docs: added more info about additional arguments in get_peaks

responding to #27

NEWS.md

@@ -2,6 +2,7 @@
 
 * Fixed bug in `plot_chroms` causing mismatched legend labels in base R plot.
 * Added additional arguments to `plot_chroms` function: `xlim`,`ylim`, and `legend_position`. 
+* Added additional information about arguments available in `get_peaks` for fine-tuning the peak-finding algorithm (in response to [#27](https://github.com/ethanbass/chromatographR/issues/27)).
 
 # chromatographR 0.5.2
 

R/get_peaks.R

@@ -5,9 +5,14 @@
 #' 
 #' Peaks are located by finding zero-crossings in the smoothed first derivative
 #' of the specified chromatographic traces (function \code{\link{find_peaks}}).
-#' At the given positions, an exponential-gaussian hybrid (or regular gaussian)
-#' function is fit to the signal using \code{\link{fit_peaks}}). The area is then
-#' calculated using a trapezoidal approximation.
+#' Additional arguments can be provided to \code{\link{find_peaks}} to fine-tune
+#' the peak-finding algorithm. For example, the \code{smooth_window} can be
+#' increased to prevent peaks from being split into multiple features. Overly
+#' aggressive smoothing may cause small peaks to be overlooked. At the given 
+#' positions, an exponential-gaussian hybrid (or regular gaussian)
+#' function is fit to the signal using \code{\link{fit_peaks}} according to the
+#' value of \code{fit}. Finally, the area is calculated using trapezoidal 
+#' approximation.
 #' 
 #' The \code{sd}, \code{FWHM}, \code{tau}, and \code{area} are returned in units
 #' determined by \code{time.units}. By defaults the units are in minutes.
@@ -35,7 +40,11 @@
 #' Either an integer specifying the number of clusters to use for parallel
 #' processing or a cluster object created by \code{\link[parallel]{makeCluster}}.
 #' Defaults to 2. On Windows integer values will be ignored.
-#' @param \dots Additional arguments to \code{\link{find_peaks}}.
+#' @param \dots Additional arguments to \code{\link{find_peaks}}. Arguments
+#' provided to \code{\link{find_peaks}} can be used to fine-tune the peak-finding
+#' algorithm. Most importantly, the \code{smooth_window} should be increased if
+#' features are being split into multiple bins. Other arguments that can be used
+#' here include \code{smooth_type}, \code{slope_thresh}, and \code{amp_thresh}.
 #' @return The result is an S3 object of class \code{peak_list}, containing a nested
 #' list of data.frames containing information about the peaks fitted for each
 #' chromatogram at each specified wavelength. The data.frame includes information
@@ -52,6 +61,10 @@
 #' function authored by Ron Wehrens (though the underlying algorithms for peak
 #' identification and peak-fitting are not the same).
 #' @references 
+#' O'Haver, Tom. Pragmatic Introduction to Signal Processing:
+#' Applications in scientific measurement.
+#' /href{https://terpconnect.umd.edu/~toh/spectrum/} (Accessed January, 2022).
+#' 
 #' Wehrens, R., Carvalho, E., Fraser, P.D. 2015. Metabolite profiling in
 #' LC–DAD using multivariate curve resolution: the alsace package for R. \emph{
 #' Metabolomics} \bold{11}:143-154. \doi{10.1007/s11306-014-0683-5}