Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

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Documentation for package ‘TIMP’ version 1.13.6

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TIMP-package a problem solving environment for fitting separable nonlinear models in physics and chemistry applications
amp Class "amp" for diagonal matrix model specification.
amp-class Class "amp" for diagonal matrix model specification.
baseIRF Baseline subtraction from a vector, usually representing an IRF.
c001 Fluorescent lifetime imaging microscopy (FLIM) data
c003 Fluorescent lifetime imaging microscopy (FLIM) data
C1 Ultrafast time-resolved fluorescence data
C2 Ultrafast time-resolved fluorescence data
C3 Ultrafast time-resolved fluorescence data
cy005c Fluorescent lifetime imaging microscopy (FLIM) data
cy006 Fluorescent lifetime imaging microscopy (FLIM) data
dat Class "dat" for model and data storage
dat-class Class "dat" for model and data storage
denS4 Time-resolved absorption data
denS5 Time-resolved absorption data
divergeZimage Plots a matrix with a diverging palette, with the center value of the palette possible to set
donorAcceptorTagged Fluorescent lifetime imaging microscopy (FLIM) data
donorTagged Fluorescent lifetime imaging microscopy (FLIM) data
efit2file Convert 'tim' FORTRAN efit files to plain matrices in ASCII files
examineFit Examines the results of a call to fitModel
fit Class "fit" to store the results of model fitting associated with all datasets analyzed.
fit-class Class "fit" to store the results of model fitting associated with all datasets analyzed.
fitModel Performs optimization of (possibly multidataset) models.
FLIMplots Functions to plot FLIM results.
getC Functions to print and return parts of the object returned by the fitting routines.
getCLP Functions to print and return parts of the object returned by the fitting routines.
getClpindepX Generic function getClpindepX in Package 'TIMP'
getClpindepX-method Generic function getClpindepX in Package 'TIMP'
getClpindepX-methods Generic function getClpindepX in Package 'TIMP'
getCLPList Functions to print and return parts of the object returned by the fitting routines.
getDAS Functions to print and return parts of the object returned by the fitting routines.
getData Functions to print and return parts of the object returned by the fitting routines.
getdim1 Functions to print and return parts of the object returned by the fitting routines.
getdim2 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.
getResiduals Functions to print and return parts of the object returned by the fitting routines.
getResults Functions to print and return parts of the object returned by the fitting routines.
getSVDData Functions to print and return parts of the object returned by the fitting routines.
getSVDResiduals Functions to print and return parts of the object returned by the fitting routines.
getTraces Functions to print and return parts of the object returned by the fitting routines.
getX Functions to print and return parts of the object returned by the fitting routines.
getXList Functions to print and return parts of the object returned by the fitting routines.
initModel Defines the model to be used in analysis.
kin Class "kin" for kinetic model storage.
kin-class Class "kin" for kinetic model storage.
kinopt Class "kinopt" stores options for fitting and plotting kinetic models
kinopt-class Class "kinopt" stores options for fitting and plotting kinetic models
mass Class "mass" for mass spectrometry model storage.
mass-class Class "mass" for mass spectrometry model storage.
massopt Class "massopt" stores options for fitting and plotting models for mass spectrometry data
massopt-class Class "massopt" stores options for fitting and plotting models for mass spectrometry data
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.
multimodel Class "multimodel" for storage of multidataset models, data and the results of fitting.
multimodel-class Class "multimodel" for storage of multidataset models, data and the results of fitting.
multitheta Class "multitheta" that stores a list with one element of class "theta" for each dataset modeled.
multitheta-class Class "multitheta" that stores a list with one element of class "theta" for each dataset modeled.
onls Functions to print and return parts of the object returned by the fitting routines.
opt Class "opt" stores options for fitting and plotting
opt-class Class "opt" stores options for fitting and plotting
outlierCorr Finds and removes outliers from a datasets
parEst Functions to print and return parts of the object returned by the fitting routines.
plotHistAmp Functions to plot FLIM results.
plotHistNormComp Functions to plot FLIM results.
plotIntenImage Functions to plot FLIM results.
plotNormComp Functions to plot FLIM results.
plotSelIntenImage Functions to plot FLIM results.
plotTau Functions to plot FLIM results.
plotter Generic function plotter in Package 'TIMP'
plotter-method Generic function plotter in Package 'TIMP'
plotter-methods Generic function plotter in Package 'TIMP'
preProcess Performs preprocessing on data stored as an objects of class dat.
readclp0 This function reads in a specification of constraints to zero on the clp.
readData This function reads in data the ivo file format
res Class "res" to store the results of model fitting associated with a single dataset.
res-class Class "res" to store the results of model fitting associated with a single dataset.
residPart Generic function residPart in Package 'TIMP'
residPart-method Generic function residPart in Package 'TIMP'
residPart-methods Generic function residPart in Package 'TIMP'
spec Class "spec" for the storage of spectral models.
spec-class Class "spec" for the storage of spectral models.
specopt Class "specopt" stores options for fitting and plotting spectral models
specopt-class Class "specopt" stores options for fitting and plotting spectral models
sumKinSpecEst Makes a summary plot of spectra associated with kinetic components alongside a plot showing parameter estimates
sumnls Functions to print and return parts of the object returned by the fitting routines.
target Ultrafast time-resolved fluorescence data
theta Class "theta" for storage of nonlinear parameter estimates
theta-class Class "theta" for storage of nonlinear parameter estimates
TIMP a problem solving environment for fitting separable nonlinear models in physics and chemistry applications
writeAverage Writes the average of scans stored in a file to a new file in the 'ivo' format