docs: small changes to titles and descriptions

fixed bracket notes

DESCRIPTION

@@ -56,7 +56,7 @@ Config/reticulate: list( packages = list(list(package = "scipy"),
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000
 Additional_repositories: https://ethanbass.github.io/drat/, https://ethanbass.r-universe.dev/
 Config/testthat/edition: 3
 Config/Needs/website: rmarkdown, ggplot2, dplyr

R/attach_metadata.R

@@ -736,7 +736,8 @@ read_waters_metadata <- function(file){
 
 #' Extract metadata
 #'
-#' Extract metadata as a data.frame from a list of chromatograms.
+#' Extract metadata as a \code{data.frame} or \code{tibble} from a list of
+#' chromatograms.
 #'
 #' @param chrom_list A list of chromatograms with attached metadata (as returned
 #' by \code{read_chroms} with \code{read_metadata = TRUE}).

R/call_aston.R

@@ -16,7 +16,7 @@
 #' or \code{raw}.
 #' @return A chromatogram in \code{data.frame} format (retention time x wavelength).
 #' @import reticulate
-#' @family {external parsers}
+#' @family external parsers
 #' @export sp_converter
 
 sp_converter <- function(path, format_out = c("matrix", "data.frame", "data.table"),
@@ -66,7 +66,7 @@ sp_converter <- function(path, format_out = c("matrix", "data.frame", "data.tabl
 #' or \code{raw}.
 #' @return A chromatogram in \code{data.frame} format (retention time x wavelength).
 #' @import reticulate
-#' @family {external parsers}
+#' @family external parsers
 #' @export uv_converter
 
 uv_converter <- function(path, format_out = c("matrix","data.frame","data.table"),

R/call_entab.R

@@ -1,5 +1,7 @@
-#' Call Entab
-#' Converts files using Entab parsers
+#' Call Entab parsers
+#'
+#' Converts files using [Entab](https://github.com/bovee/entab) parsers.
+#'
 #' @param path Path to file
 #' @param data_format Whether to return data in \code{wide} or \code{long} format.
 #' @param format_out Class of output. Either \code{matrix}, \code{data.frame},
@@ -10,7 +12,7 @@
 #' or \code{raw}.
 #' @return A chromatogram in the format specified by \code{format_out}
 #' (retention time x wavelength).
-#' @family {external parsers}
+#' @family external parsers
 #' @export
 
 call_entab <- function(path, data_format = c("wide", "long"),

R/call_openchrom.R

@@ -52,7 +52,7 @@
 #' Software for the Mass Spectrometric Analysis of Chromatographic Data. \emph{
 #' BMC Bioinformatics} \bold{11}, no. 1 (July 30, 2010): 405.
 #' \doi{10.1186/1471-2105-11-405}.
-#' @family {external parsers}
+#' @family external parsers
 #' @export
 
 call_openchrom <- function(files, path_out = NULL, format_in,
@@ -173,6 +173,9 @@ write_openchrom_batchfile <- function(files, path_out,
 
 #' Configure OpenChrom parser
 #'
+#' Configures [OpenChrom](https://lablicate.com/platform/openchrom) to use
+#' command-line interface. Requires OpenChrom version prior to 0.5.0.
+#'
 #' @name configure_openchrom
 #' @param cli Defaults to NULL. If "true", R will rewrite openchrom ini file to enable CLI.
 #' If "false", R will disable CLI. If NULL, R will not modify the ini file.
@@ -183,6 +186,7 @@ write_openchrom_batchfile <- function(files, path_out,
 #' indicating whether 'OpenChrom' is configured correctly. Otherwise, returns
 #' the path to OpenChrom command-line application.
 #' @author Ethan Bass
+#' @seealso [call_openchrom]
 #' @export
 
 configure_openchrom <- function(cli = c("null", "true", "false", "status"), path = NULL){

R/call_rainbow.R

@@ -1,4 +1,4 @@
-#' Parse Agilent or Waters files with rainbow parser
+#' Call Rainbow parsers
 #'
 #' Uses [rainbow](https://rainbow-api.readthedocs.io) parsers to read in Agilent (.D)
 #' and Waters (.raw) files. If \code{format_in} is \code{agilent_d} or
@@ -27,7 +27,7 @@
 #' @return Returns a (nested) list of \code{matrices} or \code{data.frames} according to
 #' the value of \code{format_out}. Data is ordered according to the value of
 #' \code{by}.
-#' @family {external parsers}
+#' @family external parsers
 #' @export
 
