Package: TIMP 1.13.6

Joris Snellenburg

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, as described by Mullen & van Stokkum (2007) <doi:10.18637/jss.v018.i03> for its use in fitting time resolved spectroscopy data, and as described by Laptenok et al. (2007) <doi:10.18637/jss.v018.i08> for its use in fitting Fluorescence Lifetime Imaging Microscopy (FLIM) data, in the study of Förster Resonance Energy Transfer (FRET). `TIMP` also serves as the computation backend for the `GloTarAn` software, a graphical user interface for the package, as described in Snellenburg et al. (2012) <doi:10.18637/jss.v049.i03>.

Authors:Katharine M. Mullen [aut], Joris Snellenburg [cre, ctb], Sergey P. Laptenok [ctb], David Nicolaides [ctb], Ivo H.M. van Stokkum [aut]

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TIMP.pdf |TIMP.html✨
TIMP/json (API)

# Install 'TIMP' in R:
install.packages('TIMP', repos = c('https://glotaran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/glotaran/timp/issues

Datasets:
  • C1 - Ultrafast time-resolved fluorescence data
  • C2 - Ultrafast time-resolved fluorescence data
  • C3 - Ultrafast time-resolved fluorescence data
  • c001 - Fluorescent lifetime imaging microscopy (FLIM) data
  • c003 - Fluorescent lifetime imaging microscopy (FLIM) data
  • cy005c - Fluorescent lifetime imaging microscopy (FLIM) data
  • cy006 - Fluorescent lifetime imaging microscopy (FLIM) data
  • denS4 - Time-resolved absorption data
  • denS5 - Time-resolved absorption data
  • mea_IRF - Instrument response for fluorescent lifetime imaging microscopy (FLIM) data

On CRAN:

parameter-estimation

4.62 score 2 stars 1 packages 14 scripts 408 downloads 14 mentions 137 exports 17 dependencies

Last updated 2 years agofrom:7d7be69d0c. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
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R-4.5-linux-x86_64NOTENov 07 2024
R-4.4-win-x86_64NOTENov 07 2024
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R-4.4-mac-aarch64NOTENov 07 2024
R-4.3-win-x86_64OKNov 07 2024
R-4.3-mac-x86_64OKNov 07 2024
R-4.3-mac-aarch64OKNov 07 2024

Exports:addDscaladdPreladdPrelClampapplyWeightingModelbarplot3baseCorlambdabaseCortimebaseIRFcalcBcalcCcalcCirfcalcDcalcEbsplinecalcEhiergauscompCohcompModelcompModelMasscompOscconvGausExpdatdiffAdddiffChangediffFreediffReldiffRemovedisplayEstdivergeZimagedoClpConstrdoConstrSuperdoSVDefit2fileexamineFitfillKfillResultfitfitModelfullKFgausgetAutoClp0getCgetCLPgetClpConstrgetClpindepXgetCLPListgetCohgetCohToPlotgetConToPlotgetDASgetDatagetDiffThetagetDiffThetaChangegetDiffThetaClgetDiffThetaClChangegetdim1getdim2getFixedgetGroupsgetKinConcengetModelgetOscgetPargetPrelgetPrelThetagetResidgetResidRetgetResidualsgetSelectedTracesMaxgetSpecListgetSpecToPlotgetSVDDatagetSVDResidualsgetThetagetThetaClgetTracesgetXgetXListgetXsuperinitModelinitModellistirfparFkinkinoptl2nulinloglineslinlogplotlinlogticsmassmassoptmatlinlogplotmodifyModelmultiLinmultimodelmultithetanormdatonlsoptoutlierCorrparEstplotClpplotFLIMplotHistAmpplotHistNormCompplotIntenImageplotKinBreakDownplotKinSpecEstplotNormCompplotSelIntenImageplotTauplotterplotTracesSuperpreProcessprocessOrderreadclp0readDataresrescompresidPartsample_selscaleConListsimndecay_gensimpExpsimpPolskewspecspecModelspecoptspecparFsumKinSpecEstsumnlsthetaunitstepweightNLweightPsiwriteAveragewriteEstwriteFit

Dependencies:bitopscaToolsclustercolorspacedeSolvedotCall64fieldsgclusgplotsgtoolsKernSmoothmapsminpack.lmnnlsRcppspamviridisLite

Readme and manuals

Help Manual

Help pageTopics
a problem solving environment for fitting separable nonlinear models in physics and chemistry applicationsTIMP-package TIMP
Class "amp" for diagonal matrix model specification.amp amp-class
Baseline subtraction from a vector, usually representing an IRF.baseIRF
Class "dat" for model and data storagedat dat-class
Time-resolved absorption datadenS4 denS5
Plots a matrix with a diverging palette, with the center value of the palette possible to setdivergeZimage
Fluorescent lifetime imaging microscopy (FLIM) datacy005c cy006 donorAcceptorTagged
Fluorescent lifetime imaging microscopy (FLIM) datac001 c003 donorTagged
Convert 'tim' FORTRAN efit files to plain matrices in ASCII filesefit2file
Examines the results of a call to fitModelexamineFit
Class "fit" to store the results of model fitting associated with all datasets analyzed.fit fit-class
Performs optimization of (possibly multidataset) models.fitModel
Functions to plot FLIM results.FLIMplots plotHistAmp plotHistNormComp plotIntenImage plotNormComp plotSelIntenImage plotTau
Generic function getClpindepX in Package `TIMP'getClpindepX getClpindepX,amp-method getClpindepX,kin-method getClpindepX,mass-method getClpindepX,spec-method getClpindepX-methods
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.getResid
Functions to print and return parts of the object returned by the fitting routines.getC getCLP getCLPList getDAS getData getdim1 getdim2 getResiduals getResults getSVDData getSVDResiduals getTraces getX getXList onls parEst sumnls
Defines the model to be used in analysis.initModel
Class "kin" for kinetic model storage.kin kin-class
Class "kinopt" stores options for fitting and plotting kinetic modelskinopt kinopt-class
Class "mass" for mass spectrometry model storage.mass mass-class
Class "massopt" stores options for fitting and plotting models for mass spectrometry datamassopt massopt-class
Instrument response for fluorescent lifetime imaging microscopy (FLIM) datamea_IRF
Allows the starting values for parameters associated with a model to be updated with the values found in fitting the model.modifyModel
Class "multimodel" for storage of multidataset models, data and the results of fitting.multimodel multimodel-class
Class "multitheta" that stores a list with one element of class "theta" for each dataset modeled.multitheta multitheta-class
Class "opt" stores options for fitting and plottingopt opt-class
Finds and removes outliers from a datasetsoutlierCorr
Generic function plotter in Package `TIMP'plotter plotter,kin-method plotter,mass-method plotter,spec-method plotter-methods
Performs preprocessing on data stored as an objects of class dat.preProcess
This function reads in a specification of constraints to zero on the clp.readclp0
This function reads in data the ivo file formatreadData
Class "res" to store the results of model fitting associated with a single dataset.res res-class
Generic function residPart in Package `TIMP'residPart residPart,amp-method residPart,kin-method residPart,mass-method residPart,spec-method residPart-methods
Class "spec" for the storage of spectral models.spec spec-class
Class "specopt" stores options for fitting and plotting spectral modelsspecopt specopt-class
Makes a summary plot of spectra associated with kinetic components alongside a plot showing parameter estimatessumKinSpecEst
Ultrafast time-resolved fluorescence dataC1 C2 C3 target
Class "theta" for storage of nonlinear parameter estimatestheta theta-class
Writes the average of scans stored in a file to a new file in the 'ivo' formatwriteAverage