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TIMP

TIMP is an R package for fitting superposition models that implements the partitioned variable projection algorithm. The package has been extensively applied to modeling spectroscopy and Fluorescence Lifetime Imaging Microscopy (FLIM) datasets. This is the git managed codebase of the r-forge TIMP project.

https://github.com/glotaran/timp

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 14 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: scholar.google
  • ✓
    Committers with academic emails
    2 of 6 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

parameter-estimation r
Last synced: 6 months ago · JSON representation

Repository

TIMP is an R package for fitting superposition models that implements the partitioned variable projection algorithm. The package has been extensively applied to modeling spectroscopy and Fluorescence Lifetime Imaging Microscopy (FLIM) datasets. This is the git managed codebase of the r-forge TIMP project.

Basic Info
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 1
  • Open Issues: 2
  • Releases: 3
Topics
parameter-estimation r
Created about 11 years ago · Last pushed about 3 years ago
Metadata Files
Readme License

README.md

TIMP

TIMP is an R package developed by Mullen and van Stokkum for fitting models to data arising from time-resolved spectroscopy, Fluorescence Lifetime Imaging Microscopy (FLIM) and mass spectroscopy experiments.

The package provides a comprehensive problem solving environment (PSE) for fitting separable nonlinear models to a variety of datasets. It is used for modeling multiway spectroscopic measurements, and allows users to simultaneously analyze datasets collected under a range of experimental conditions. To do this efficiently it implements the partitioned variable projection algorithm.

Installation

TIMP is available from CRAN. To install, from an R Console type:

R install.packages("TIMP")

The Glotaran Ecosystem

TIMP is part of the Glotaran ecosystem (glotaran.org). It functions as the computational back-end of glotaran-legacy, the original Java-based GUI for TIMP, released under the name Glotaran. Additionally it is used as the backend for paramGUI, a R Shiny web app for teaching parameter estimation by examples.

Cite

TIMP can be cited as:

Mullen KM, van Stokkum IHM (2007). TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements. Journal of Statistical Software, 18(3). URL https://doi.org/10.18637/jss.v018.i03/.

See also citation.html on CRAN

Contributors

TIMP has its origins in more than 15 years of software development for applications in computational physics by Ivo van Stokkum.

Katharine Mullen created the package during her PhD studies and was the primary developer for many years. She's now at UCLA.

Sergey Laptenok has contributed options for FLIM data and invaluable experience and testing on the MS Windows OS, co-creator of the Glotaran GUI.

David Nicolaides has contributed options for modeling reaction kinetics as described by kinetic theory models.

Alessandro Marin has contributed testing and ideas for new options.

Ilya Stepanenko has implemented PPViewer, a LabVIEW application for interactive exploration of data and model fit that is useful for examining TIMP datafiles and model fit output.

The members of the biophysics group of the Department of Physics and Astronomy of the Vrije Universiteit Amsterdam have motivated much of the development of TIMP.

The package is currently maintained by Joris Snellenburg, who also created and maintains the Glotaran GUI for TIMP.

Package statistics

| TIMP | Downloads | | --- | ---: | | Last day | | | Last week | | | Last month | | | Total | | | Citations | Citation Badge |

Download count thanks to the cranlogs.app service.

Citations thanks to Jules Kreuer's Citation Badge.

Notes

  • TIMP 1.0 was published January 10th 2007.
  • TIMP 1.2 is the earliest version on CRAN, published 1st of May 2007.
  • The grand-total download count, is only from from October 2012 (5 year of stats missing).

Owner

  • Name: GloTarAn
  • Login: glotaran
  • Kind: organization
  • Email: github@glotaran.org
  • Location: Amsterdam

Modeling frameworks for global and target analysis (GloTarAn)

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 137
  • Total Committers: 6
  • Avg Commits per committer: 22.833
  • Development Distribution Score (DDS): 0.555
Past Year
  • Commits: 8
  • Committers: 1
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kmm k****m@e****b 61
jsnel j****l@e****b 34
Joris Snellenburg j****g@v****l 21
Joris Snellenburg j****l 19
Ivo van Stokkum i****m@v****l 1
stefan7th s****h@e****b 1
Committer Domains (Top 20 + Academic)
vu.nl: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 9
  • Average time to close issues: 3 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.33
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jsnel (8)
Pull Request Authors
  • jsnel (9)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 265 last-month
  • Total docker downloads: 21,777
  • Total dependent packages: 1
  • Total dependent repositories: 2
  • Total versions: 19
  • Total maintainers: 1
cran.r-project.org: TIMP

Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

  • Versions: 19
  • Dependent Packages: 1
  • Dependent Repositories: 2
  • Downloads: 265 Last month
  • Docker Downloads: 21,777
Rankings
Docker downloads count: 12.7%
Dependent packages count: 18.3%
Dependent repos count: 19.4%
Forks count: 21.2%
Average: 21.4%
Stargazers count: 25.6%
Downloads: 30.9%
Maintainers (1)
j.snellenburg@vu.nl
Last synced: 6 months ago

Dependencies

.github/workflows/lint.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/r.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 2.10.0 depends
  • fields >= 4.1 depends
  • methods * depends
  • colorspace * imports
  • deSolve * imports
  • gclus * imports
  • gplots * imports
  • grDevices * imports
  • graphics * imports
  • minpack.lm >= 1.1 imports
  • nnls >= 1.1 imports
  • splines * imports
  • stats * imports
  • utils * imports