Merge pull request #71 from r-hyperspec/feature-38/preparation

Preparation to rename functions

DESCRIPTION

@@ -143,6 +143,7 @@ Collate:
     'as_hyperSpec.R'
     'barbiturates.R'
     'bind.R'
+    'calculate_stacked_offsets.R'
     'colMeans.R'
     'collapse.R'
     'cov_pooled.R'
@@ -168,13 +169,12 @@ Collate:
     'paracetamol.R'
     'laser.R'
     'hyperspec-package.R'
+    'identify_spc.R'
     'labels.R'
-    'plotmap.R'
+    'plot_map.R'
     'levelplot.R'
-    'makeraster.R'
     'map_identify.R'
-    'map_sel_poly.R'
-    'mark_dendrogram.R'
+    'mark_groups_in_dendrogram.R'
     'mark_peak.R'
     'mean_sd.R'
     'merge.R'
@@ -183,11 +183,12 @@ Collate:
     'palette_colorblind.R'
     'palette_matlab.R'
     'plot.R'
-    'plotc.R'
-    'plotmat.R'
-    'plotspc.R'
-    'plotvoronoi.R'
+    'plot_and_get.R'
+    'plot_c.R'
+    'plot_mat.R'
+    'plot_voronoi.R'
     'quantile.R'
+    'raster.R'
     'rbind.fill.R'
     'read_txt_long.R'
     'read_txt_wide.R'
@@ -199,14 +200,13 @@ Collate:
     'show.R'
     'spc_bin.R'
     'spc_fix_colnames.R'
-    'spc_identify.R'
     'spc_loess.R'
     'spc_na_approx.R'
     'spc_spline.R'
     'split.R'
     'subset.R'
     'sweep.R'
-    'trellis.factor.key.R'
+    'trellis_factor_key.R'
     'vandermonde.R'
     'wl.R'
     'wl_fix_unit_name.R'
@@ -216,4 +216,3 @@ Collate:
     'write_txt_long.R'
     'write_txt_wide.R'
     'zzz.R'
-

R/plotspc.R → R/calculate_stacked_offsets.R

@@ -45,7 +45,7 @@
 #'        accidentally plotting of large numbers of spectra).
 #' @param func a function to apply to each wavelength in order to calculate
 #'        summary spectra such as mean, min, max, etc.
-#' @param func.args `list` with furter arguments for `func`
+#' @param func.args `list` with further arguments for `func`
 #' @param add if `TRUE`, the output is added to the existing plot
 #' @param bty see [graphics::par()]
 #' @param col see [graphics::par()]. `col` might be a vector giving individual

R/spc_identify.R → R/identify_spc.R

@@ -5,7 +5,7 @@
 #' Function [spc.identify()] allows to identify the spectrum and the wavelength
 #' of a point in a plot produced by [plotspc()].
 #'
-#' @rdname spc_identify
+#' @rdname identify_spc
 #'
 #' @aliases spc.identify
 #'          spc.label.default
@@ -267,7 +267,7 @@ spc.identify <- function(x, y = NULL,
 
 # Function -------------------------------------------------------------------
 
-#' @rdname spc_identify
+#' @rdname identify_spc
 #'
 #' @param wl The wavelength to label.
 #' @param spc The intensity to label.
@@ -279,21 +279,21 @@ spc.point.max <- function(wl, spc, wlclick) {
   c(wl = wl[i], spc = spc[i])
 }
 
-#' @rdname spc_identify
+#' @rdname identify_spc
 #' @export
 spc.point.default <- function(wl, spc, wlclick) {
   i <- round(approx(wl, seq_along(wl), wlclick, rule = 2)$y)
   c(wl = wl[], spc = spc[i])
 }
 
-#' @rdname spc_identify
+#' @rdname identify_spc
 #' @export
 spc.point.min <- function(wl, spc, wlclick) {
   i <- which.min(spc)
   c(wl = wl[i], spc = spc[i])
 }
 
-#' @rdname spc_identify
+#' @rdname identify_spc
 #' @export
 spc.point.sqr <- function(wl, spc, wlclick, delta = 1L) {
   i <- which.max(spc)
@@ -318,7 +318,7 @@ spc.point.sqr <- function(wl, spc, wlclick, delta = 1L) {
 
 # Function -------------------------------------------------------------------
 
-#' @rdname spc_identify
+#' @rdname identify_spc
 #'
 #' @param ispc If a selection of spectra was plotted, their indices can be
 #'        given in `ispc`. In this case `ispc[i]` is returned rather than `i`.
@@ -329,7 +329,7 @@ spc.label.default <- function(ispc, wl, spc, digits = 3) {
   sprintf(" %i, %s ", ispc, format(wl, digits = digits))
 }
 
-#' @rdname spc_identify
+#' @rdname identify_spc
 #' @export
 spc.label.wlonly <- function(ispc, wl, spc, digits = 3) {
   sprintf(" %s ", format(wl, digits = digits))

R/levelplot.R

@@ -100,7 +100,7 @@ setMethod("levelplot",
 #'   legend?
 #' @param contour,useRaster see  [lattice::levelplot()]
 #'
-#' @include plotmap.R
+#' @include plot_map.R
 #' @importFrom lattice levelplot
 #' @export
 #'

R/map_identify.R

@@ -1,5 +1,5 @@
 #' @aliases levelplot,hyperSpec,missing-method
-#' @include plotmap.R
+#' @include plot_map.R
 #' @rdname levelplot
 #'
 #' @export

R/map_sel_poly.R → R/plot_and_get.R

@@ -4,7 +4,7 @@
 #' [grid::grid.locator()]). Polygon will be drawn closed.
 #'
 #' `map.sel.poly` is a convenience wrapper for [plotmap()], `sel.poly`,
-#' and [sp::point.in.polygon()]. For custiomized plotting, the plot can be produced by
+#' and [sp::point.in.polygon()]. For customized plotting, the plot can be produced by
 #' [plotmap()], [plotvoronoi()] or [levelplot()], and the result of
 #' that plot command handed over to `map.sel.poly`, see the example below.
 #'

R/plotc.R → R/plot_c.R

@@ -1,4 +1,4 @@
-### -----------------------------------------------------------------------------
+### --------------------------------------------------------------------------
 ###
 ###  plotc - plot timeseries, concentration, ...
 ###

R/makeraster.R → R/raster.R

@@ -6,7 +6,7 @@
 #' `x` values: The differences between the values of `x` are calculated (possible step
 #' sizes). For each of those step sizes, different points are tried (until all points have been
 #' covered by a raster) and the parameter combination leading to the best coverage (i.e. most points
-#' on the grid) ist used.
+#' on the grid) is not used.
 #'
 #' Note that only differences between the sorted values of x are considered as step size.
 #' @param x numeric to be fitted with a raster