(fixed missing edits from last commit)

NAMESPACE

@@ -77,7 +77,9 @@ export(reanalyzeFailpeaks)
 export(recalibrate)
 export(recalibrate.addMS1data)
 export(recalibrate.identity)
+export(recalibrate.linear)
 export(recalibrate.loess)
+export(recalibrate.mean)
 export(recalibrateSingleSpec)
 export(recalibrateSpectra)
 export(resetInfolists)

R/leMsMs.r

@@ -2063,6 +2063,10 @@ recalibrate.addMS1data <- function(spec,mode="pH", recalibrateMS1Window =
 #' which predicts 0 for all input values. This can be used if the user wants to
 #' skip recalibration in the RMassBank workflow.
 #' 
+#' #' \code{recalibrate.mean()} and \code{recalibrate.linear()} are simple recalibrations
+#' which return a constant shift or a linear recalibration. They will be only useful
+#' in particular cases.
+#' 
 #' \code{recalibrate()} itself is only a dummy function and does not do anything.
 #' 
 #' Alternatively other functions can be defined. Which functions are used for recalibration
@@ -2070,11 +2074,15 @@ recalibrate.addMS1data <- function(spec,mode="pH", recalibrateMS1Window =
 #' \code{recalibrator: MS1} value is irrelevant, since for a common curve generated with
 #' the function specified in \code{recalibrator: MS2} will be used.)
 #' 
-#' @aliases recalibrate.loess recalibrate recalibrate.identity
+#' @aliases recalibrate.loess recalibrate recalibrate.identity recalibrate.mean recalibrate.linear
 #' @usage recalibrate.loess(rcdata)
 #' 
 #' 		recalibrate.identity(rcdata)
 #' 
+#' 		recalibrate.mean(rcdata)
+#' 
+#' 		recalibrate.linear(rcdata)
+#' 
 #' @param rcdata A data frame with at least the columns \code{recalfield} and
 #' 			\code{mzFound}. \code{recalfield} will usually contain delta(ppm) or
 #' 			delta(mz) values and is the target parameter for the recalibration.
@@ -2134,6 +2142,18 @@ recalibrate.identity <- function(rcdata)
 	return(lm(recalfield ~ 0, data=rcdata))
 }
 
+#' @export 
+recalibrate.mean <- function(rcdata)
+{
+  return(lm(recalfield ~ 1, data=rcdata))
+}
+
+#' @export 
+recalibrate.linear <- function(rcdata)
+{
+  return(lm(recalfield ~ mzFound, data=rcdata))
+}
+
 #' Standard progress bar hook.
 #' 
 #' This function provides a standard implementation for the progress bar in RMassBank.

man/recalibrate.Rd

 \name{recalibrate}
 \alias{recalibrate}
 \alias{recalibrate.identity}
+\alias{recalibrate.linear}
 \alias{recalibrate.loess}
+\alias{recalibrate.mean}
 \title{Predefined recalibration functions.}
 \usage{
   recalibrate.loess(rcdata)
 
   recalibrate.identity(rcdata)
+
+  recalibrate.mean(rcdata)
+
+  recalibrate.linear(rcdata)
 }
 \arguments{
   \item{rcdata}{A data frame with at least the columns
@@ -34,6 +40,11 @@
   all input values. This can be used if the user wants to
   skip recalibration in the RMassBank workflow.
 
+  #' \code{recalibrate.mean()} and
+  \code{recalibrate.linear()} are simple recalibrations
+  which return a constant shift or a linear recalibration.
+  They will be only useful in particular cases.
+
   \code{recalibrate()} itself is only a dummy function and
   does not do anything.