resurrected pairwise_ratio but kept it internal

R/graveyard.R

@@ -1,85 +1,67 @@
-#' ################################################################################
-#' #
-#' ################################################################################
+#' Pairwise index combinations
 #'
-#' #' Pairwise index combinations
-#' #'
-#' #' \code{i_index_pairwise_combn} returns the split pairwise combination of idxs
-#' #' in a matrix
-#' #'
-#' #' @param n number of indices
-#' #' @return list of matrices. For each focal index up to n - 1, a matrix with the
-#' #' other indexes it interacts with (2nd col) and the "absolute position" of that
-#' #' pairwise interaction (1st column) is returned.
-#' #'
-#' #' @author Jose Eduardo Meireles
-#' #' @keywords internal
-#' i_index_pairwise_combn = function(n){
+#' \code{i_index_pairwise_combn} returns the split pairwise combination of idxs
+#' in a matrix
 #'
-#'     if( ! i_is_whole(n) | n < 2 ){
-#'         stop("n must be an integer > 1")
-#'     }
+#' @param n number of indices
+#' @return list of matrices. For each focal index up to n - 1, a matrix with the
+#' other indexes it interacts with (2nd col) and the "absolute position" of that
+#' pairwise interaction (1st column) is returned.
 #'
-#'     focal_seq = seq.int(1, n - 1)
-#'     focal_idx = rep.int(focal_seq, rev(focal_seq))
+#' @author Jose Eduardo Meireles
+#' @keywords internal
+i_index_pairwise_combn = function(n){
+
+    if( ! i_is_whole(n) | n < 2 ){
+        stop("n must be an integer > 1")
+    }
+
+    focal_seq = seq.int(1, n - 1)
+    focal_idx = rep.int(focal_seq, rev(focal_seq))
+
+    iter_seq  = seq.int(2, n)
+    iter_idx  = unlist(sapply(iter_seq, function(x){ seq.int(x, n)} ))
+
+    pos_idx   = seq.int(along.with = iter_idx)
+
+    pcomb = data.frame("pos" = pos_idx,  "iter" = iter_idx, check.names = FALSE)
+    split(pcomb, focal_idx)
+}
+
+
+#' Pairwise value ratios
 #'
-#'     iter_seq  = seq.int(2, n)
-#'     iter_idx  = unlist(sapply(iter_seq, function(x){ seq.int(x, n)} ))
+#' \code{pairwise_ratio} computes pairwise ratios between bands
 #'
-#'     pos_idx   = seq.int(along.with = iter_idx)
+#' @param x spectra
+#' @param simplify coerce to matrix or keep result as list
+#' @return list or matrix
 #'
-#'     pcomb = data.frame("pos" = pos_idx,  "iter" = iter_idx, check.names = FALSE)
-#'     split(pcomb, focal_idx)
-#' }
+#' @author Jose Eduardo Meireles
+#' @keywords internal
 #'
+#' @examples
+#' library(spectrolab)
 #'
-#' #' Pairwise value ratios -- Deprecated!
-#' #'
-#' #' \code{ratio} computes pairwise ratios between bands
-#' #'
-#' #'  Deprecated!
-#' #'
-#' #' @param x spectra
-#' #' @param simplify coerce to matrix or keep result as list
-#' #' @return list or matrix
-#' #'
-#' #' @author Jose Eduardo Meireles
-#' #'
-#' #' @examples
-#' #' library(spectrolab)
-#' #'
-#' #' # Ratios of visible part of the spectrum
-#' #' spec = as_spectra(spec_matrix_example, name_idx = 1)[ , 400:700 ]
-#' #' spec_ratio_mat = ratio(spec)
-#' ratio = function(x, simplify = FALSE){
-#'     warning("Deprecated!")
-#'     UseMethod("ratio")
-#' }
-#'
-#'
-#' #' @describeIn ratio Compute pairwise value ratios
-#' ratio.spectra = function(x, simplify = FALSE){
-#'     message("ratio may take a while...")
-#'     spm  = as.matrix(x)
-#'     wvl  = bands(x)
-#'     pwc  = i_index_pairwise_combn(ncol(x))
-#'
-#'     res  = lapply(names(pwc), function(y){
-#'         i   = as.numeric(y)
-#'         j   = pwc[[y]][ , "iter"]
-#'         mat = spm[ , i]  / spm[ , j, drop = FALSE]
-#'         colnames(mat) = paste(wvl[i], wvl[j], sep = "/")
-#'         mat
-#'     })
-#'
-#'     names(res) = wvl[ as.numeric(names(pwc)) ]
-#'
-#'     if(simplify){
-#'         res = do.call(cbind, res)
-#'     }
-#'     res
-#' }
-#'
-#' ################################################################################
-#' #
-#' ################################################################################
+#' # Ratios of visible part of the spectrum
+pairwise_ratio = function(x, simplify = FALSE){
+    message("ratio may take a while...")
+    spm  = as.matrix(x)
+    wvl  = bands(x)
+    pwc  = i_index_pairwise_combn(ncol(x))
+
+    res  = lapply(names(pwc), function(y){
+        i   = as.numeric(y)
+        j   = pwc[[y]][ , "iter"]
+        mat = spm[ , i]  / spm[ , j, drop = FALSE]
+        colnames(mat) = paste(wvl[i], wvl[j], sep = "/")
+        mat
+    })
+
+    names(res) = wvl[ as.numeric(names(pwc)) ]
+
+    if(simplify){
+        res = do.call(cbind, res)
+    }
+    res
+}