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 09:13:13
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 R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TIMP", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

amp-class: Class "amp" for diagonal matrix model specification.
dat-class: Class "dat" for model and data storage
internals: TIMP function used internally
kin-class: Class "kin" for kinetic model storage.
mea_IRF: Instrument response for fluorescent lifetime imaging...
multimodel-class: Class "multimodel" for storage of multidataset models, data...
plotter: Generic function plotter in Package 'TIMP'
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

C1 Man page
C2 Man page
C3 Man page
FLIMplots Man page
Internals Man page
TIMP Man page
TIMP-package Man page
addDscal Man page
addPrel Man page
addPrelCl Man page
amp Man page
amp-class Man page
applyWeighting Man page
applyWeightingModel Man page
barplot3 Man page Source code
baseCorlambda Man page
baseCortime Man page
baseIRF Man page
c001 Man page
c003 Man page
calcB Man page
calcC Man page
calcCirf Man page
calcD Man page
calcEbspline Man page
calcEhiergaus Man page
compCoh Man page
compModel Man page
compModelMass Man page
compOsc Man page
convGausExp Man page
convolveUnitStep Source code
cy005c Man page
cy006 Man page
dat Man page
dat-class Man page
denS4 Man page
denS5 Man page
diffAdd Man page
diffChange Man page
diffFree Man page
diffRel Man page
diffRemove Man page
displayEst Man page
divergeZimage Man page
doClpConstr Man page
doConstrSuper Man page
doSVD Man page
donorAcceptorTagged Man page
donorTagged Man page
doubleDiff Source code
efit2file Man page Source code
examineFit Man page
fillK Man page
fillResult Man page
fit Man page
fit-class Man page
fitModel Man page
fullKF Man page
gaus Man page
getAutoClp0 Man page
getC Man page Source code
getCLP Man page Source code
getCLPList Man page Source code
getClpConstr Man page
getClpList Man page
getClpindepX Man page
getClpindepX,amp-method Man page
getClpindepX,kin-method Man page
getClpindepX,mass-method Man page
getClpindepX,spec-method Man page
getClpindepX-methods Man page
getCoh Man page
getCohToPlot Man page
getConToPlot Man page
getDAS Man page Source code
getData Man page Source code
getDiffTheta Man page
getDiffThetaChange Man page
getDiffThetaCl Man page
getDiffThetaClChange Man page
getFixed Man page
getGroups Man page
getKinConcen Man page
getModel Man page
getOsc Man page
getPar Man page
getPrel Man page
getPrelTheta Man page
getResid Man page
getResidRet Man page
getResiduals Man page Source code
getResults Man page
getSVDData Man page Source code
getSVDResiduals Man page Man page Source code
getSelectedTracesMax Man page
getSpecList Man page
getSpecToPlot Man page
getTheta Man page
getThetaCl Man page
getTraces Man page Source code
getX Man page Source code
getXList Man page Source code
getXsuper Man page
getdim1 Man page Source code
getdim2 Man page Source code
initModel Man page
initModellist Man page
irfparF Man page
jacobian Source code
kin Man page
kin-class Man page
kinopt Man page
kinopt-class Man page
l2nu Man page
linloglines Man page
linlogplot Man page
linlogtics Man page
mass Man page
mass-class Man page
massopt Man page
massopt-class Man page
matlinlogplot Man page
mea_IRF Man page
modifyModel Man page
multiLin Man page
multimodel Man page
multimodel-class Man page
multitheta Man page
multitheta-class Man page
normdat Man page
onls Man page Source code
opt Man page
opt-class Man page
outlierCorr Man page
p.nls.convInfo Source code
parEst Man page Source code
plotClp Man page
plotEst Man page
plotFLIM Man page
plotHistAmp Man page
plotHistNormComp Man page
plotIntenImage Man page
plotKinBreakDown Man page
plotKinSpecEst Man page
plotNormComp Man page
plotSelIntenImage Man page
plotSelectedSpectra Man page
plotSelectedTraces Man page
plotSelectedTracesSuper Man page
plotTau Man page
plotTraces Man page
plotTracesSuper Man page
plotter Man page
plotter,kin-method Man page
plotter,mass-method Man page
plotter,spec-method Man page
plotter-methods Man page
preProcess Man page
print.summary.timp.nls Source code
print.summary.timp.nls.lm Source code
print.summary.timp.optim Source code
print.timp.nls Source code
print.timp.nls.lm Source code
print.timp.optim Source code
processOrder Man page
readData Man page
readclp0 Man page
res Man page
res-class Man page
rescomp Man page
residPart Man page
residPart,amp-method Man page
residPart,kin-method Man page
residPart,mass-method Man page
residPart,spec-method Man page
residPart-methods Man page
sample_sel Man page
scaleConList Man page
simndecay_gen Man page
simpExp Man page
simpPol Man page
skew Man page
spec Man page
spec-class Man page
specModel Man page
specopt Man page
specopt-class Man page
specparF Man page
stdErrTransform Source code
sumKinSpecEst Man page
summary.timp.nls Source code
summary.timp.nls.lm Source code
summary.timp.optim Source code
sumnls Man page Source code
target Man page
theta Man page
theta-class Man page
timpErrors Man page
unitstep Man page
weightNL Man page
weightPsi Man page
weightSM Man page
writeAverage Man page Source code
writeData Source code
writeEst Man page
writeFit Man page

