TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

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
http://timp.r-forge.r-project.org/ http://timpgui.org/

View on CRAN

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...

Files in this package

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

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