taxaToGuild.R

#    Copyright 2013 Chen-Pan Liao 
#    This program 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
#    any later version.
#    
#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.


############################################
## taxaToGuild.r
## Author: Chen-Pan Liao (2013)
## License: Public domain
## Environment: R (ver. 2.15+)
## Usage:
##  new.dataframe <- taxaToGuild(
##    taxa.file.csv,
##    taxa.file.csv.row.num,
##    guild.file.csv,
##    guild.file.csv.row.num,
##    guild.system.row.num
##  )
############################################



taxaToGuild <- function (

  taxa.file.csv,
  taxa.file.csv.row.num,
  guild.file.csv,
  guild.file.csv.row.num,
  guild.system.row.num


#  taxa.file.csv = "taxa.csv",
#  taxa.file.csv.row.num = 1,
#  guild.file.csv = "guild.csv",
#  guild.file.csv.row.num = 1,
#  guild.system.row.num = 1


){

  guild.data <- read.csv(guild.file.csv, row.names = guild.file.csv.row.num)
  taxa.data <- read.csv("taxa.csv", row.names = taxa.file.csv.row.num)
  
  guild.list.taxa <- row.names(guild.data)
  guild.list.guild <- guild.data[, guild.system.row.num]
  taxa.list <- names(taxa.data)
  
  taxa.list.ind <- numeric(length(taxa.list))
  taxa.unknown <- 0
  for(n in 1:length(taxa.list)){
    if (sum(taxa.list[n] == guild.list.taxa) > 0) {
      taxa.list.ind[n] <- which(taxa.list[n] == guild.list.taxa)
    } else {
      taxa.list.ind[n] <- NA
      taxa.unknown[length(taxa.unknown) + 1] <- n
    }
  }
  
  new.guild.list <- unique(guild.list.guild[taxa.list.ind])
  taxa.unknown <- taxa.unknown[-1]
  
  #new.taxa.data <- taxa.data
  #names(new.taxa.data) <- guild.list.guild[taxa.list.ind]
  
  
  ## new taxa matrix initiation 
  newer.taxa.data <- data.frame (
    matrix(
      0,
      nrow = nrow(taxa.data),
      ncol = length(new.guild.list)
    ),
    row.names = row.names(taxa.data)
  )
  names(newer.taxa.data) <- new.guild.list
  
  
  ## subsum of new taxa matrix
  for(n in 1:length(new.guild.list)){
    if (!is.na(new.guild.list[n])) {
      newer.taxa.data[,n] <- rowSums(
        data.frame(
          taxa.data[
            ,
            which(new.guild.list[n] == guild.list.guild[taxa.list.ind])
          ]
        )
      )
    } else {
      newer.taxa.data[,n] <- rowSums(
        data.frame(
          taxa.data[ , taxa.unknown]
        )
      )
    }
  }
  cat(
    sprintf(
      "The guild system is %s.\n",
      names(guild.data)[guild.system.row.num]
    )
  )
  cat(
    sprintf(
      "Warning: the following taxa is merged into guild NA due to no reference: %s.\n",
      taxa.list[taxa.unknown]
    )
  )
  
  return(newer.taxa.data)

}