Zofia Tillman 2025-05-28
Code used to run analysis and create visualizations/tables for ‘Rapid monitoring of fermentations – a feasibility study on biological 2,3-butanediol production’
Tillman, Z., Peterson, D.J., Dowe, N. et al. Rapid monitoring of fermentations: a feasibility study on biological 2,3-butanediol production. Biotechnol. Biofuels Bioprod. 18, 60 (2025).
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Clone Repository
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Download the research data used to perform this analysis from data.nrel.gov - Data for “Rapid monitoring of fermentations- a feasibility study of biological 2,3-butanediol production” and save data to data/raw folder within repository
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Produce Models by working through the following scripts:
- laboratoryatline_full_modelbuild.R (lab grade full models)
- laboratoryatline_lowcostfeasibility_modelbuild.R (lab grade low cost feasibility models)
- laboratoryatline_onlinefeasibility_modelbuild.R (lab grade on line feasibility models)
- lowcostatline_modelbuild.R (low cost at line models)
- laboratoryonline_modelbuild.R (laboratory grade on line models)
- Produce Figures and Tables describing the models by working through the following scripts:
- figure_(1-S11).R code used to generate each figure in the manuscript
- table_(S1-5).R code used to generate each table in the manuscript
- R version 4.4.2 (2024-10-31 ucrt)
tidyverse(v. 2.0.0)pls(v. 2.8.5)prospectr(v. 0.2.7)ggpmisc(v. 0.6.1)openxlsx(v. 4.2.8)egg(v. 0.4.5)ggsci(v. 3.2.0)caret(v. 7.0.1)ggtext(v. 0.1.2)GGally(v. 2.2.1)patchwork(v. 1.3.0)Hmisc(v. 5.2.2)rmarkdown(v. 2.29)
## R version 4.4.2 (2024-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 11 x64 (build 22631)
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## Matrix products: default
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##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
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## time zone: America/Denver
## tzcode source: internal
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] Hmisc_5.2-2 patchwork_1.3.0 GGally_2.2.1 ggtext_0.1.2
## [5] caret_7.0-1 lattice_0.22-6 ggsci_3.2.0 egg_0.4.5
## [9] gridExtra_2.3 openxlsx_4.2.8 ggpmisc_0.6.1 ggpp_0.5.8-1
## [13] prospectr_0.2.7 pls_2.8-5 lubridate_1.9.4 forcats_1.0.0
## [17] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
## [21] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
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## loaded via a namespace (and not attached):
## [1] polynom_1.4-1 pROC_1.18.5 rlang_1.1.5
## [4] magrittr_2.0.3 compiler_4.4.2 vctrs_0.6.5
## [7] reshape2_1.4.4 quantreg_6.00 pkgconfig_2.0.3
## [10] fastmap_1.2.0 backports_1.5.0 rmarkdown_2.29
## [13] prodlim_2024.06.25 tzdb_0.4.0 MatrixModels_0.5-3
## [16] xfun_0.50 recipes_1.1.0 parallel_4.4.2
## [19] cluster_2.1.6 R6_2.5.1 stringi_1.8.4
## [22] RColorBrewer_1.1-3 parallelly_1.41.0 rpart_4.1.23
## [25] Rcpp_1.0.14 iterators_1.0.14 knitr_1.49
## [28] future.apply_1.11.3 base64enc_0.1-3 Matrix_1.7-1
## [31] splines_4.4.2 nnet_7.3-19 timechange_0.3.0
## [34] tidyselect_1.2.1 rstudioapi_0.17.1 yaml_2.3.10
## [37] timeDate_4041.110 codetools_0.2-20 listenv_0.9.1
## [40] plyr_1.8.9 withr_3.0.2 evaluate_1.0.3
## [43] foreign_0.8-87 future_1.34.0 survival_3.7-0
## [46] ggstats_0.8.0 zip_2.3.1 xml2_1.3.6
## [49] pillar_1.10.1 checkmate_2.3.2 foreach_1.5.2
## [52] stats4_4.4.2 generics_0.1.3 mathjaxr_1.6-0
## [55] hms_1.1.3 munsell_0.5.1 scales_1.3.0
## [58] globals_0.16.3 class_7.3-22 glue_1.8.0
## [61] tools_4.4.2 data.table_1.16.4 SparseM_1.84-2
## [64] ModelMetrics_1.2.2.2 gower_1.0.2 grid_4.4.2
## [67] ipred_0.9-15 colorspace_2.1-1 nlme_3.1-166
## [70] htmlTable_2.4.3 Formula_1.2-5 cli_3.6.3
## [73] lava_1.8.1 gtable_0.3.6 digest_0.6.37
## [76] htmlwidgets_1.6.4 farver_2.1.2 htmltools_0.5.8.1
## [79] lifecycle_1.0.4 hardhat_1.4.0 gridtext_0.1.5
## [82] MASS_7.3-61