fix: fix documentation and vignette

R/kendrickMass.R

@@ -1,67 +1,68 @@
-#' @title m/z matching
+#' @title Kendrick mass defects
 #'
 #' @name calculateKendrickMass
-#' 
-
+#'
 #' @description
 #'
 #' Kendrick mass defect analysis is a way to analyze high-resolution MS data in
-#' order to identify homologous series. The Kendrick mass (KM) is calculated by 
+#' order to identify homologous series. The Kendrick mass (KM) is calculated by
 #' choosing a specific molecular fragment (e.g. CH2) and settings its mass to an
-#' integer mass. In case of CH2 the mass of 14.01565 would be set to 14.The 
-#' Kendrick mass defect (KMD) is defined as the difference between the KM and 
-#' the nominial (integer) KM. All molecules of homologoues series, e.g. only 
+#' integer mass. In case of CH2 the mass of 14.01565 would be set to 14.The
+#' Kendrick mass defect (KMD) is defined as the difference between the KM and
+#' the nominial (integer) KM. All molecules of homologoues series, e.g. only
 #' differing in the number of CH2, will have an identical KMD. In an additional
-#' step the KMD can be referenced to the mass defect of specific lipid backbone 
-#' and by this normalize values to the referenced KMD (RKMD). This leads to 
+#' step the KMD can be referenced to the mass defect of specific lipid backbone
+#' and by this normalize values to the referenced KMD (RKMD). This leads to
 #' values of 0 for saturated species or -1, -2, -3, etc for unsaturated species.
-#' 
+#'
 #' Available functoins are:
-#' 
-#' - `calculateKm`: calculates the Kendrick mass from an exact mass for a 
-#'   specific molecular fragment, e.g. "CH2".
+#'
+#' - `calculateKm`: calculates the Kendrick mass from an exact mass for a
+#'   specific molecular fragment, e.g. `"CH2"`.
 #' - `calculateKmd`: calculates the Kendrick mass defect from an exact mass for
-#'   a specific molecular fragment, e.g. "CH2"
-#' - `calculateRkmd`: calculates the referenced Kendrick mass defect from an 
-#'   exact mass for a specific molecular fragment, e.g. "CH2", and a reference
+#'   a specific molecular fragment, e.g. `"CH2"`.
+#' - `calculateRkmd`: calculates the referenced Kendrick mass defect from an
+#'   exact mass for a specific molecular fragment, e.g. `"CH2"`, and a reference
 #'   KMD.
 #' - `isRkmd`: Checks if a calculated RKMD falls within a specific error range
-#'   around an negative integer corresponding the number of double bonds, in 
+#'   around an negative integer corresponding the number of double bonds, in
 #'   case of CH2 as fragment.
-#'   
-#' @param x `numeric` Vector with exact masses or calculated RKMDs in case of 
-#'     `isRkmd`
-#' @param framgent `numeric(1)` or `character(1)` corresponding factor or molecular
-#'     formula of molecular fragment, e.g. 14  /14.01565 or "CH2" for CH2.
-#' @param rkmd `numeric(1)` KMD used for referencing of KMDs
-#' @param rkmdTolerance `numeric(1)` Tolerance to check if RKMD fall around a 
+#'
+#' @param x `numeric` with exact masses or calculated RKMDs in case of `isRkmd`.
+#'
+#' @param fragment `numeric(1)` or `character(1)` corresponding factor or
+#'     molecular formula of molecular fragment, e.g. `14 / 14.01565` or `"CH2"`
+#'     for CH2.
+#'
+#' @param rkmd `numeric(1)` KMD used for referencing of KMDs.
+#'
+#' @param rkmdTolerance `numeric(1)` Tolerance to check if RKMD fall around a
 #'     negative integer corresponding to the number of double bonds
-#' 
-#' @return `numeric` or `boolean` All functions, except `isRkmd` return a numeric
-#'     with same length as the input corresponding to the KM, KMD or RMKD. 
-#'     `isRkmd` returns a list TRUE or FALSE indicating if the RKMD falls within
-#'      a specific range around a negative integer corresponding to the number
-#'      of double bonds
-#' 
-#' 
+#'
+#' @return `numeric` or `boolean`. All functions, except `isRkmd` return a
+#'     `numeric` with same length as the input corresponding to the KM, KMD or
+#'     RMKD.
+#'     `isRkmd` returns a `logical` with `TRUE` or `FALSE` indicating if the
+#'      RKMD falls within a specific range around a negative integer
+#'      corresponding to the number of double bonds.
+#'
 #' @author Michael Witting
-#' 
+#'
 #' @examples
 #'
 #' calculateKm(760.5851)
 #'
 #' calculateKmd(760.5851)
 #'
 #' calculateRkmd(760.5851, rkmd = 0.749206)
-#' 
-#' isRkmd(calculateRkmd(760.5851, rkmd = 0.749206))
 #'
+#' isRkmd(calculateRkmd(760.5851, rkmd = 0.749206))
 #'
 NULL
 
