add ISTDLists

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: patRoonData
 Type: Package
 Title: Example Data For The patRoon Package 
-Version: 2.0.0
+Version: 2.1.0
 Authors@R: c(
     person("Rick", "Helmus", email = "[email protected]", role = c("aut", "cre")),
     person("Narain-Ford", "Dominique", role = "aut"),
@@ -14,7 +14,7 @@ Suggests: patRoon
 License: CC0
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 URL: https://github.com/rickhelmus/patRoonData
 BugReports: https://github.com/rickhelmus/patRoonData/issues
 Depends: R (>= 2.10)

R/patRoonData.R

@@ -57,6 +57,7 @@ exampleAnalysisInfo <- function(polarity = "positive")
 #' @name suspects
 #' @author Dominique Narain-Ford, Samira Absalah, Rick Helmus and Vittorio Albergamo
 #' @keywords datasets
+#' @seealso \link{ISTDList}
 NULL
 
 #' @format 
@@ -68,3 +69,27 @@ NULL
 #' @aliases suspectsNeg
 #' @rdname suspects
 "suspectsNeg"
+
+#' Example internal standard lists
+#'
+#' The \code{ISTDListPos} and \code{ISTDListNeg} datasets are example lists with internal standards for a set of
+#' environmental contaminants (measured in positive and negative ionization, respectively). The datasets can be directly
+#' used with the \code{\link[patRoon]{normInts}} function.
+#'
+#' @format A \code{data.frame} with column \code{name}, \code{formula} and \code{rt}, specifying the analyte name,
+#'   formula and retention time (in seconds), respectively.
+#' @name ISTDList
+#' @author Dominique Narain-Ford, Samira Absalah, Rick Helmus and Vittorio Albergamo
+#' @keywords datasets
+#' @seealso \link{suspects}
+NULL
+
+#' @format 
+#' @aliases ISTDListPos
+#' @rdname ISTDList
+"ISTDListPos"
+
+#' @format 
+#' @aliases ISTDListNeg
+#' @rdname ISTDList
+"ISTDListNeg"

README.md

@@ -1,7 +1,7 @@
 # patRoonData
 
 This R package contains example to test and demonstrate the [patRoon R package][patRoon].
-The data is used in the [package vignette][patRoon-tutorial] to demonstrate the various functionalities of patRoon regarding mass spectrometry based non-target analysis.
+The data is used in the [package vignette][patRoon-tutorial] to demonstrate the various functionality of patRoon regarding mass spectrometry based non-target analysis.
 
 This data package contains
 * a triplicate analysis of a blank solvent (useful for blank subtraction)

data-raw/istds-neg.csv

@@ -0,0 +1,10 @@
+name,formula,rt
+Clofibric-D4 acid,C10[2]H4H7ClO3,339.1
+Diclofenac-13C6,C8[13]C6H11Cl2NO2,375.8
+"Fipronil-(pyrazole-13C3, cyano-13C)",C8[13]C4H4Cl2F6N4OS,350.4
+Furosemide-D5,C12[2]H5H6ClN2O5S,327.7
+Ibuprofen-D3,C13[2]H3H15O2,363.4
+MCPA-D3,C9[2]H3H6ClO3,336.5
+Methoxyfenozide-D3,C22[2]H3H25N2O3,363.6
+Pentachlorophenol-13C6,[13]C6HCl5O,378.8
+Sulfamethoxazole-13C6,C4[13]C6H11N3O3S,292.3

data-raw/istds-pos.csv

@@ -0,0 +1,25 @@
+name,formula,rt
+1H-benzotriazole-D4,C6[2]H4HN3,268.1
+Atenolol-D7,C14[2]H7H15N2O3,213.5
+Atrazine-D5,C8[2]H5H9ClN5,336.5
+Bezafibrate-D6,C19[2]H6H14ClNO4,351.7
+Climbazole-D4,C15[2]H4H13ClN2O2,359.1
+DEET-D6,C12[2]H6H11NO,354.5
+Diglyme-D14,C6[2]H14O3,246.1
+Diuron-D6,C9[2]H6H4Cl2N2O,335.2
+Flufenacet-D4,C14[2]H4H9F4N3O2S,371.8
+Hexazinone-D6,C12[2]H6H14N4O2,351.3
+Irgarol-D9,C11[2]H9H10N5S,368.3
+Isoproturon-D6,C12[2]H6H12N2O,339.6
+Linuron-D6,C9[2]H6H4Cl2N2O2,347.7
+Methiocarb-D3,C11[2]H3H12NO2S,360.1
+Metoprolol-D7,C15[2]H7H18NO3,294.7
+Monuron-D6,C9[2]H6H5ClN2O,316.1
+Prometryne-D7,C10[2]H7H12N5S,367.6
+Sotalol-D7,C12[2]H7H13N2O3S,211.2
+Sulfamethazine-13C6,C6[13]C6H14N4O2S,300.8
+Sulfamethoxazole-13C6,C4[13]C6H11N3O3S,292.3
+Triazophos-D5,C12[2]H5H11N3O3PS,379.8
+Triethyl phosphate-D15,C6[2]H15O4P,309.6
+Trimethoprim-D9,C14[2]H9H9N4O3,262
+Venlafaxine-D6,C17[2]H6H21NO2,323.3

data-raw/prepare-data.R

@@ -0,0 +1,9 @@
+devtools::load_all(".")
+
+suspectsPos <- read.csv(system.file("data-raw", "suspects-pos.csv", package = "patRoonData"), stringsAsFactors = FALSE)
+suspectsNeg <- read.csv(system.file("data-raw", "suspects-neg.csv", package = "patRoonData"), stringsAsFactors = FALSE)
+
+ISTDListPos <- read.csv(system.file("data-raw", "istds-pos.csv", package = "patRoonData"), stringsAsFactors = FALSE)
+ISTDListNeg <- read.csv(system.file("data-raw", "istds-neg.csv", package = "patRoonData"), stringsAsFactors = FALSE)
+
+usethis::use_data(suspectsPos, suspectsNeg, ISTDListPos, ISTDListNeg, overwrite = TRUE)