# (C) Copyright 2019 Sur Herrera Paredes
#
# This file is part of HMVAR.
#
# HMVAR is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# HMVAR is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with HMVAR. If not, see <http://www.gnu.org/licenses/>.
#' Format HMMCP phylotype taxonomy for AMOR
#'
#' @param x A character vector, one element per taxa
#' @param split.char A character string indicating the field
#' delimiter character
#'
#' @return A character vector
#'
#' @author Sur Herrera Paredes
#'
#' @export
phylotype2rdp <- function(x, split.char = ';'){
for(i in 1:length(x)){
x[i] <- gsub(pattern = "\\(\\d+\\)", replacement = "", x = x[i], perl = TRUE)
}
return(x)
}
#' Phylotype to RDP version 2
#'
#' Slow version
#'
#' @param x A character vector, one element per taxa
#' @param split.char A character string indicating the field
#' delimiter character
phylotype2rdp2 <- function(x, split.char = ';'){
sapply(strsplit(x, split = split.char), function(x){
# Get last quality
# last <- x[ length(x) ]
# pat <- "\\((\\d+)\\)"
# match <- regexpr(pattern = pat, text = last, perl = TRUE)
# start.match <- attr(x = match, which = "capture.start")
# length.match <- attr(x = match, which = "capture.length")
# q <- substr(x = last, start = start.match, stop = start.match + length.match - 1)
#return(q)
# Clean
x <- paste(gsub(pattern = pat, replacement = "", x = x), collapse = ";")
return(x)
})
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.