TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy
Version 1.13.0

A problem-solving environment (PSE) for fitting separable nonlinear models to measurements arising in physics and chemistry experiments; has been extensively applied to time-resolved spectroscopy and FLIM-FRET data.

AuthorKatharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Date of publication2015-10-19 18:07:01
MaintainerJoris J. Snellenburg <j.snellenburg@vu.nl>
LicenseGPL (>= 2)
Version1.13.0
URL http://timp.r-forge.r-project.org/ http://timpgui.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TIMP")

Getting started

Package overview

Popular man pages

donorTagged: Fluorescent lifetime imaging microscopy (FLIM) data
fit-class: Class "fit" to store the results of model fitting associated...
internals: TIMP function used internally
multitheta-class: Class "multitheta" that stores a list with one element of...
res-class: Class "res" to store the results of model fitting associated...
specopt-class: Class "specopt" stores options for fitting and plotting...
target: Ultrafast time-resolved fluorescence data
See all...

All man pages Function index File listing

Man pages

amp-class: Class "amp" for diagonal matrix model specification.
baseIRF: Baseline subtraction from a vector, usually representing an...
dat-class: Class "dat" for model and data storage
denS4: Time-resolved absorption data
divergeZimage: Plots a matrix with a diverging palette, with the center...
donorAcceptorTagged: Fluorescent lifetime imaging microscopy (FLIM) data
donorTagged: Fluorescent lifetime imaging microscopy (FLIM) data
efit2file: covert 'tim' FORTRAN efit files to plain matrices in ASCII...
examineFit: Examines the results of a call to fitModel
fit-class: Class "fit" to store the results of model fitting associated...
fitModel: Performs optimization of (possibly multidataset) models.
FLIMplots: Functions to plot FLIM results.
getClpindepX: Generic function getClpindepX in Package 'TIMP'
getResid: For data correction, fits a model (but ignores plotting...
getResults: Functions to print and return parts of the object returned by...
initModel: Defines the model to be used in analysis.
internals: TIMP function used internally
kin-class: Class "kin" for kinetic model storage.
kinopt-class: Class "kinopt" stores options for fitting and plotting...
mass-class: Class "mass" for mass spectrometry model storage.
massopt-class: Class "massopt" stores options for fitting and plotting...
mea_IRF: Instrument response for fluorescent lifetime imaging...
modifyModel: Allows the starting values for parameters associated with a...
multimodel-class: Class "multimodel" for storage of multidataset models, data...
multitheta-class: Class "multitheta" that stores a list with one element of...
opt-class: Class "opt" stores options for fitting and plotting
outlierCorr: Finds and removes outliers from a datasets
plotter: Generic function plotter in Package 'TIMP'
preProcess: Performs preprocessing on data stored as an objects of class...
readclp0: This function reads in a specification of constraints to zero...
readData: This function reads in data the ivo file format
res-class: Class "res" to store the results of model fitting associated...
residPart: Generic function residPart in Package 'TIMP'
spec-class: Class "spec" for the storage of spectral models.
specopt-class: Class "specopt" stores options for fitting and plotting...
sumKinSpecEst: Makes a summary plot of spectra associated with kinetic...
target: Ultrafast time-resolved fluorescence data
theta-class: Class "theta" for storage of nonlinear parameter estimates
TIMP-package: a problem solving environment for fitting separable nonlinear...
writeAverage: Writes the average of scans stored in a file to a new file in...

