merged master and fixed examples

RECETOX · Dec 21, 2023 · b2ac5a6 · b2ac5a6
1 parent 425c281
commit b2ac5a6
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Showing 47 changed files with 649 additions and 202 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,6 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: knitr,
     	  rmarkdown,
-		  datacomparer (>= 0.1.4),
 		  patrick (>= 0.2.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -24,4 +24,19 @@ export(RecalList)
 export(SNplot)
 export(Valence)
 export(ValidFormula)
+export(bind_and_filter_data)
+export(calculate_variables)
+export(compare_bad_and_filter)
+export(compute_pairs)
+export(create_data_chunks)
+export(create_pairs)
+export(extract_mono_and_iso_pairs)
+export(filter_and_arrange_data)
+export(filter_pairs)
+export(merge_and_filter_abundances)
+export(merge_and_filter_pairs)
+export(processMassList)
+export(process_carbon_isotoping)
+export(process_sulfur)
+export(sulfur_check)
 import(ggplot2)
diff --git a/R/IsoFiltR.R b/R/IsoFiltR.R
@@ -153,8 +153,6 @@ combine_isotopes <- function(Isotopes) {
 #' @return list(Monolist, Isolist):
 #'   Monolist - monoistopic and non-matched masses,
 #'   Isolist - isotopic masses
-#' @examples
-#' IsoFiltR(peaks = df)
 #' @export
 IsoFiltR <- function(
     peaks,

diff --git a/R/MFAssign.R b/R/MFAssign.R
@@ -504,19 +504,19 @@ records <- vector("list")
                 }
 
                 loop[CompFactorToInt2("Br")] <- unlist(loop[CompFactorToInt2("Br")]) + 1
-                if (loop[CompFactorToInt2("Br")] > HighMoles2("Br",Br=Brx)) {
+                if (loop[CompFactorToInt2("Br")] > HighMoles("Br",Br=Brx)) {
                   break
                 }
                     }
 
                     loop[CompFactorToInt2("Br81")] <- unlist(loop[CompFactorToInt2("Br81")]) + 1
-                    if (loop[CompFactorToInt2("Br81")] > HighMoles2("Br81",Br81=Br81x)) {
+                    if (loop[CompFactorToInt2("Br81")] > HighMoles("Br81",Br81=Br81x)) {
                       break
                     }
                   }
 
                   loop[CompFactorToInt2("I")] <- unlist(loop[CompFactorToInt2("I")]) + 1
-                  if (loop[CompFactorToInt2("I")] > HighMoles2("I",I=Ix)) {
+                  if (loop[CompFactorToInt2("I")] > HighMoles("I",I=Ix)) {
                     break
                   }
                 }
@@ -635,15 +635,15 @@ records <- vector("list")
                             max_H = C * 2 + 2, H_test = round(H / max_H, 1),
 
                             Senior2 = Pval + Nval + N15val + Valence("H")  +
-                              Valence("Cl") + Valence("Cl37")+Valence("Fl") + Valence2("Br") + Valence2("Br81") +
-                              Valence2("I"),
+                              Valence("Cl") + Valence("Cl37")+Valence("Fl") + Valence("Br") + Valence("Br81") +
+                              Valence("I"),
 
                             Senior3Atom = C + H + O + N + S + P + N15 + Cl + Cl37 + S34 + Br + Br81 + I,
 
                             Senior3Val = C*Valence("C") + H*Valence("H") + O*Valence("O") + N*Nval +
                               S*Sval + P*Pval + S34*S34val + Fl*Valence("Fl")+
-                              N15*N15val + Cl*Valence("Cl") + Cl37*Valence("Cl37") + Br *Valence2("Br")+
-                              Br81 *Valence2("Br81") + I * Valence2("I")
+                              N15*N15val + Cl*Valence("Cl") + Cl37*Valence("Cl37") + Br *Valence("Br")+
+                              Br81 *Valence("Br81") + I * Valence("I")
 
   )
 
@@ -1122,15 +1122,15 @@ records <- vector("list")
                             max_H = C * 2 + 2, H_test = round(H / max_H,1),
 
                             Senior2 = Pval + Nval + N15val + Valence("H")  +
-                              Valence("Cl") + Valence("Cl37")+Valence("Fl") + Valence2("Br") + Valence2("Br81") +
-                              Valence2("I"),
+                              Valence("Cl") + Valence("Cl37")+Valence("Fl") + Valence("Br") + Valence("Br81") +
+                              Valence("I"),
 
