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TIMP (version 1.5)

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

280

Version

1.5

License

GPL (>= 2)

Maintainer

Katharine M Mullen

Last Published

December 12th, 2022

Functions in TIMP (1.5)

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
kin-class

Class "kin" for kinetic model storage.
fitModel

Performs optimization of (possibly multidataset) models.
amp-class

Class "amp" for diagonal matrix model specification.
baseIRF

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

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

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

Examines the results of a call to fitModel
theta-class

Class "theta" for storage of nonlinear parameter estimates
plotter-methods

Generic function plotter in Package `TIMP'
getClpindepX-methods

Generic function getClpindepX in Package `TIMP'
getResults

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

Class "mass" for mass spectrometry model storage.
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.
residPart-methods

Generic function residPart in Package `TIMP'
spec-class

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

Class "opt" stores options for fitting and plotting
fit-class

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

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

This function reads in data the ivo file format
modifyModel

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

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

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

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

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

TIMP function used internally
initModel

Defines the model to be used in analysis.
readclp0

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

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

Finds and removes outliers from a datasets