Files

COPYING
DESCRIPTION
NAMESPACE
NEWS
R
R/addDscal.R
R/addOutlierWeights.R
R/addPrel.R
R/addPrelCl.R
R/amp.R
R/applyKinScalSpecialFun.R
R/applyWeightingModel.R
R/barplot3.R
R/baseCorlambda.R
R/baseCortime.R
R/baseIRF.R
R/calcAniSignal.R
R/calcB.R
R/calcC.R
R/calcCirf.R
R/calcD.R
R/calcEbspline.R
R/calcEhiergaus.R
R/compCoh.R
R/compModel.R
R/compModelMass.R
R/compOsc.R
R/convGausExp.R
R/convolveUnitStep.R
R/dat.R
R/diffAdd.R
R/diffChange.R
R/diffFree.R
R/diffRel.R
R/diffRemove.R
R/displayEst.R
R/divergeZimage.R
R/doClpConstr.R
R/doConstrSuper.R
R/doSVD.R
R/doubleDiff.R
R/efit2file.R
R/examineFit.R
R/fillK.R
R/fillResult.R
R/fit.R
R/fitModel.R
R/fullKF.R
R/gaus.R
R/getAniA.R
R/getAniK.R
R/getAniSuper.R
R/getAnisotropy.R
R/getAutoClp0.R
R/getClpConstr.R
R/getCoh.R
R/getCohToPlot.R
R/getConToPlot.R
R/getConstrained.R
R/getDiffTheta.R
R/getDiffThetaChange.R
R/getDiffThetaCl.R
R/getDiffThetaClChange.R
R/getFixed.R
R/getGroups.R
R/getJac.R
R/getKinConcen.R
R/getLightDiff.R
R/getModel.R
R/getMvec.R
R/getOsc.R
R/getPar.R
R/getPrel.R
R/getPrelBetweenDatasets.R
R/getPrelTheta.R
R/getResid.R
R/getResidRet.R
R/getResults.R
R/getSelectedTracesMax.R
R/getSpecList.R
R/getSpecToPlot.R
R/getStartTri.R
R/getStdErrClp.R
R/getStreakBacksweep.R
R/getTheta.R
R/getThetaCl.R
R/getXList.R
R/getXsuper.R
R/init.dat.R
R/init.fit.R
R/init.multimodel.R
R/init.multitheta.R
R/init.opt.R
R/init.res.R
R/init.theta.R
R/initModel.R
R/initModellist.R
R/initOneModel.R
R/irfparF.R
R/jacobian.R
R/kin.R
R/kinopt.R
R/l2nu.R
R/linloglines.R
R/linlogplot.R
R/linlogtics.R
R/mass.R
R/massopt.R
R/matlinlogplot.R
R/modifyModel.R
R/multiLin.R
R/multimodel.R
R/multitheta.R
R/normdat.R
R/opt.R
R/outlierCorr.R
R/plotClp.R
R/plotFLIM.R
R/plotFLIMresid.R
R/plotKinBreakDown.R
R/plotKinSpecEst.R
R/plotMassSpec.R
R/plotResids.R
R/plotSpecKin.R
R/plotSpectraSuper.R
R/plotTracesResids.R
R/plotTracesSuper.R
R/plotTri.R
R/preProcess.R
R/processOrder.R
R/readData.R
R/readclp0.R
R/res.R
R/rescomp.R
R/sample_sel.R
