Analysis for

Estimation of biodiversity with short-range multispectral imaging in a temperate calcareous grassland

Jackson, J, Lawson, C. S., Adelmant, C., Huhtala, E., Fernandes, P., Hodgson, R., King, H., Williamson, L., Maseyk, K., Hawes, N., Hector, A., & Salguero-Gómez, R

2022-09-02

Repository created by John Jackson

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Full analysis for our study on the link between spectral diversity and biodiversity in a calcareous grassland in Wytham Woods, Oxfordshire. Here we use multispectral image data from a commercially available UAV monitoring system at short range and fine spatial resolution. For the manuscript please see the bioRxiv entry. Package version info for this analysis is given below.

Analysis scripts can be found in the code/ sub-repository, manuscript figures and output in the output/ sub-repository, and analysis data in the data/ sub-repository. Raw cropped image data (which is unsuitable for storage online) is available on request from John Jackson.

Scripts are labeled A-E in order of the analysis, and are as follows:

1. A_biodiversity_data_processing.R - data cleaning and wrangling of raw biodiversity data for June 2021.
2. B_raster_extraction_uncalibrated.R - pipeline for image analysis to calculate spectral distribution characteristics from cropped image data.
3. C_raster_band_plot.R - plotting of example raster data for manuscript figure 1. Script C2 is repeated but with a black background.
4. D_biodiversity_spectral_uncalibrated_models.R - Bayesian linear modeling framework linking spectral diversity and biodiversity.
5. E_biodiversity_spectral_uncalibrated_supplementary.R - supplementary figures and stats for the manuscript.

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System Information and Package Versions

Click here to expand

R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] viridis_0.5.1       viridisLite_0.3.0   rnaturalearth_0.1.0 brms_2.15.0        
 [5] Rcpp_1.0.7          cowplot_1.1.1       ggdist_3.0.0        ggridges_0.5.3     
 [9] flextable_0.6.7     psych_2.1.6         rasterVis_0.50.3    latticeExtra_0.6-29
[13] lattice_0.20-41     terra_1.3-4         raster_3.4-13       sp_1.4-5           
[17] patchwork_1.1.1     forcats_0.5.1       stringr_1.4.0       dplyr_1.0.5        
[21] purrr_0.3.4         readr_1.4.0         tidyr_1.1.3         tibble_3.1.0       
[25] ggplot2_3.3.5       tidyverse_1.3.1    

loaded via a namespace (and not attached):
  [1] uuid_0.1-4           readxl_1.3.1         backports_1.2.1      systemfonts_1.0.2   
  [5] plyr_1.8.6           igraph_1.2.6         splines_4.0.5        crosstalk_1.1.1     
  [9] rstantools_2.1.1     inline_0.3.19        digest_0.6.27        htmltools_0.5.1.1   
 [13] rsconnect_0.8.24     fansi_0.4.2          magrittr_2.0.1       modelr_0.1.8        
 [17] RcppParallel_5.1.4   matrixStats_0.60.0   officer_0.3.19       xts_0.12.1          
 [21] prettyunits_1.1.1    jpeg_0.1-9           colorspace_2.0-0     rvest_1.0.1         
 [25] xfun_0.29            haven_2.3.1          callr_3.7.0          crayon_1.4.1        
 [29] jsonlite_1.7.2       hexbin_1.28.2        lme4_1.1-27.1        zoo_1.8-9           
 [33] glue_1.4.2           gtable_0.3.0         emmeans_1.6.2-1      V8_3.4.2            
 [37] distributional_0.2.2 ggdark_0.2.1         pkgbuild_1.2.0       rstan_2.21.2        
 [41] abind_1.4-5          scales_1.1.1         mvtnorm_1.1-1        DBI_1.1.1           
 [45] miniUI_0.1.1.1       xtable_1.8-4         units_0.7-2          tmvnsim_1.0-2       
 [49] proxy_0.4-26         stats4_4.0.5         StanHeaders_2.21.0-7 DT_0.18             
 [53] htmlwidgets_1.5.3    httr_1.4.2           threejs_0.3.3        RColorBrewer_1.1-2  
 [57] ellipsis_0.3.2       farver_2.1.0         pkgconfig_2.0.3      loo_2.4.1           
 [61] dbplyr_2.1.1         utf8_1.2.1           tidyselect_1.1.1     rlang_0.4.11        
 [65] reshape2_1.4.4       later_1.2.0          munsell_0.5.0        cellranger_1.1.0    
 [69] tools_4.0.5          cli_3.0.1            generics_0.1.0       broom_0.7.9         
 [73] evaluate_0.14        fastmap_1.1.0        knitr_1.33           processx_3.5.2      
 [77] fs_1.5.0             zip_2.2.0            nlme_3.1-152         mime_0.11           
 [81] projpred_2.0.2       xml2_1.3.2           compiler_4.0.5       bayesplot_1.8.1     
 [85] shinythemes_1.2.0    rstudioapi_0.13      curl_4.3.2           gamm4_0.2-6         
 [89] png_0.1-7            e1071_1.7-8          reprex_2.0.1         stringi_1.5.3       
 [93] ps_1.6.0             Brobdingnag_1.2-6    gdtools_0.2.3        Matrix_1.3-2        
 [97] classInt_0.4-3       nloptr_1.2.2.2       markdown_1.1         shinyjs_2.0.0       
[101] vctrs_0.3.8          pillar_1.6.2         lifecycle_1.0.0      bridgesampling_1.1-2
[105] estimability_1.3     data.table_1.14.0    httpuv_1.6.1         R6_2.5.0            
[109] promises_1.2.0.1     KernSmooth_2.23-18   gridExtra_2.3        codetools_0.2-18    
[113] boot_1.3-27          colourpicker_1.1.0   MASS_7.3-53.1        gtools_3.8.2        
[117] assertthat_0.2.1     withr_2.4.2          shinystan_2.5.0      mnormt_2.0.2        
[121] mgcv_1.8-34          parallel_4.0.5       hms_1.1.0            grid_4.0.5          
[125] class_7.3-18         coda_0.19-4          minqa_1.2.4          rmarkdown_2.10      
[129] sf_1.0-2             shiny_1.6.0          lubridate_1.7.10     base64enc_0.1-3     
[133] dygraphs_1.1.1.6