                             Senior3Atom = C + H + O + N + S + P + N15 + Cl + Cl37 + S34 + Br + Br81 + I,
 
                             Senior3Val = C*Valence("C") + H*Valence("H") + O*Valence("O") + N*Nval +
                               S*Sval + P*Pval + S34*S34val + Fl*Valence("Fl")+
-                              N15*N15val + Cl*Valence("Cl") + Cl37*Valence("Cl37") + Br * Valence2("Br") +
-                              Br81 * Valence2("Br81") + I * Valence2("I")
+                              N15*N15val + Cl*Valence("Cl") + Cl37*Valence("Cl37") + Br * Valence("Br") +
+                              Br81 * Valence("Br81") + I * Valence("I")
   )
 
   records1$NM <- ifelse(abs(floor(records1$Exp_mass)-records1$Exp_mass) >= min_def & abs(floor(records1$Exp_mass)-records1$Exp_mass) <= max_def,
@@ -1870,15 +1870,15 @@ records <- vector("list")
                              max_H = C * 2 + 2, H_test = round(H / max_H,1),
 
                              Senior2 = Pval + Nval + N15val + Valence("H")  +
-                               Valence("Cl") + Valence("Cl37")+Valence("Fl") + Valence2("Br") + Valence2("Br81") +
-                               Valence2("I"),
+                               Valence("Cl") + Valence("Cl37")+Valence("Fl") + Valence("Br") + Valence("Br81") +
+                               Valence("I"),
 
                              Senior3Atom = C + H + O + N + S + P + N15 + Cl + Cl37 + S34,
 
                              Senior3Val = C*Valence("C") + H*Valence("H") + O*Valence("O") + N*Nval +
                                S*Sval + P*Pval + S34*S34val + Fl*Valence("Fl")+
-                               N15*N15val + Cl*Valence("Cl") + Cl37*Valence("Cl37") + Br * Valence2("Br") +
-                               Br81 * Valence2("Br81") + I * Valence2("I")
+                               N15*N15val + Cl*Valence("Cl") + Cl37*Valence("Cl37") + Br * Valence("Br") +
+                               Br81 * Valence("Br81") + I * Valence("I")
   )
 
 

diff --git a/R/MFAssignCHO.R b/R/MFAssignCHO.R
@@ -290,8 +290,6 @@ MFAssignCHO <- function(peaks, isopeaks = "none", ionMode, lowMW=100,highMW=1000
 
             loop[CompFactorToInt("M")] <- 0 #LowMoles("M")
             repeat {
-
-
                               loop[CompFactorToInt("E")] <- 0 #LowMoles("E")
                               repeat {
 

diff --git a/R/RecalFunctions.R b/R/RecalFunctions.R
@@ -45,7 +45,7 @@ plot_spectrum <- function(plotpeak, RecalPlot) {
 #' @examples
 #' data <- data.frame(Exp_mass = c(100, 150, 200))
 #' processed_data <- processMassList(data)
-#'
+#' @export
 processMassList <- function(data) {
   data$NM <- round(data$Exp_mass)
 

diff --git a/R/Utilities.R b/R/Utilities.R
@@ -540,11 +540,6 @@ Even <- function(x) {
 #'
 #' @return boolean
 #'
-#' @examples
-#' ValidFormula(moles)
-#'
-#' ValidFormula(c(2, 3, 1, 0, 0, 0, 0, 0, 1))
-#'
 #' @export
 #'
 ValidFormula <- function(moles) {

diff --git a/man/AddCalculatedSummary.Rd b/man/AddCalculatedSummary.Rd
diff --git a/man/CompFactorToInt.Rd b/man/CompFactorToInt.Rd
diff --git a/man/CompFactorToInt2.Rd b/man/CompFactorToInt2.Rd
diff --git a/man/CompIntToFactor.Rd b/man/CompIntToFactor.Rd
diff --git a/man/CompIntToFactor2.Rd b/man/CompIntToFactor2.Rd
diff --git a/man/EM.Rd b/man/EM.Rd
diff --git a/man/EM2.Rd b/man/EM2.Rd
diff --git a/man/Even.Rd b/man/Even.Rd
diff --git a/man/FilterAndMerge.Rd b/man/FilterAndMerge.Rd
diff --git a/man/FindCoreFormulae2_Halo.Rd b/man/FindCoreFormulae2_Halo.Rd
diff --git a/man/HighMoles.Rd b/man/HighMoles.Rd
diff --git a/man/HighMoles2.Rd b/man/HighMoles2.Rd
diff --git a/man/LowMoles.Rd b/man/LowMoles.Rd