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TIMP (version 1.13.6)

Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

Description

A problem solving environment (PSE) for fitting separable nonlinear models to measurements arising in physics and chemistry experiments, as described by Mullen & van Stokkum (2007) for its use in fitting time resolved spectroscopy data, and as described by Laptenok et al. (2007) for its use in fitting Fluorescence Lifetime Imaging Microscopy (FLIM) data, in the study of Förster Resonance Energy Transfer (FRET). `TIMP` also serves as the computation backend for the `GloTarAn` software, a graphical user interface for the package, as described in Snellenburg et al. (2012) .

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Install

install.packages('TIMP')

Monthly Downloads

350

Version

1.13.6

License

GPL (>= 2)

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Repository

https://github.com/glotaran/TIMP

Maintainer

Joris J Snellenburg

Last Published

December 12th, 2022

Functions in TIMP (1.13.6)

Performs optimization of (possibly multidataset) models.

getClpindepX-methods

Generic function getClpindepX in Package `TIMP'

Class "kinopt" stores options for fitting and plotting kinetic models

Class "kin" for kinetic model storage.

Examines the results of a call to fitModel

Defines the model to be used in analysis.

Class "fit" to store the results of model fitting associated with all datasets analyzed.

Functions to print and return parts of the object returned by the fitting routines.

For data correction, fits a model (but ignores plotting commands) in order to obtain the SVD of the residuals, which then can be used in data-correction.

TIMP function used internally

Instrument response for fluorescent lifetime imaging microscopy (FLIM) data

Allows the starting values for parameters associated with a model to be updated with the values found in fitting the model.

Class "opt" stores options for fitting and plotting

plotter-methods

Generic function plotter in Package `TIMP'

Finds and removes outliers from a datasets

Class "massopt" stores options for fitting and plotting models for mass spectrometry data

Class "mass" for mass spectrometry model storage.

Performs preprocessing on data stored as an objects of class dat.

multitheta-class

Class "multitheta" that stores a list with one element of class "theta" for each dataset modeled.

multimodel-class

Class "multimodel" for storage of multidataset models, data and the results of fitting.

Makes a summary plot of spectra associated with kinetic components alongside a plot showing parameter estimates

Class "specopt" stores options for fitting and plotting spectral models

Class "theta" for storage of nonlinear parameter estimates

Class "spec" for the storage of spectral models.

This function reads in data the ivo file format

Class "res" to store the results of model fitting associated with a single dataset.

This function reads in a specification of constraints to zero on the clp.

Ultrafast time-resolved fluorescence data

residPart-methods

Generic function residPart in Package `TIMP'

Writes the average of scans stored in a file to a new file in the 'ivo' format

Convert 'tim' FORTRAN efit files to plain matrices in ASCII files

Baseline subtraction from a vector, usually representing an IRF.

Class "amp" for diagonal matrix model specification.

Fluorescent lifetime imaging microscopy (FLIM) data

donorAcceptorTagged

Fluorescent lifetime imaging microscopy (FLIM) data

Plots a matrix with a diverging palette, with the center value of the palette possible to set

a problem solving environment for fitting separable nonlinear models in physics and chemistry applications

Time-resolved absorption data

Functions to plot FLIM results.

Class "dat" for model and data storage