 call_rainbow <- function(path,

R/read_agilent_d.R

@@ -1,11 +1,6 @@
 #' Read files from 'ChemStation' .D directories
 #'
-#' Agilent \code{.ch} files come in several different varieties. This parser
-#' can automatically detect and read several versions of these files from
-#' 'Agilent ChemStation' and 'Agilent OpenLab', including versions \code{30} and
-#' \code{130}, which are generally produced by ultraviolet detectors, as well as
-#' \code{81}, \code{179}, and \code{181} which are generally produced by flame
-#' ionization (FID) detectors.
+#' Reads files from 'Agilent' \code{.D} directories.
 #'
 #' @param path Path to \code{.ch} file
 #' @param what Whether to extract chromatograms (\code{chroms}), DAD data
@@ -30,7 +25,7 @@
 #' Metadata can be attached to the chromatogram as \code{\link{attributes}} if
 #' \code{read_metadata} is \code{TRUE}.
 #' @author Ethan Bass
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 
 read_agilent_d <- function(path, what = c("chroms", "dad", "peak_table"),

R/read_asm.R

@@ -1,6 +1,7 @@
-#' Read Allotrope Simple Model (ASM) 2D chromatograms
+#' Read 'Allotrope Simple Model' (ASM) 2D chromatograms
 #'
-#' A parser for reading 'Allotrope Simple Model' files into R.
+#' A parser for reading ['Allotrope Simple Model'](https://www.allotrope.org/asm)
+#' files.
 #'
 #' @param path Path to ASM \code{.json} file.
 #' @param format_out Matrix or data.frame.

R/read_cdf.R

@@ -1,6 +1,6 @@
-#' Read CDF file
+#' Read CDF
 #'
-#' Parser for Analytical Data Interchange (ANDI) netCDF files.
+#' Reads 'Analytical Data Interchange' (ANDI) netCDF (\code{.cdf}) files.
 #'
 #' @param path Path to ANDI netCDF file.
 #' @param format_out Class of output. Either \code{matrix}, \code{data.frame},

R/read_chemstation_ch.R

@@ -1,6 +1,8 @@
-#' Read 'ChemStation' CH files
+#' Read 'Agilent ChemStation' CH files
 #'
-#' Agilent \code{.ch} files come in several different varieties. This parser
+#' Reads 'Agilent ChemStation' \code{.ch} files.
+#'
+#' Agilent \code{.ch} files come in several different formats. This parser
 #' can automatically detect and read several versions of these files from
 #' 'Agilent ChemStation' and 'Agilent OpenLab', including versions \code{30} and
 #' \code{130}, which are generally produced by ultraviolet detectors, as well as
@@ -30,7 +32,7 @@
 #' @note This function was adapted from the
 #' \href{https://github.com/chemplexity/chromatography}{Chromatography Toolbox}
 #' (&copy James Dillon 2014).
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 #' @md
 
@@ -454,7 +456,13 @@ get_agilent_offsets <- function(version){
   offsets
 }
 
-#' Parser for reading Agilent ('.dx') files into R
+#' Read 'Agilent' DX files
+#'
+#' Reads 'Agilent' \code{.dx} files.
+#'
+#' This function unzips 'Agilent'  \code{.dx} into a temporary directory using
+#' \code{\link{unzip}} and calls \code{\link{read_chemstation_ch}}.
+#'
 #' @importFrom utils unzip
 #' @param path Path to \code{.dx} file.
 #' @param path_out Path to directory to export unzipped files.
@@ -466,7 +474,7 @@ get_agilent_offsets <- function(version){
 #' @return A chromatogram in the format specified by \code{format_out}
 #' (retention time x wavelength).
 #' @author Ethan Bass
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 read_agilent_dx <-  function(path, path_out = NULL,
                              format_out = c("matrix", "data.frame", "data.table"),

R/read_chemstation_csv.R

@@ -1,6 +1,6 @@
 #' Read Chemstation CSV
 #'
-#' Reads 'Agilent Chemstation' CSV files into R.
+#' Reads 'Agilent Chemstation' \code{.csv} files.
 #'
 #' 'Agilent Chemstation' CSV files are encoded in UTF-16.
 #'
@@ -12,7 +12,7 @@
 #' @return A chromatogram in the format specified by \code{format_out}
 #' (retention time x wavelength).
 #' @author Ethan Bass
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 
 read_chemstation_csv <- function(path, format_out = c("matrix", "data.frame", "data.table")){

