xos_ms_dataandcode

Zofia Tillman 2024-08-07

Data and code used to run analysis and create visualizations/tables for ‘Rapid measurement of soluble xylo-oligomers using near-infrared spectroscopy (NIRS) and multivariate statistics: calibration model development and practical approaches to model optimization’ (Biotechnology for Biofuels and Bioproducts 2024, https://doi.org/10.1186/s13068-024-02558-6)

How to Reproduce Analysis

1. Open R studio and change to version 4.2.3 via Tools -> Global Options -> R version -> Change…
2. In R studio, source, ./code/runAnalysis.R

Dependencies

• R version 4.2.3 (2023-03-15 ucrt)
  • tidyverse (v. 2.0.0)
  • pls (v. 2.8.1)
  • prospectr (v. 0.2.6)
  • ggfortify (v. 0.4.16)
  • ggpmisc (v. 0.5.2)
  • rmarkdown (v. 2.21)
  • openxlsx (v. 4.2.5.2)
  • ggh4x (v. 0.2.8)
  • ggmagnify (v. 0.4.0.9000)
  • patchwork (v. 1.2.0)
  • egg (v. 0.4.5)

My Computer

## R version 4.2.3 (2023-03-15 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## 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    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] patchwork_1.2.0      egg_0.4.5            gridExtra_2.3       
##  [4] ggmagnify_0.4.0.9000 ggh4x_0.2.8          openxlsx_4.2.5.2    
##  [7] ggpmisc_0.5.2        ggpp_0.5.2           ggfortify_0.4.16    
## [10] prospectr_0.2.6      pls_2.8-1            lubridate_1.9.2     
## [13] forcats_1.0.0        stringr_1.5.0        dplyr_1.1.2         
## [16] purrr_1.0.1          readr_2.1.4          tidyr_1.3.0         
## [19] tibble_3.2.1         ggplot2_3.4.4        tidyverse_2.0.0     
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.0   xfun_0.39          splines_4.2.3      lattice_0.21-8    
##  [5] colorspace_2.1-0   vctrs_0.6.3        generics_0.1.3     htmltools_0.5.5   
##  [9] yaml_2.3.7         survival_3.5-5     utf8_1.2.3         rlang_1.1.1       
## [13] pillar_1.9.0       glue_1.6.2         withr_3.0.0        foreach_1.5.2     
## [17] lifecycle_1.0.4    MatrixModels_0.5-1 munsell_0.5.0      gtable_0.3.4      
## [21] zip_2.3.0          codetools_0.2-19   evaluate_0.20      knitr_1.42        
## [25] SparseM_1.81       tzdb_0.3.0         fastmap_1.1.1      quantreg_5.95     
## [29] fansi_1.0.4        Rcpp_1.0.11        polynom_1.4-1      scales_1.3.0      
## [33] hms_1.1.3          digest_0.6.33      stringi_1.7.12     grid_4.2.3        
## [37] mathjaxr_1.6-0     cli_3.6.1          tools_4.2.3        magrittr_2.0.3    
## [41] pkgconfig_2.0.3    MASS_7.3-59        Matrix_1.5-4       timechange_0.2.0  
## [45] rmarkdown_2.21     rstudioapi_0.15.0  iterators_1.0.14   R6_2.5.1          
## [49] compiler_4.2.3