R: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

# Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

## Documentation for package ‘TIMP’ version 1.13.6

- DESCRIPTION file

## Help Pages

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