 
 #' @rdname calculateKendrickMass
-#' 
+#'
 #' @export
 calculateKm <- function(x, fragment = 14.00000 / 14.01565) {
   if(is.numeric(fragment)) {
@@ -74,27 +75,23 @@ calculateKm <- function(x, fragment = 14.00000 / 14.01565) {
 }
 
 #' @rdname calculateKendrickMass
-#' 
+#'
 #' @export
 calculateKmd <- function(x, fragment = 14.00000 / 14.01565) {
   kendrick <- calculateKm(x, fragment)
   kendrick - as.integer(kendrick)
 }
 
 #' @rdname calculateKendrickMass
-#' 
+#'
 #' @export
 calculateRkmd <- function(x, fragment = 14.00000 / 14.01565, rkmd = 0.749206) {
-
   (calculateKmd(x) - rkmd) / 0.013399
-
 }
 
 #' @rdname calculateKendrickMass
-#' 
+#'
 #' @export
 isRkmd <- function(x, rkmdTolerance = 0.1) {
-
   abs(round(x, digits = 0) - x) < rkmdTolerance
-
-}
+}

vignettes/MetaboCoreUtils.Rmd

@@ -129,23 +129,23 @@ countElements(frml)
 ## Kendrick mass defect calculation
 
 Lipids and other homologous series based on fatty acyls can be found in data by
-using Kendrick mass defects (KMD) or referenced kendrick mass defects (RKMD). The 
-`MetaboCoreUtils` package provides functions to calculate everything around
-Kendrick mass defects. The following example calculates the KMD and RKMD for
-three lipids (PC(16:0/18:1(9Z)), PC(16:0/18:0), PS(16:0/18:1(9Z))) and checks,
-if they fit the RKMD of PCs detected as [M+H]+ adducts.
+using Kendrick mass defects (KMD) or referenced kendrick mass defects
+(RKMD). The `MetaboCoreUtils` package provides functions to calculate everything
+around Kendrick mass defects. The following example calculates the KMD and RKMD
+for three lipids (PC(16:0/18:1(9Z)), PC(16:0/18:0), PS(16:0/18:1(9Z))) and
+checks, if they fit the RKMD of PCs detected as [M+H]+ adducts.
 
 ```{r}
 lipid_masses <- c(760.5851, 762.6007, 762.5280)
-calculateKendrickMassDefect(lipid_masses)
+calculateKmd(lipid_masses)
 ```
 
 Next the RKMD is calculated and checked if it fits to a specific range. RKMDs
 are either 0 or negative integers according to the number of double bonds in the
 lipids, e.g. -2 if two double bonds are present in the lipids.
 
 ```{r}
-lipid_rkmd <- calculateReferencedKendrickMassDefect(lipid_masses)
+lipid_rkmd <- calculateRkmd(lipid_masses)
 isRkmd(lipid_rkmd)
 ```