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.

Author
Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Date of publication
2015-10-19 09:13:13
Maintainer
Joris J. Snellenburg <j.snellenburg@vu.nl>
License
GPL (>= 2)
Version
1.13.0
URLs

View on R-Forge

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