R/read_chemstation_ms.R

@@ -1,6 +1,6 @@
 #' Read 'Agilent ChemStation' MS file.
 #'
-#' Parser to read Agilent Chemstation 'MSD Spectral Files' beginning with
+#' Reads 'Agilent ChemStation MSD Spectral Files' beginning with
 #' \code{x01/x32/x00/x00}.
 #'
 #' @param path Path to \code{.ms} file
@@ -28,7 +28,7 @@
 #' @note Many thanks to Evan Shi and Eugene Kwan for providing helpful
 #' information on the structure of these files in the
 #' \href{https://rainbow-api.readthedocs.io/en/latest/agilent/ms.html}{rainbow documentation}.
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 
 read_chemstation_ms <- function(path, what = c("MS1", "BPC", "TIC"),

R/read_chemstation_report.R

@@ -1,4 +1,4 @@
-#' Read 'Agilent ChemStation' Reports
+#' Read 'Agilent ChemStation' report files.
 #' @param paths Paths to 'ChemStation' report files.
 #' @param data_format Format to output data. Either \code{chromatographr} or
 #' \code{chemstation}.
@@ -7,7 +7,7 @@
 #' @return A data.frame containing the information from the specified
 #' 'ChemStation' report.
 #' @author Ethan Bass
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 
 read_chemstation_reports <- function(paths, data_format = c("chromatographr",

R/read_chemstation_uv.R

@@ -1,6 +1,6 @@
-#' Read 'ChemStation' DAD files
+#' Read 'Agilent ChemStation' DAD files
 #'
-#' Agilent \code{.uv} files come in several different varieties. This parser can
+#' Agilent \code{.uv} files come in several different formats. This parser can
 #' automatically detect and read several versions of these files from
 #' 'Agilent ChemStation' and 'Agilent OpenLab', including versions \code{31} and
 #' \code{131}.
@@ -27,7 +27,7 @@
 #' @note This function was adapted from the parser in the rainbow project
 #' licensed under GPL 3 by Evan Shi
 #' \url{https://rainbow-api.readthedocs.io/en/latest/agilent/uv.html}.
-#' @family {'Agilent' parsers}
+#' @family 'Agilent' parsers
 #' @export
 
 read_chemstation_uv <- function(path, format_out = c("matrix", "data.frame",

R/read_chromeleon.R

@@ -1,7 +1,7 @@
 
-#' Chromeleon ASCII reader
+#' Read 'Chromeleon' ASCII files
 #'
-#' Reads 'Thermo Fisher Chromeleon™ CDS' files into R.
+#' Reads 'Thermo Fisher Chromeleon™ CDS' ASCII (\code{.txt}) files.
 #'
 #' @importFrom utils tail read.csv
 #' @param path Path to file

R/read_mdf.R

@@ -1,4 +1,7 @@
-#' Read 'Lumex' MDF files into R
+#' Read 'Lumex' MDF
+#'
+#' Reads 'Lumex' \code{.mdf} files.
+#'
 #' @param path The path to a 'Lumex' \code{.mdf} file.
 #' @param format_out Class of output. Either \code{matrix}, \code{data.frame},
 #' or \code{data.table}.

R/read_mzml.R

@@ -1,4 +1,4 @@
-#' Extract data from mzML files
+#' Read mzML files
 #'
 #' Extracts data from \code{mzML} files using parsers from either RaMS or mzR.
 #' The RaMS parser (default) will only return data in tidy (long) format. The

R/read_shimadzu_ascii.R

@@ -1,6 +1,6 @@
-#' Shimadzu ascii reader
+#' Read 'Shimadzu' ASCII
 #'
-#' Reads 'Shimadzu' ascii files into R. These files can be exported from
+#' Reads 'Shimadzu' ASCII (\code{.txt}) files. These files can be exported from
 #' 'Shimadzu LabSolutions' by right clicking on samples in the sample list and
 #' selecting \code{File Conversion:Convert to ASCII}.
 #'
@@ -31,7 +31,7 @@
 #' the value of \code{what}. Chromatograms are returned in the format specified
 #' by \code{format_out} (retention time x wavelength).
 #' @author Ethan Bass
-#' @family {'Shimadzu' parsers}
+#' @family 'Shimadzu' parsers
 #' @export
 
 read_shimadzu <- function(path, what = "chroms",

R/read_shimadzu_gcd.R

@@ -1,6 +1,6 @@
-#' Shimadzu GCD parser
+#' Read 'Shimadzu' GCD
 #'
-#' Read chromatogram data streams from 'Shimadzu' GCD files.
+#' Read chromatogram data streams from 'Shimadzu' \code{.gcd} files.
 #'
 #' A parser to read chromatogram data streams from 'Shimadzu' \code{.gcd} files.
 #' GCD files are encoded as 'Microsoft' OLE documents. The parser relies on the
@@ -39,7 +39,7 @@
 #' according to the value of \code{data_format}.
 #' @note This parser is experimental and may still need some work. It is not
 #' yet able to interpret much metadata from the files.
-#' @family {'Shimadzu' parsers}
+#' @family 'Shimadzu' parsers
 #' @export
 
