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predmicror: Fitting Predictive Microbiology Models

Provides predictive microbiology model functions and convenience wrappers for fitting primary growth, microbial inactivation, dynamic, omnibus, and cardinal parameter models to experimental data using nonlinear least squares and related mixed-effects or time-varying workflows. Includes helper functions for extracting fitted values, calculating model diagnostics, and comparing fitted models. Implemented model families include those described by: Zwietering et al. (1990) <doi:10.1128/AEM.56.6.1875-1881.1990>, Baranyi and Roberts (1994) <doi:10.1016/0168-1605(94)90157-0>, Baranyi and Roberts (1995) <doi:10.1016/0168-1605(94)00121-L>, Buchanan et al. (1997) <doi:10.1006/fmic.1997.0125>, Richards (1959) <doi:10.1093/jxb/10.2.290>, Fang et al. (2012) <doi:10.1111/j.1750-3841.2012.02873.x>, Fang et al. (2013) <doi:10.1016/j.fm.2012.12.005>, Huang (2008) <doi:10.1111/j.1750-3841.2008.00785.x>, Huang (2009) <doi:10.1016/j.jfoodeng.2008.07.011>, Huang (2013) <doi:10.1016/j.foodcont.2012.11.019>, Geeraerd et al. (2005) <doi:10.1016/j.ijfoodmicro.2004.11.038>, van Boekel (2002) <doi:10.1016/S0168-1605(01)00742-5>, Peleg (1999) <doi:10.1016/S0963-9969(99)00081-2>, Mafart et al. (2002) <doi:10.1016/S0168-1605(01)00624-9>, Albert and Mafart (2005) <doi:10.1016/j.ijfoodmicro.2004.10.016>, Rosso et al. (1993) <doi:10.1006/jtbi.1993.1099>, Rosso et al. (1995) <doi:10.1128/AEM.61.2.610-616.1995>, and Rosso et al. (1996) <doi:10.4315/0362-028X-59.9.944>.

Version: 1.3.2
Depends: R (≥ 3.4.0)
Imports: graphics, gslnls, nlme, Rdpack, stats, utils
Suggests: knitr, rmarkdown, htmltools, commonmark, shinyAce, testthat (≥ 3.0.0), ggplot2, deSolve, FME, minpack.lm, reshape2, readxl, shiny
Published: 2026-06-19
DOI: 10.32614/CRAN.package.predmicror
Author: Vasco Cadavez ORCID iD [aut, cre], Ursula Gonzales-Barron ORCID iD [aut]
Maintainer: Vasco Cadavez <vcadavez at ipb.pt>
BugReports: https://github.com/fsqanalytics/predmicror/issues
License: GPL (≥ 3)
URL: https://fsqanalytics.github.io/predmicror/, https://github.com/fsqanalytics/predmicror
NeedsCompilation: no
Citation: predmicror citation info
Materials: README, NEWS
CRAN checks: predmicror results

Documentation:

Reference manual: predmicror.html , predmicror.pdf
Vignettes: Cardinal parameter models (source, R code)
Data Transformation in predmicror (source, R code)
Dynamic predictive microbiology models (source, R code)
Fitting growth models using predmicror (source, R code)
Microbial inactivation models (source, R code)
Comparing fitted predmicror models (source, R code)
Omnibus predictive microbiology models (source, R code)
Introduction to predmicror (source)

Downloads:

Package source: predmicror_1.3.2.tar.gz
Windows binaries: r-devel: predmicror_1.3.2.zip, r-release: predmicror_1.3.2.zip, r-oldrel: not available
macOS binaries: r-release (arm64): predmicror_1.3.2.tgz, r-oldrel (arm64): predmicror_1.3.2.tgz, r-release (x86_64): predmicror_1.3.2.tgz, r-oldrel (x86_64): predmicror_1.3.2.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.