docs: fix minor roxygen mistakes

R/fit_peaks.R

@@ -172,9 +172,9 @@ find_peaks <- function(y, smooth_type = c("gaussian", "box", "savgol",
 #'
 #' * Naish, P. J. & Hartwell, S. 1988. Exponentially Modified Gaussian functions - A
 #' good model for chromatographic peaks in isocratic HPLC? \emph{Chromatographia},
-#' /bold{26}: 285-296. \doi{10.1007/BF02268168}.
+#' \bold{26}: 285-296. \doi{10.1007/BF02268168}.
 #' @export fit_peaks
-
+#' @md
 fit_peaks <- function (x, lambda, pos = NULL, sd.max = 50,
                        fit = c("egh", "gaussian", "raw"),  max.iter = 1000, 
                        estimate_purity = TRUE, noise_threshold = .001, ...){

R/get_peaktable.R

@@ -54,7 +54,7 @@
 #' weight given to spectral correlation if \code{sp.rt} is selected.
 #' @param deepSplit Logical. Controls sensitivity to cluster splitting. If
 #' \code{TRUE}, function will return more smaller clusters. See documentation for
-#' \code{\link{cutreeDynamic}} for additional information.
+#' \code{\link[dynamicTreeCut]{cutreeDynamic}} for additional information.
 #' @param verbose Logical. Whether to print warning when combining peaks into 
 #' single time window. Defaults to \code{FALSE}.
 #' @param out Specify `data.frame` or `matrix` as output. Defaults to

R/get_purity.R

@@ -20,7 +20,7 @@
 #' @references
 #' Stahl, Mark. “Peak Purity Analysis in HPLC and CE Using Diode-Array Technology.”
 #' Agilent Technologies, April 1, 2003, 16.
-#' /href{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
+#' \url{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
 #' @author Ethan Bass
 #' @keywords internal
 #' @export
@@ -98,7 +98,7 @@ find_noise <- function(x, noise_threshold = 0.01, lambdas){
 #' @references
 #' Stahl, Mark. “Peak Purity Analysis in HPLC and CE Using Diode-Array Technology.”
 #' Agilent Technologies, April 1, 2003, 16.
-#' /href{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
+#' \url{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
 #' @author Ethan Bass
 #' @keywords internal
 #' @export
@@ -131,7 +131,7 @@ get_agilent_threshold <- function(x, pos, weight = 1, noise_variance = NULL,
 #' @references
 #' Stahl, Mark. “Peak Purity Analysis in HPLC and CE Using Diode-Array Technology.”
 #' Agilent Technologies, April 1, 2003, 16.
-#' /href{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
+#' \url{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
 #' @author Ethan Bass
 #'@noRd
 
@@ -155,7 +155,7 @@ get_spectral_similarity <- function(x, pos){
 #' @references
 #' Stahl, Mark. “Peak Purity Analysis in HPLC and CE Using Diode-Array Technology.”
 #' Agilent Technologies, April 1, 2003, 16.
-#' /href{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
+#' \url{https://www.agilent.com/cs/library/applications/5988-8647EN.pdf}
 #' @author Ethan Bass
 #' @noRd