build URL edits, dependencies and usage: data("modifications"0 instead of just calling modifications

Author: guideflandre

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PTMods
 Type: Package
 Version: 0.99.0
-Title: Managing post-translational modifications in R
+Title: Managing Post-Translational Modifications in R
 Authors@R: c(person("Laurent", "Gatto", role = "aut",
                     email = "laurent.gatto@uclouvain.be",
                     comment = c(ORCID = "0000-0002-1520-2268")),
@@ -15,11 +15,11 @@ Description: An interface to the community supported database for
              amino acid/protein modifications using mass
              spectrometry.
 Depends: R (>= 4.5.0), methods
-Suggests: xml2, testthat, knitr, BiocStyle
+Suggests: xml2, testthat, knitr, BiocStyle, Biostrings
 License: GPL-3
 VignetteBuilder: knitr
 biocViews: Proteomics, MassSpectrometry
-BugReports: https://github.com/RforMassSpectrometry/unimod/issues
-URL: https://github.com/RforMassSpectrometry/unimod
+BugReports: https://github.com/RforMassSpectrometry/PTMods/issues
+URL: https://github.com/RforMassSpectrometry/PTMods
 RoxygenNote: 7.3.3
-Encoding: UTF-8
+Encoding: UTF-8

R/datasets.R

@@ -33,6 +33,7 @@
 #' PTMods:::.createDataSets()
 #' ```
 #'
+#' @usage data("elements")
 #' @format A `data.frame` with 4 columns (Name, FullName, AvgMass, MonoMass) for
 #' the chemical elements.
 #' @source Taken from the unimod database: http://www.unimod.org/xml/unimod.xml.
@@ -52,6 +53,7 @@
 #' PTMods:::.createDataSets()
 #' ```
 #'
+#' @usage data("aminoacids")
 #' @format A `data.frame` with 11 columns (OneLetter, ThreeLetter, FullName,
 #' AvgMass, MonoMass, H, C, N, O S, Se) for the aminoacids. The H/C/N/O/S/Se
 #' columns contain the number of elements that build the aminoacid.
@@ -72,6 +74,7 @@
 #' PTMods:::.createDataSets()
 #' ```
 #'
+#' @usage data("modifications")
 #' @format A `data.frame` with 15 columns (Id (created by
 #' Name:(Position-)Site(:NeutralLoss) because unimod id is not unique),
 #' UnimodId, Name, Description, AvgMass, MonoMass, Site, Position,