R/scaleConList.R
R/setGenerics.R
R/set_getClpindepX_amp.R
R/set_getClpindepX_kin.R
R/set_getClpindepX_mass.R
R/set_getClpindepX_spec.R
R/set_initModelClass_amp.R
R/set_initModelClass_kin.R
R/set_initModelClass_mass.R
R/set_initModelClass_spec.R
R/set_plotter_kin.R
R/set_plotter_mass.R
R/set_plotter_spec.R
R/set_residPart_amp.R
R/set_residPart_kin.R
R/set_residPart_mass.R
R/set_residPart_spec.R
R/simndecay_gen.R
R/simpExp.R
R/simpPol.R
R/skew.R
R/spec.R
R/specModel.R
R/specopt.R
R/specparF.R
R/sumKinSpecEst.R
R/summary.R
R/superLogistic.R
R/theta.R
R/triResolve.R
R/unitstep.R
R/weightNL.R
R/weightPsi.R
R/weightSM.R
R/writeAverage.R
R/writeData.R
R/writeEst.R
R/writeFit.R
R/zzz.R
data
data/denS4.rda
data/denS5.rda
data/donorAcceptorTagged.rda
data/donorTagged.rda
data/mea_IRF.rda
data/target.rda
inst
inst/CITATION
man
man/FLIMplots.Rd
man/TIMP-package.Rd
man/amp-class.Rd
man/baseIRF.Rd
man/dat-class.Rd
man/denS4.Rd
man/divergeZimage.Rd
man/donorAcceptorTagged.Rd
man/donorTagged.Rd
man/efit2file.Rd
man/examineFit.Rd
man/fit-class.Rd
man/fitModel.Rd
man/getClpindepX.Rd
man/getResid.Rd
man/getResults.Rd
man/initModel.Rd
man/internals.Rd
man/kin-class.Rd
man/kinopt-class.Rd
man/mass-class.Rd
man/massopt-class.Rd
man/mea_IRF.Rd
man/modifyModel.Rd
man/multimodel-class.Rd
man/multitheta-class.Rd
man/opt-class.Rd
man/outlierCorr.Rd
man/plotter.Rd
man/preProcess.Rd
man/readData.Rd
man/readclp0.Rd
man/res-class.Rd
man/residPart.Rd
man/spec-class.Rd
man/specopt-class.Rd
man/sumKinSpecEst.Rd
man/target.Rd
man/theta-class.Rd
man/writeAverage.Rd
src
src/ntr.c
tests
tests/25_650-75_2700.txt
tests/PCP1.-50000fs.PP.txt
tests/cp432704.txt
tests/cp8b.txt
tests/example2nd.R
tests/kin_ir_simult_script.RRRR
tests/kin_sim_large_script.R
tests/kin_simple_ir_script.R
tests/kin_simple_visible_script.R
tests/kin_target_script.R
tests/psitspec.txt
tests/sim1.txt
tests/spectral_script.R
TIMP documentation built on May 21, 2017, 12:41 a.m.

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