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TIMP (version 1.6)

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

Description

TIMP is a problem solving environment for fitting separable nonlinear models to measurements arising in physics and chemistry experiments, and has been extensively applied to time-resolved spectroscopy and FLIM-FRET data.

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Version

Install

install.packages('TIMP')

Monthly Downloads

384

Version

1.6

License

GPL (>= 2)

Maintainer

Katharine M Mullen

Last Published

December 12th, 2022

Functions in TIMP (1.6)

dat-class

Class "dat" for model and data storage
TIMP-package

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

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

Defines the model to be used in analysis.
getClpindepX-methods

Generic function getClpindepX in Package `TIMP'
opt-class

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

Generic function plotter in Package `TIMP'
kin-class

Class "kin" for kinetic model storage.
getResults

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

Performs optimization of (possibly multidataset) models.
baseIRF

Baseline subtraction from a vector, usually representing an IRF.
outlierCorr

Finds and removes outliers from a datasets
preProcess

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

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

Class "mass" for mass spectrometry model storage.
multimodel-class

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

TIMP function used internally
residPart-methods

Generic function residPart in Package `TIMP'
readclp0

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

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

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

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

Class "amp" for diagonal matrix model specification.
examineFit

Examines the results of a call to fitModel
efit2file

covert 'tim' FORTRAN efit files to a plain matrices
spec-class

Class "spec" for the storage of spectral models.
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.
res-class

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

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

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

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

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

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

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