R/curves.R

Defines functions read_grp_curves read_curves

Documented in read_curves read_grp_curves

# This file is a part of zonator package

# Copyright (C) 2012-2014 Joona Lehtomaki <[email protected]>. All rights
# reserved.

# This program is open source software; you can redistribute it and/or modify
# it under the terms of the FreeBSD License (keep this notice):
# http://en.wikipedia.org/wiki/BSD_licenses

# 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.

# Helper function to decide whether given names in indexes exist. Returns
# a vector of indexes if names/indexes are actually found.

#' Read in performance curves produced by Zonation.
#'
#' Header is automatically generated based on the number of features in the
#' file. If you need to read in grouped curves files, use
#' \code{\link{read_grp_curves}} instead.
#'
#' @keywords zonation, results
#' @author Joona Lehtomaki <[email protected]@gmail.com>
#'
#' @param infile Character file path to .curves.txt file.
#'
#' @return Curves object with all the information in the curves file. If the
#'   requested file does not exist, return NA.
#'
#' @importFrom utils read.table
#' @importFrom methods new
#'
#' @export
#' @seealso \code{\link{read_grp_curves}}
#'
read_curves <- function(infile) {

  if (is.na(infile)) {
    return(NA)
  }

  if(!file.exists(infile)) {
    return(NA)
  }

  # Read in the curves file skipping the header line, we'll construct this
  # later on
  curves <- read.table(infile, as.is=TRUE, header=FALSE, skip=1)
  # Standard header entries

  # The header has a set of standard components + proportion for each species
  # remaining at level of removal (created dynamically)
  header <- c("pr_lost",          # 1
              "cost",             # 2
              "min_pr",           # 3
              "ave_pr",           # 4
              "w_pr",             # 5
              "ext1",            # 6
              "ext2")            # 7

  # Populate the rest of the header lines with sp headers and assign it
  header <- c(header, paste("f", 1:(ncol(curves) - length(header)), sep=""))
  colnames(curves) <- header
  # Convert into a curves object
  curves <- new("ZCurvesDataFrame", curves,
                is.feature=c(rep(FALSE, 7), rep(TRUE, ncol(curves) - 7)))
  return(curves)
}

#' Read in performance curves for grouped features produced by Zonation.
#'
#' Header is automatically generated based on the number of groups in the
#' file. If you need to read in individual curves files, use
#' \code{\link{read_curves}} instead.
#'
#' @keywords zonation, results
#' @author Joona Lehtomaki <[email protected]@gmail.com>
#'
#' @param infile Character file path to .curves.txt file.
#'
#' @return A DataFrame with all the information in the curves file. If the
#'   requested file does not exist, return NA.
#'
#' @export
#' @seealso \code{\link{read_curves}}
#'
read_grp_curves <- function(infile) {

  if (is.na(infile)) {
    return(NA)
  }

  if(!file.exists(infile)) {
    return(NA)
  }

  grp.curves <- read.table(infile, header=TRUE)

  # standard part of the header
  header <- c("pr_lost", "cost")

  # Repeating parts of the group curves header
  rep.header <- c("min", "mean", "max", "w.mean", "ext2")
  times <- (ncol(grp.curves) - length(header)) / length(rep.header)
  rep.header <- paste(rep(rep.header, times), paste0("group",
                                                     rep(1:times,
                                                         each=length(rep.header))),
                      sep=".")
  header <- c(header, rep.header)
  colnames(grp.curves) <- header

  grp.curves <- new("ZGroupCurvesDataFrame", grp.curves,
                    is.group=c(rep(FALSE, 2), rep(TRUE, ncol(grp.curves) - 2)))

  return(grp.curves)
}

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zonator documentation built on Dec. 17, 2017, 5:03 p.m.