R/PACKAGE-NMR.Utils.R

In jmstrat/NMR.Utils: Importing and processing Bruker NMR data

#' @author Josh Stratford
#'
#' @import Plotting.Utils
#' @section Importing NMR data:
#' Use the function \code{\link{read.nmr}} to import 1D or 2D nmr data. Use \code{plot} or \code{iplot} to plot the data.
#'
#' @section In situ NMR data:
#'
#' \itemize{
#'   \item Import the NMR data using \code{\link{read.nmr}}; import the echem data using \code{\link[Echem.Data]{read.echem}}.
#'   \item Set the time for each scan using \code{\link{storeOffsets}}. These times can be automatically generated from an ATMC log file
#' using \code{\link{read.ATMC}} or without a log file using \code{\link{noATMoffsets}}.
#'   \item Combine the NMR and echem data with \code{\link{associate_echem_with_nmr}}.
#'   \item If complex, data can then be phased (\code{\link{apkpseudo2d}}), and made real (\code{\link{makeReal}}).
#'   \item Baseline subtraction can be performed using \code{\link[jms.classes]{make_background}} OR \code{\link{correct_baseline}}
#'   \item Use \code{plot} to plot the data -- see \code{\link{plot.nmr2dinsitu.data.object}} for options.
#' }
#' Any / all of these steps can be performed graphically using the command \code{\link{insitu_gui}} or any of the
#' \code{interactive} family of commands (\code{\link{interactiveImport}}, \code{\link{interactivePhase}},
#' \code{\link{interactiveBaseline}} and \code{\link{interactivePlotting}}).\cr
#' Data can be exported as a csv file using the \code{\link[jms.classes]{export}} function.
#'
#' @section Fitting in situ NMR data:
#' Import and process the data as described in the in situ NMR section. Note that it is very important that the baseline is 0 for fitting,
#' if your baseline is reasonably flat the command \code{data = correct_baseline(data, method="modpolyfit",degree=1)} will fit a straight
#' line to the data. Otherwise consider using \code{\link{interactiveBaseline}}.\cr\cr
#'
#' Create a fit object using \code{\link{new_fit}}, e.g.\cr
#' \code{fit = new_fit(integration_range=c(-50, 50))} \cr\cr
#' Create one or more peaks using \code{\link{new_model}}, e.g.:\cr
#' \code{electrolyte = new_model(pseudoVoigt, height=1e6, centre=0.2, hwhm=2.0, shape=0.5)}\cr\cr
#' Define which parameters of the model will be fitted using \code{\link{add_constraint_to_model}}, e.g.:\cr
#' \code{electrolyte = add_constraint_to_model(electrolyte, parameter='height', constraint_type='vary', constraint=1e5)}\cr\cr
#' Add each model to the fit using \code{\link{add_model_to_fit}}, e.g.:\cr
#' \code{fit = add_model_to_fit(fit, electrolyte)}\cr\cr
#' Run the fit using \code{\link{run_fit_for_data}}.\cr\cr
#' Results are available in the fit object under \code{result}, e.g. \code{fit$result}. These can be exported to a csv file
#' using \code{\link[jms.classes]{export}}. A simple plot can be made using \code{plot(fit)}, or an animation as described below.
#'
#' @section Animations:
#' A simple animation of in situ NMR data can be made using \code{\link{save_animation}}, optionally including a fit.
"_PACKAGE"

.onLoad <- function(libname, pkgname) {
  jms.classes::create_data_type("nmr", "ppm", "", envir=asNamespace("NMR.Utils"))
  jms.classes::create_data_type("nmr2d", "ppm", "", inherits="nmr", envir=asNamespace("NMR.Utils"))
  jms.classes::create_data_type("nmr2dinsitu", "ppm", "", inherits=c("nmr2d", "nmr"), envir=asNamespace("NMR.Utils"))
}