 read_shimadzu_gcd <- function(path, what = "chroms",

R/read_shimadzu_lcd.R

@@ -1,6 +1,6 @@
-#' Shimadzu LCD parser
+#' Read 'Shimadzu' LCD
 #'
-#' Read 3D PDA or 2D chromatogram streams from 'Shimadzu' LCD files.
+#' Read 3D PDA or 2D chromatogram streams from 'Shimadzu' \code{.lcd} files.
 #'
 #' A parser to read data from 'Shimadzu' \code{.lcd} files. LCD files are
 #' encoded as 'Microsoft' OLE documents. The parser relies on the
@@ -57,7 +57,7 @@
 #' \code{read_metadata} is \code{TRUE}.
 #' @note My parsing of the date-time format seems to be a little off, since
 #' the acquisition times diverge slightly from the ASCII file.
-#' @family {'Shimadzu' parsers}
+#' @family 'Shimadzu' parsers
 #' @export
 
 read_shimadzu_lcd <- function(path, what, format_out = c("matrix", "data.frame",
@@ -118,9 +118,9 @@ read_shimadzu_lcd <- function(path, what, format_out = c("matrix", "data.frame",
   dat
 }
 
-#' Shimadzu LCD 3D parser
+#' Read 'Shimadzu' LCD 3D data
 #'
-#' Read 3D PDA data stream from 'Shimadzu' LCD files.
+#' Reads 3D PDA data stream from 'Shimadzu' \code{.lcd} files.
 #'
 #' A parser to read PDA data from 'Shimadzu' \code{.lcd} files. LCD files are
 #' encoded as 'Microsoft' OLE documents. The parser relies on the
@@ -161,7 +161,7 @@ read_shimadzu_lcd <- function(path, what, format_out = c("matrix", "data.frame",
 #' \code{data.frame} format, according to the value of \code{format_out}.
 #' The chromatograms will be returned in \code{wide} or \code{long} format
 #' according to the value of \code{data_format}.
-#' @family {'Shimadzu' parsers}
+#' @family 'Shimadzu' parsers
 #' @export
 
 read_sz_lcd_3d <- function(path, format_out = "matrix",
@@ -209,9 +209,9 @@ read_sz_lcd_3d <- function(path, format_out = "matrix",
   dat
 }
 
-#' Shimadzu LCD 2D parser
+#' Read 'Shimadzu' LCD 2D data
 #'
-#' Read 2D PDA data stream from 'Shimadzu' LCD files.
+#' Reads 2D PDA data stream from 'Shimadzu' \code{.lcd} files.
 #'
 #' A parser to read chromatogram data streams from 'Shimadzu' \code{.lcd} files.
 #' LCD files are encoded as 'Microsoft' OLE documents. The parser relies on the
@@ -254,7 +254,7 @@ read_sz_lcd_3d <- function(path, format_out = "matrix",
 #' \code{format_out}. If multiple chromatograms are found, they will be returned
 #' as a list of matrices or data.frames. The chromatograms will be returned in
 #' \code{wide} or \code{long} format according to the value of \code{data_format}.
-#' @family {'Shimadzu' parsers}
+#' @family 'Shimadzu' parsers
 #' @export
 
 read_sz_lcd_2d <- function(path, format_out = "data.frame",

R/read_shimadzu_qgd.R

@@ -1,6 +1,6 @@
 #' Read 'Shimadzu' QGD
 #'
-#' Parser for 'Shimadzu GCMSsolution' \code{.qgd} files.
+#' Reads 'Shimadzu GCMSsolution' \code{.qgd} GC-MS data files.
 #'
 #' The MS data is stored in the "GCMS Raw Data" storage, which contains a
 #' \code{MS Raw Data} stream with MS scans, a \code{TIC Data} stream containing
@@ -48,7 +48,7 @@
 #' attached to the chromatogram as \code{\link{attributes}} if
 #' \code{read_metadata} is \code{TRUE}.
 #' @author Ethan Bass
-#' @family {'Shimadzu' parsers}
+#' @family 'Shimadzu' parsers
 #' @export
 
 read_shimadzu_qgd <- function(path, what = c("MS1", "TIC"),