R/pcaAnalyseData.r

In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes

#' @export

  pcaAnalyseData = function(X, t0, t1, fname, vars=NULL, newnames=NULL,OFN=NULL,...) {
    
    if (!is.null(vars)) X = X[, vars ]
    if (!is.null(newnames) ) names(X) = newnames
    X = X[ which( rowSums( X, na.rm=T) !=0 ) ,]
    X = X[ which( as.numeric(rownames(X)) >= t0 ) ,]
    X = X[ which( as.numeric(rownames(X)) <= t1 ) ,]
    X = scale( X, center=T, scale=T )
    X.stats = lobSortedOrdination( X, outfileroot=fname ,outfilenames=OFN,...) # look in work directory for figures and data outputs
    return( X.stats ) 
  }