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TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements

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  • Mullen, Katharine M.
  • van Stokkum, Ivo H. M.

Abstract

TIMP is an R package for modeling multiway spectroscopic measurements. The package allows for the simultaneous analysis of datasets collected under different experimental conditions in terms of a wide variety of parametric models. Models arising in spectroscopy data analysis often have some parameters that are intrinstically nonlinear, and some parameters that are conditionally linear on estimates of the nonlinear parameters. TIMP fits such separable nonlinear models using partitioned variable projection, a variant of the variable projection algorithm that is described here for the first time. The of the partitioned variable projection algorithm allows fitting many models for spectroscopy datasets using much less memory as compared to under the standard variable projection algorithm that is implemented in nonlinear optimization routines (e.g., the plinear option of the R function nls), as is shown here. An overview of modeling with TIMP is also given that includes several case studies in the application of the package.

Suggested Citation

  • Mullen, Katharine M. & van Stokkum, Ivo H. M., 2007. "TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i03).
    • Handle: RePEc:jss:jstsof:v:018:i03
    DOI: http://hdl.handle.net/10.18637/jss.v018.i03
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    References listed on IDEAS

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    1. Laptenok, Sergey & Mullen, Katharine M. & Borst, Jan Willem & van Stokkum, Ivo H. M. & Apanasovich, Vladimir V. & Visser, Antonie J. W. G., 2007. "Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i08).
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    Cited by:

    1. Chong Wang & Bo Wu & Yang Li & Shen Zhou & Conghui Wu & Tianyang Dong & Ying Jiang & Zihui Hua & Yupeng Song & Wei Wen & Jianxin Tian & Yongqiang Chai & Rui Wen & Chunru Wang, 2024. "Aggregation promotes charge separation in fullerene-indacenodithiophene dyad," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Adelina Bärligea & Philipp Hochstaffl & Franz Schreier, 2023. "A Generalized Variable Projection Algorithm for Least Squares Problems in Atmospheric Remote Sensing," Mathematics, MDPI, vol. 11(13), pages 1-20, June.
    3. Dianne O’Leary & Bert Rust, 2013. "Variable projection for nonlinear least squares problems," Computational Optimization and Applications, Springer, vol. 54(3), pages 579-593, April.
    4. repec:jss:jstsof:18:i08 is not listed on IDEAS
    5. Wei Wen & Guocai Liu & Xiaofang Wei & Haojie Huang & Chong Wang & Danlei Zhu & Jianzhe Sun & Huijuan Yan & Xin Huang & Wenkang Shi & Xiaojuan Dai & Jichen Dong & Lang Jiang & Yunlong Guo & Hanlin Wang, 2024. "Biomimetic nanocluster photoreceptors for adaptative circular polarization vision," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    6. Laptenok, Sergey & Mullen, Katharine M. & Borst, Jan Willem & van Stokkum, Ivo H. M. & Apanasovich, Vladimir V. & Visser, Antonie J. W. G., 2007. "Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i08).

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