R/extract.profiles.R

In cttedwards/seabird2: Read and write SeaBird files in R

#' Extracts data from a casal -p run
#'
#' Outputs a list with one component for each parameter that is profiled
#' Each component is a list with components
#' values = n x 2 matrix with columns Value (parameter value) and
#'          Objective (objective function at that value)
#'          for n points in profile
#' header = string containing description of parameter vector
#' parameters = n x npar matrix contining parameter values at each profile point
#' @author R.I.C.C. Francis
#' @export
"extract.profiles" <- function(filename)
{
    string.match <- function(x, y) return((1:length(y))[regexpr(x, y, F) > 0])
    profile.list <- list()
    file <- SeaBird.convert.to.lines(filename)
    file <- file[file != "Dumping Taylor tape to disk - see BB"]
    name.lines <- string.match("Profile of parameter", file)
    parameter.lines <- string.match("Parameter estimates for profile of parameter", file)
    n.profiles <- length(name.lines)
    header.split <- SeaBird.string.to.vector.of.words(file[parameter.lines[1] + 1])
    colnames <- c()
    k <- 1
    while (k < length(header.split)) {
        if (SeaBird.is.whole.number(header.split[k + 1])) {
            n.reps <- as.numeric(header.split[k + 1])
            colnames <- c(colnames, paste(rep(header.split[k], n.reps), 1:n.reps, sep = "."))
            k <- k + 2
        }
        else {
            colnames <- c(colnames, header.split[k])
            k <- k + 1
        }
    }
    if (k == length(header.split))
        colnames <- c(colnames, header.split[length(header.split)])
    for (i in 1:n.profiles) {
        profile <- list()
        par.name <- SeaBird.string.to.vector.of.words(file[parameter.lines[i]])[7]
        par.name <- substring(par.name, 1, nchar(par.name) - 1)
        subfile <- file[(name.lines[i] + 2):(parameter.lines[i] - 1)]
        n.values <- length(subfile)
        profile$values <- matrix(0, n.values, 2, dimnames = list(NULL, c("Value", "Objective")))
        for (j in 1:n.values)
            profile$values[j,  ] <- SeaBird.string.to.vector.of.numbers(subfile[j])
        profile$header <- paste(header.split, collapse = " ")
        profile$parameters <- matrix(0, n.values, length(colnames), dimnames = list(NULL, colnames))
        subfile <- file[(parameter.lines[i] + 2):(parameter.lines[i] + n.values + 1)]
        for (j in 1:n.values)
            profile$parameters[j,  ] <- SeaBird.string.to.vector.of.numbers(subfile[j])
        profile.list[[par.name]] <- profile
    }
    return(profile.list)
}