#' RvegCombine
#'
#' Merging species or layers in the database
#'
#' @param database name of the loading database
#' @param export name of the exported database
#' @param checklist checklist to be used
#'
#' @returns export two csv files, one for releve and one for header
#'
#' @examples
#' ## NOT RUN
#' if (interactive()) {
#' RvegCombine(database = paste0(
#' path.package("Rveg"),
#' "/extdata/example_db"
#' ))
#' read.csv("exportREL.csv", row.names = 1)
#' }
#'
#' @export
#'
RvegCombine <- function(database, export = "export", checklist = "default") {
if (export == "export") {
export <- file.path(tempdir(), "export")
}
if (checklist == "default") {
checklist <- paste0(path.package("Rveg"), "/extdata/DANIHELKA2012rko.txt")
}
DATA <- read.csv(paste0(database, "REL.csv"), row.names = 1)
HeaderDATA <- read.csv(paste0(database, "HEAD.csv"), row.names = 1)
while (TRUE) {
a <- toupper(readline("Combine?(LAYER/SPEC/PRINTREL/N) ")) # layer selection
if (a == "LAYER") {
while (TRUE) {
b <- toupper(readline("Which layer?(3/2/1/0/J) "))
c <- toupper(readline("To which layer?(3/2/1/0/J) "))
if (any(c(b, c) %in% c(1, 2, 3, "J", 0))) {
for (i in DATA$ShortName) {
if (i == paste0(substr(i, 1, 7), "_", b) && any(DATA$ShortName == paste0(substr(i, 1, 7), "_", c))) {
l1 <- DATA[DATA$ShortName == i, -1]
l2 <- DATA[DATA$ShortName == paste0(substr(i, 1, 7), "_", c), -1]
l3 <- round(l1 + (l2 * (1 - (l1 / 100))))
DATA <- DATA[DATA$ShortName != paste0(substr(i, 1, 7), "_", b), ]
DATA[DATA$ShortName == paste0(substr(i, 1, 7), "_", c), -1] <- l3
write.csv(DATA, paste0(export, "REL.csv"))
write.csv(HeaderDATA, paste0(export, "HEAD.csv")) # merge Two existing layerss
} else if (i == paste0(substr(i, 1, 7), "_", b) && !any(DATA$ShortName == paste0(substr(i, 1, 7), "_", c))) {
DATA[DATA$ShortName == i, 1] <- paste0(substr(i,1,7),"_", c) # changing single layer
SpLIST <- makeSpLIST(checklist)
for (i in 1:nrow(DATA)) {
rownames(DATA)[i] <- row.names(SpLIST)[SpLIST$ShortName==DATA$ShortName[i]]
}
}
}
break
} else {
warning("wrong layers input")
}
}
} else if (a == "SPEC") {
while (TRUE) {
b <- toupper(readline("Which specie?(GenuSpe_L) "))
c <- toupper(readline("To which layer?(GenuSpe_L) "))
if (nchar(b) == 9 & nchar(c) == 9) {
l1 <- DATA[DATA$ShortName == b, -1]
l2 <- DATA[DATA$ShortName == c, -1]
l3 <- round(l1 + (l2 * (1 - (l1 / 100)))) # propability shared cover
DATA <- DATA[DATA$ShortName != b, ]
DATA[DATA$ShortName == c, -1] <- l3
write.csv(DATA, paste0(export, "REL.csv"))
write.csv(HeaderDATA, paste0(export, "HEAD.csv"))
break
} else {
warning("wrong species input")
}
}
} else if (a == "PRINTREL") {
print(DATA)
} else if (a == "N") {
break
}
}
}
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