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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.packages('TIMP')

Monthly Downloads

402

Version

1.13.6

License

GPL (>= 2)

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Last Published

December 12th, 2022

Functions in TIMP (1.13.6)

fitModel

Performs optimization of (possibly multidataset) models.
getClpindepX-methods

Generic function getClpindepX in Package `TIMP'
kinopt-class

Class "kinopt" stores options for fitting and plotting kinetic models
kin-class

Class "kin" for kinetic model storage.
examineFit

Examines the results of a call to fitModel
initModel

Defines the model to be used in analysis.
fit-class

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

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

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.
Internals

TIMP function used internally
mea_IRF

Instrument response for fluorescent lifetime imaging microscopy (FLIM) data
modifyModel

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

Class "opt" stores options for fitting and plotting
plotter-methods

Generic function plotter in Package `TIMP'
outlierCorr

Finds and removes outliers from a datasets
massopt-class

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

Class "mass" for mass spectrometry model storage.
preProcess

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.
sumKinSpecEst

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

Class "specopt" stores options for fitting and plotting spectral models
theta-class

Class "theta" for storage of nonlinear parameter estimates
spec-class

Class "spec" for the storage of spectral models.
readData

This function reads in data the ivo file format
res-class

Class "res" to store the results of model fitting associated with a single dataset.
readclp0

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

Ultrafast time-resolved fluorescence data
residPart-methods

Generic function residPart in Package `TIMP'
writeAverage

Writes the average of scans stored in a file to a new file in the 'ivo' format
efit2file

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

Baseline subtraction from a vector, usually representing an IRF.
amp-class

Class "amp" for diagonal matrix model specification.
donorTagged

Fluorescent lifetime imaging microscopy (FLIM) data
donorAcceptorTagged

Fluorescent lifetime imaging microscopy (FLIM) data
divergeZimage

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

a problem solving environment for fitting separable nonlinear models in physics and chemistry applications
denS4

Time-resolved absorption data
FLIMplots

Functions to plot FLIM results.
dat-class

Class "dat" for model and data storage