Functions

Files

COPYING
inst
inst/CITATION
tests
tests/25_650-75_2700.txt
tests/sim1.txt
tests/spectral_script.R
tests/PCP1.-50000fs.PP.txt
tests/kin_sim_large_script.R
tests/psitspec.txt
tests/_paramEst.txt
tests/_summary.ps
tests/example2nd.R
tests/cp8b.txt
tests/kin_target_script.R
tests/kin_ir_simult_script.RRRR
tests/kin_simple_ir_script.R
tests/cp432704.txt
tests/kin_simple_visible_script.R
tests/_selectedtraces.ps
src
src/ntr.c
NAMESPACE
NEWS
data
data/donorTagged.rda
data/donorAcceptorTagged.rda
data/target.rda
data/denS5.rda
data/mea_IRF.rda
data/denS4.rda
R
R/linlogtics.R
R/getPrelBetweenDatasets.R
R/massopt.R
R/baseCortime.R
R/calcB.R
R/set_initModelClass_amp.R
R/set_residPart_kin.R
R/jacobian.R
R/getSpecList.R
R/normdat.R
R/plotTracesResids.R
R/applyWeightingModel.R
R/set_plotter_mass.R
R/set_getClpindepX_amp.R
R/initModel.R
R/calcD.R
R/plotFLIMresid.R
R/sumKinSpecEst.R
R/res.R
R/getResults.R
R/l2nu.R
R/examineFit.R
R/doConstrSuper.R
R/calcAniSignal.R
R/plotClp.R
R/mass.R
R/set_getClpindepX_kin.R
R/getStreakBacksweep.R
R/specparF.R
R/kinopt.R
R/getResid.R
R/opt.R
R/getClpConstr.R
R/getSelectedTracesMax.R
R/getXsuper.R
R/weightNL.R
R/plotFLIM.R
R/init.multitheta.R
R/getStdErrClp.R
R/getDiffThetaCl.R
R/dat.R
R/getAniSuper.R
R/calcC.R
R/writeFit.R
R/set_plotter_spec.R
R/specopt.R
R/init.theta.R
R/getFixed.R
R/init.opt.R
R/diffChange.R
R/plotSpecKin.R
R/preProcess.R
R/matlinlogplot.R
R/getMvec.R
R/doClpConstr.R
R/weightPsi.R
R/writeAverage.R
R/set_residPart_spec.R
R/initModellist.R
R/weightSM.R
R/fullKF.R
R/getDiffThetaClChange.R
R/set_getClpindepX_spec.R
R/getAnisotropy.R
R/writeData.R
R/diffRel.R
R/barplot3.R
R/getJac.R
R/irfparF.R
R/getDiffThetaChange.R
R/diffAdd.R
R/set_plotter_kin.R
R/getModel.R
R/set_residPart_mass.R
R/amp.R
R/specModel.R
R/plotKinBreakDown.R
R/gaus.R
R/convolveUnitStep.R
R/getConstrained.R
R/plotMassSpec.R
R/processOrder.R
R/set_initModelClass_spec.R
R/init.dat.R
R/getPrel.R
R/fillResult.R
R/multitheta.R
R/fitModel.R
R/theta.R
R/fit.R
R/outlierCorr.R
R/convGausExp.R
R/divergeZimage.R
R/getXList.R
R/init.multimodel.R
R/initOneModel.R
R/calcCirf.R
R/initModelClassTest.R
R/calcEhiergaus.R
R/getDiffTheta.R
R/compModelMass.R
R/skew.R
R/addOutlierWeights.R
R/getResidRet.R
R/getTheta.R
R/init.res.R
R/baseIRF.R
R/doubleDiff.R
R/getPar.R
R/readData.R
R/getOsc.R
R/plotTracesSuper.R
R/compOsc.R
R/unitstep.R
R/applyKinScalSpecialFun.R
R/diffFree.R
R/fillK.R
R/rescomp.R
R/set_getClpindepX_mass.R
R/scaleConList.R
R/simpPol.R
R/addDscal.R
R/getAniA.R
R/set_residPart_amp.R
R/linloglines.R
R/getCoh.R
R/calcEbspline.R
R/writeEst.R
R/doSVD.R
R/getStartTri.R
R/diffRemove.R
R/simndecay_gen.R
R/set_initModelClass_mass.R
R/compCoh.R
R/summary.R
R/modifyModel.R
R/multiLin.R
R/getGroups.R
R/getSpecToPlot.R
R/addPrelCl.R
R/getLightDiff.R
R/set_initModelClass_kin.R
R/triResolve.R
R/spec.R
R/displayEst.R
R/getConToPlot.R
R/init.fit.R
R/getKinConcen.R
R/getAutoClp0.R
R/setGenerics.R
R/simpExp.R
R/compModel.R
R/readclp0.R
R/plotKinSpecEst.R
R/kin.R
R/plotTri.R
R/linlogplot.R
R/plotResids.R
R/multimodel.R
R/getPrelTheta.R
R/getCohToPlot.R
R/efit2file.R
R/sample_sel.R
R/zzz.R
R/superLogistic.R
R/getThetaCl.R
R/plotSpectraSuper.R
R/addPrel.R
R/baseCorlambda.R
R/getAniK.R
MD5
DESCRIPTION
man
man/donorTagged.Rd
man/specopt-class.Rd
man/massopt-class.Rd
man/mea_IRF.Rd
man/getClpindepX.Rd
man/preProcess.Rd
man/fitModel.Rd
man/donorAcceptorTagged.Rd
man/examineFit.Rd
man/outlierCorr.Rd
man/residPart.Rd
man/writeAverage.Rd
man/readData.Rd
man/kin-class.Rd
man/res-class.Rd
man/amp-class.Rd
man/TIMP-package.Rd
man/denS4.Rd
man/sumKinSpecEst.Rd
man/plotter.Rd
man/fit-class.Rd
man/multitheta-class.Rd
man/getResid.Rd
man/internals.Rd
man/kinopt-class.Rd
man/target.Rd
man/modifyModel.Rd
man/baseIRF.Rd
man/theta-class.Rd
man/spec-class.Rd
man/dat-class.Rd
man/FLIMplots.Rd
man/initModel.Rd
man/divergeZimage.Rd
man/mass-class.Rd
man/multimodel-class.Rd
man/opt-class.Rd
man/readclp0.Rd
man/getResults.Rd
man/efit2file.Rd
TIMP documentation built on May 19, 2017, 10:55 a.m.

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