updates

R/normalize.R

@@ -35,15 +35,10 @@
 #'      spectra, Trends in Analytical Chemistry, 28(10):1201-1222.
 #'
 #' @param x A numeric matrix or data frame containing the spectra.
-#' @param method A character vector specifying the normalization method to apply.
-#'   Available methods are: "area", "background", and "internal".
-#' @param bkg A numeric matrix or data frame of the same dimension as `x`, specifying
-#'   the intensity of the continuum radiation (background emission) used for
-#'   normalizing `x`. Required for "background" method.
-#' @param wlength A character vector of the selected wavelength(s) related to the
-#'   internal standard(s) peak intensity. Optional for "background" method.
-#' @param drop.na A logical value indicating whether to remove missing values before
-#'   normalizing (default: `TRUE`).
+#' @param method A character vector specifying the normalization method to apply. Available methods are: "area", "background", and "internal".
+#' @param bkg A numeric matrix or data frame of the same dimension as `x`, specifying the intensity of the continuum radiation (background emission) used for normalizing `x`. Required for "background" method.
+#' @param wlength A character vector of the selected wavelength(s) related to the internal standard(s) peak intensity. Optional for "background" method.
+#' @param drop.na A logical value indicating whether to remove missing values before normalizing. Default is `TRUE`.
 #'
 #' @return A data frame of normalized spectra.
 #'

R/outlierplot.R

@@ -60,13 +60,19 @@ outlierplot <- function(x, quan = 1/2, alpha = 0.025, show.outlier = TRUE, show.
   if (!is.numeric(quan) || quan < 0.5 || quan > 1) {
     stop("'quan' must be a numeric value between 0.5 and 1")
   }
+  if (!is.logical(show.outlier)) {
+    stop("'show.outlier' must be of type boolean (TRUE or FALSE)")
+  }
+  if (!is.logical(show.mahal)) {
+    stop("'show.mahal' must be of type boolean (TRUE or FALSE)")
+  }
 
   if (is.data.frame(x) || tibble::is_tibble(x)) {
     x <- as.matrix(x)
   }
 
   rob <- robustbase::covMcd(x, alpha = quan)
-  xarw <- adapt_reweight(x, rob$center, rob$cov, alpha = alpha)
+  xarw <- covARW(x, rob$center, rob$cov, alpha = alpha)
 
   if (xarw$cn != Inf) {
     alpha <- sqrt(c(xarw$cn, stats::qchisq(c(0.75, 0.5, 0.25), ncol(x))))
@@ -160,7 +166,7 @@ outlierplot <- function(x, quan = 1/2, alpha = 0.025, show.outlier = TRUE, show.
 }
 
 
-adapt_reweight <- function(x, m0, c0, alpha, pcrit){
+covARW <- function(x, m0, c0, alpha, pcrit){
   n <- nrow(x)
   p <- ncol(x)
 

_pkgdown.yml

@@ -9,10 +9,7 @@ reference:
   contents:
   - zscore
   - iqrMethod
-  - outlierplot
-  - adjusted_boxplot
   - directOutlyingness
-  - generalized_boxplot
 
 - title: Multivariate filtering
 
@@ -50,10 +47,13 @@ reference:
 
 - title: Data visualization
   desc: >
-    Functions that help visualize the state of the data.
+    Functions that help assess data visually.
   contents:
   - plotfit
   - plotSpec
+  - outlierplot
+  - adjusted_boxplot
+  - generalized_boxplot
 
 - title: Smoothing
   desc: >