R/growthPhenoUtilities.r

In growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

#Definition needed for probeSmooths and friends
smooth.cols <- c("Type","TunePar","TuneVal","Tuning","Method")

#Function to force an error if a set of Names is not present in an object 
checkNamesInData <- function(Names, data)
{
  if (!all(Names %in% names(data)))
  { 
    mess <- paste0("The following required columns are not in data: ", #deparse(substitute(data)))
                   paste0(Names[!(Names %in% names(data))], collapse = ", "), ".\n")
    callingFuncs = as.list(sys.call(-1))
    if (any(callingFuncs %in% c("traitSmooth", "probeSmooths")))
      mess <- paste0(mess, "Perhaps add the column names to the keep.columns argument\n")
    stop(mess)
  }
  invisible()
}

#Function to allow testing for NULL when objects of length > 1 are possible
is.allnull <- function(x) all(is.null(x))


"check.arg.values" <- function(arg.val, options)
  #Function to check that arg.val is one of the allowed values
  #and to return the position of the argument in the set of values
  #that is stored in options
{ 
  kopt <- pmatch(arg.val, options)
  if (any(is.na(kopt)))
    stop("Value `",paste(arg.val, collapse = ","), "' is either not unique or is not an allowed option for its argument")
  if (length(kopt) > 1)
  {
    warning(paste("Only one value allowed for argument where", 
                  paste(arg.val, collapse = ","), "have been supplied", 
            sep = " "))
    kopt <- kopt[1]
  }
  return(kopt)
}

facet.char2formula <- function(facet.x, facet.y)
{ 
  form <- as.formula(paste(paste(facet.y, collapse = " + "),
                           paste(facet.x, collapse = " + "),sep="~"))
  return(form)
}

#Function to convert a set of times from factor/character to numeric
convertTimes2numeric <- function(times)
{
  if (!is.numeric(times))
  {
    if (inherits(times, what = "factor"))
      times <- dae::as.numfac(times)
    if (inherits(times, what = "character"))
      times <- as.numeric(times)
  }
  return(times)
}

#Function to convert a set of times to factor/character from numeric
convertTimesExnumeric <- function(x, times.data)
{
  if (!inherits(times.data, what = "numeric"))
  {
    if (inherits(times.data, what = "factor"))
      x <- factor(x)
    if (inherits(times.data, what = "character"))
      x <- as.character(x)
  }
  return(x)
}



#Get a list of the factors in a formula, converting a character with a list of factors to a formula
"fac.getinFormula" <- function(formula = NULL, data = NULL, ...)
{ 
  if (is.character(formula))
  { 
    formula <- as.formula(paste0("~ ",paste(formula, collapse = " + ")))
  }
  else
  { 
    if (!is.null(formula))  
      formula <- as.formula(formula)
  }
  if (is.null(formula))
    facs <- NULL
  else
    facs <- rownames(attr(terms(with(data, formula)), which="factor"))
  return(facs)
}

remove.repeats <- function(x, column = 1, tolerance = 1E-06)
# function to remove repeated values that differ by no more than tolerance  
#If x is two-dimensional then column specifies which column of x is to be tested for repeats
{ 
  ndim <- length(dim(x))
  if (ndim <= 1)
  {
    n <- length(x)
    if (n > 1)
    { 
      repeats <-   c(FALSE, abs(x[2:n] - x[1:(n-1)]) < tolerance)
      x <- x[!repeats]
    }
  } else
  {
    if (ndim == 2)
    {
      repeats <-   c(FALSE, abs(x[2:n, column] - x[1:(n-1), column]) < tolerance)
      x <- x[!repeats,]
      
    } else
    {
      stop("remove.repeats cannot handle objects of more than two dimensions")
    }
  }
  return(x)
}

"ginv" <- function(x, tol = .Machine$double.eps ^ 0.5)
{ 
  # computes Moore-Penrose inverse of a matrix
  if (!is.matrix(x) | length(dim(x)) != 2 )
  {
    if (length(x) == 1)
      if (abs(x) < tol)
        geninv.x <- Inf
      else
        geninv.x <- 1/x
      else
        stop("x must be a matrix")
  }
  else
  {
    svd.x <- svd(x)
    nonzero.x <- (svd.x$d > svd.x$d[1] * tol)
    rank.x <- sum(nonzero.x)
    geninv.x <- matrix(0, dim(x)[1], dim(x)[2])
    if (rank.x)
    { i <- matrix((1:length(nonzero.x))[nonzero.x], rank.x, 2)
    geninv.x[i] <- 1/svd.x$d[nonzero.x]
    if (all(nonzero.x))
      geninv.x <- svd.x$v %*% geninv.x %*% t(svd.x$u)
    else 
      geninv.x <- svd.x$v[, nonzero.x] %*% geninv.x[nonzero.x, nonzero.x] %*% 
      t(svd.x$u[, nonzero.x])
    }
  }
  geninv.x
}