docs: fix typos in markdown, formatting

R/chromatographR-package.R

@@ -1,11 +1,9 @@
-
-
 #' chromatographR
 #' 
 #' chromatographR
 #' 
 #' \tabular{ll}{ Package: \tab chromatographR\cr Type: \tab Package\cr Version:
-#' \tab 0.4.5 \cr Date: \tab 2022-11-05\cr License: GPL (>= 2) }
+#' \tab 0.5.3 \cr Date: \tab 2023-08-17\cr License: GPL (>= 2) }
 #' 
 #' @name chromatographR-package
 #' @aliases chromatographR-package chromatographR

R/correct_rt.R

@@ -71,7 +71,7 @@
 #' 
 #' * 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}
+#' Metabolomics}, \bold{11}:143-154. \doi{10.1007/s11306-014-0683-5}.
 #' 
 #' @examplesIf interactive()
 #' data(Sa_pr)

R/fit_peaks.R

@@ -33,10 +33,10 @@
 #' 1, window will be interpreted as a proportion of points to include. Otherwise,
 #' the window will be the absolute number of points to include in the window.
 #' (Defaults to .001).
-#' @param slope_thresh Minimum threshold for peak slope. (Defaults to 0).
-#' @param amp_thresh Minimum threshold for peak amplitude. (Defaults to 0).
+#' @param slope_thresh Minimum threshold for peak slope. (Defaults to \code{0}).
+#' @param amp_thresh Minimum threshold for peak amplitude. (Defaults to \code{0}).
 #' @param bounds Logical. If TRUE, includes peak boundaries in data.frame.
-#' (Defaults to TRUE).
+#' (Defaults to \code{TRUE}).
 #' @return If bounds == TRUE, returns a data.frame containing the center, start,
 #' and end of each identified peak. Otherwise, returns a numeric vector of peak
 #' centers. All locations are expressed as indices.
@@ -50,8 +50,8 @@
 #' find_peaks(Sa_pr[[1]][,"220"])
 #' @seealso \code{\link{fit_peaks}}, \code{\link{get_peaks}}
 #' @references O'Haver, Tom. Pragmatic Introduction to Signal Processing:
-#' Applications in scientific measurement.
-#' /href{https://terpconnect.umd.edu/~toh/spectrum/} (Accessed January, 2022).
+#' Applications in scientific measurement. \url{https://terpconnect.umd.edu/~toh/spectrum/}
+#' (Accessed January, 2022).
 #' @export find_peaks
 find_peaks <- function(y, smooth_type=c("gaussian", "box", "savgol", "mva","tmva","none"),
                        smooth_window = .001, slope_thresh = 0, amp_thresh = 0,
@@ -139,7 +139,7 @@ find_peaks <- function(y, smooth_type=c("gaussian", "box", "savgol", "mva","tmva
 #' \item{height}{height of the peak (y)}
 #' \item{area}{peak area}
 #' \item{r.squared}{r-squared value for linear fit of model to data.}
-#' #' \item{purity}{spectral purity of peak as assessed by \code{\link{get_purity}}.}
+#' \item{purity}{spectral purity of peak as assessed by \code{\link{get_purity}}.}
 #' Again, the first five elements (rt, start, end, sd and FWHM) are expressed
 #' as indices, so not in terms of the real retention times. The transformation
 #' to "real" time is done in function \code{get_peaks}.
@@ -154,11 +154,11 @@ find_peaks <- function(y, smooth_type=c("gaussian", "box", "savgol", "mva","tmva
 #' fit_peaks(Sa_pr[[1]], lambda="220")
 #' @seealso \code{\link{find_peaks}}, \code{\link{get_peaks}}
 #' @references
-#' Lan, K. & Jorgenson, J. W. 2001. A hybrid of exponential and gaussian
+#' * Lan, K. & Jorgenson, J. W. 2001. A hybrid of exponential and gaussian
 #' functions as a simple model of asymmetric chromatographic peaks. \emph{Journal of
 #' Chromatography A} \bold{915}:1-13. \doi{10.1016/S0021-9673(01)00594-5}.
 #'
-#' Naish, P. J. & Hartwell, S. 1988. Exponentially Modified Gaussian functions - A
+#' * 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}.
 #' @export fit_peaks

R/get_peaks.R

@@ -56,26 +56,27 @@
 #' peak values to the raw data. This approach is not really statistically valid
 #' but it can still be useful as a rough metric for "goodness-of-fit").
 #' @author Ethan Bass
-#' @note The function is adapted from the
+#' @note This function is adapted from the
 #' \href{https://github.com/rwehrens/alsace/blob/master/R/getAllPeaks.R}{getAllPeaks}
 #' 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}
-#' 
-#' #' Lan, K. & Jorgenson, J. W. 2001. A hybrid of exponential and gaussian
+#' * Lan, K. & Jorgenson, J. W. 2001. A hybrid of exponential and gaussian
 #' functions as a simple model of asymmetric chromatographic peaks. \emph{Journal of
 #' Chromatography A} \bold{915}:1-13. \doi{10.1016/S0021-9673(01)00594-5}.
 #'
-#' Naish, P. J. & Hartwell, S. 1988. Exponentially Modified Gaussian functions - A
+#' * 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}.
+#'
+#' * O'Haver, Tom. Pragmatic Introduction to Signal Processing:
+#' Applications in scientific measurement.
+#' \url{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}.
+#' 
 #' @examplesIf interactive()
 #' data(Sa_pr)
 #' pks <- get_peaks(Sa_pr, lambdas = c('210'), sd.max=50, fit="egh")

R/get_peaktable.R

@@ -71,18 +71,18 @@
 #' * `args`: A vector of arguments given to \code{\link{get_peaktable}} to generate
 #' the peak table.
 #' @author Ethan Bass
-#' @note Adapted from
+#' @note This function is adapted from
 #' \href{https://github.com/rwehrens/alsace/blob/master/R/getPeakTable.R}{getPeakTable}
 #' function in the alsace package by Ron Wehrens.
 #' @md
 #' @references
 #' * Broeckling, C. D., Afsar F.A., Neumann S., Ben-Hur A., and Prenni J.E. 2014.
 #' RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based
 #' Annotation for Metabolomics Data. \emph{Anal. Chem.}
-#' \bold{86}:6812-6817. \doi{10.1021/ac501530d}
+#' \bold{86}:6812-6817. \doi{10.1021/ac501530d}.
 #' * 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}
+#' Metabolomics} \bold{11}:143-154. \doi{10.1007/s11306-014-0683-5}.
 #' @examplesIf interactive()
 #' data(Sa_pr)
 #' pks <- get_peaks(Sa_pr, lambdas = c('210'))

R/plot_spectrum.R

@@ -12,8 +12,7 @@
 #' @importFrom utils head tail
 #' @param loc The name of the peak or retention time for which you wish to
 #' extract spectral data.
-#' @param peak_table The peak table (output from \code{\link{get_peaktable}}
-#' function).
+#' @param peak_table The peak table (output from \code{\link{get_peaktable}}).
 #' @param chrom_list A list of chromatograms in matrix format (timepoints x
 #' wavelengths). If no argument is provided here, the function will try to find
 #' the \code{chrom_list} object used to create the provided \code{peak_table}.