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#' @method left_join treedata
#' @importFrom cli cli_warn
#' @export
left_join.treedata <- function(x, y, by = NULL, copy = FALSE, suffix=c("", ".y"), ...){
dat <- .extract_annotda.treedata(x)
ornm <- colnames(dat)
msg <- c("The {.arg suffix} requires a character vector containing 2 different elements,",
"The first element must be \"\", and the second element must not be \"\",",
"it was set {.code suffix=c(\"\", \".y\")} automatically.")
if (all(nchar(suffix)!=0)){
cli::cli_warn(msg)
suffix[1] = ""
}
if (all(nchar(suffix)==0)){
cli::cli_warn(msg)
suffix[2] = ".y"
}
if (nchar(suffix[1])!=0 && nchar(suffix[2])==0){
cli::cli_warn(msg)
suffix <- rev(suffix[seq_len(2)])
}
da <- dplyr::left_join(dat, y, by = by, copy = copy, suffix = suffix, ...)
if (any(duplicated(da$node))){
da %<>% .internal_nest(keepnm=ornm)
}
tr <- .update.td.join(td=x, da=da)
return(tr)
}
#' @method left_join phylo
#' @export
left_join.phylo <- function(x, y, by=NULL, copy=FALSE, ...){
x <- treedata(phylo=x)
tr <- x %>% left_join(y, by = by, copy = copy, ...)
return(tr)
}
#' @method left_join tbl_tree
#' @export
left_join.tbl_tree <- function(x, y, by = NULL, copy = FALSE,
suffix = c(".x", ".y"), ..., keep = NULL){
x <- NextMethod()
if (!valid.tbl_tree2(x)){
x <- drop_class(x, 'tbl_tree')
}
return(x)
}
#' @keywords internal
#' @param td treedata object
#' @param da tbl_df after left_join.
#' @noRd
.update.td.join <- function(td, da){
aa <- names(attributes(td@phylo))
aa <- aa[!aa %in% c("names", "class", "order", "reroot", "node_map")]
data.nm <- get.fields.data(td)
if (length(data.nm)==1 && data.nm==""){
td@data <- tibble()
}else{
td@data <- da %>% select(c("node", data.nm))
}
extra.nm <- colnames(da)[!colnames(da) %in% c("node", "label", "isTip", data.nm, aa)]
if (length(extra.nm) > 0){
td@extraInfo <- da %>% select(c("node", extra.nm))
}
return(td)
}
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