Last updated: 2019-05-25

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Predicted defoliation (absolute)

Predicted defoliation by XGBOOST on 20 m spatial resolution in the Basque Country.

With an RMSE of 36 % (for a range of 0 - 100), the model focuses its prediction to the mean of the response range (0 - 100) to achieve acceptable performance results on the test set.

The following vegetation indices have been used, selected by the internal variable importance rating of XGBOOST:

  • EVI
  • GDVI4
  • GDVI3
  • GDVI2
  • D1
  • mNDVI
  • mSR

Optimization path of hyperparameter tuning

The following shows the optimization path (RMSE) of the hyperparameter tuning for the XGBOOST model using 20 MBO iterations (with a starting design of 30).

 [1] 43.17171 44.46635 43.42093 43.82827 44.53159 43.86555 41.70989
 [8] 37.23756 37.77271 37.66704 39.38304 40.50224 36.66701 36.22678
[15] 38.25126 36.93972 39.12485 42.45889 38.05913 39.47527

Some more details on the optimization path are presented below:

Version Author Date
39ea046 pat-s 2019-05-22

Predicted Defoliation (relative)

Since these absolute values do not reflect the truth, we decided to create a relative Index from the predicted absolute values.

This was done by calling

scale(data$defoliation, center = FALSE,
      scale = max(data$defoliation, na.rm = TRUE)/100)

which re-scales the data from 0 - 100. The code was adapted from this Stackoverflow answer.

Defoliation evaluation

Absolute defoliation

Maps

2017

Version Author Date
39ea046 pat-s 2019-05-22

2018

Version Author Date
39ea046 pat-s 2019-05-22

Histograms

2017

Version Author Date
39ea046 pat-s 2019-05-22

2018

Version Author Date
39ea046 pat-s 2019-05-22

Relative defoliation

Maps

2017

Version Author Date
39ea046 pat-s 2019-05-22

2018

Version Author Date
39ea046 pat-s 2019-05-22

Histograms

2017

Version Author Date
39ea046 pat-s 2019-05-22

2018

Version Author Date
39ea046 pat-s 2019-05-22 

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/openblas-0.3.5-zncvk4jccaqyfl4z3vszaboeps6hyzta/lib/libopenblas_zen-r0.3.5.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] gridExtra_2.3        tidyselect_0.2.5     workflowr_1.3.0     
 [4] here_0.1             ggpubr_0.1.6         ggspatial_1.0.3     
 [7] gdalUtils_2.0.1.7    getSpatialData_0.0.4 knitr_1.21          
[10] rgenoud_5.8-3.0      parallelMap_1.3      mlrMBO_1.1.2        
[13] smoof_1.5.1          checkmate_1.9.1      BBmisc_1.11         
[16] mapview_2.3.0        stringr_1.4.0        fs_1.2.6            
[19] curl_3.3             mlrCPO_0.3.4-2       mlr_2.13.9000       
[22] ParamHelpers_1.12    data.table_1.12.0    magrittr_1.5        
[25] future.apply_1.1.0   future.callr_0.4.0   furrr_0.1.0.9002    
[28] future_1.11.1.1      R.utils_2.8.0        R.oo_1.22.0         
[31] R.methodsS3_1.7.1    glue_1.3.0           purrr_0.3.0         
[34] sf_0.7-3             dplyr_0.8.0.1        hsdar_0.5.2         
[37] caret_6.0-81         ggplot2_3.1.0        lattice_0.20-38     
[40] signal_0.7-6         rootSolve_1.7        rgdal_1.4-3         
[43] raster_2.8-19        sp_1.3-1             drake_7.3.0         

loaded via a namespace (and not attached):
  [1] backports_1.1.3    fastmatch_1.1-0    mapedit_0.4.3     
  [4] plyr_1.8.4         igraph_1.2.4       lazyeval_0.2.1    
  [7] splines_3.5.2      storr_1.2.1        crosstalk_1.0.0   
 [10] listenv_0.7.0      leaflet_2.0.2      usethis_1.4.0     
 [13] digest_0.6.18      foreach_1.4.4      htmltools_0.3.6   
 [16] memoise_1.1.0      base64url_1.4      remotes_2.0.2     
 [19] recipes_0.1.4      globals_0.12.4     gower_0.1.2       
 [22] prettyunits_1.0.2  colorspace_1.4-0   xfun_0.5          
 [25] DiceKriging_1.5.6  callr_3.1.1        crayon_1.3.4      
 [28] jsonlite_1.6       survival_2.43-3    iterators_1.0.10  
 [31] gtable_0.2.0       ipred_0.9-8        webshot_0.5.1     
 [34] pkgbuild_1.0.2     abind_1.4-5        scales_1.0.0      
 [37] GGally_1.4.0       DBI_1.0.0          Rcpp_1.0.0        
 [40] viridisLite_0.3.0  xtable_1.8-3       units_0.6-2       
 [43] stats4_3.5.2       lava_1.6.5         prodlim_2018.04.18
 [46] htmlwidgets_1.3    httr_1.4.0         RColorBrewer_1.1-2
 [49] reshape_0.8.8      pkgconfig_2.0.2    nnet_7.3-12       
 [52] RJSONIO_1.3-1.1    labeling_0.3       rlang_0.3.4       
 [55] reshape2_1.4.3     later_0.8.0        munsell_0.5.0     
 [58] tools_3.5.2        cli_1.1.0          generics_0.0.2    
 [61] devtools_2.0.1     evaluate_0.13      yaml_2.2.0        
 [64] ModelMetrics_1.2.2 processx_3.2.1     satellite_1.0.1   
 [67] nlme_3.1-137       whisker_0.3-2      mime_0.6          
 [70] xml2_1.2.0         compiler_3.5.2     prettymapr_0.2.2  
 [73] plotly_4.8.0       png_0.1-7          e1071_1.7-0.1     
 [76] testthat_2.0.1     RPostgreSQL_0.6-2  tibble_2.0.1      
 [79] lhs_1.0.1          stringi_1.3.1      ps_1.3.0          
 [82] desc_1.2.0         plot3D_1.1.1       Matrix_1.2-15     
 [85] classInt_0.3-1     rosm_0.2.4         pillar_1.3.1      
 [88] httpuv_1.4.5.1     R6_2.4.0           promises_1.0.1    
 [91] sessioninfo_1.1.1  codetools_0.2-16   MASS_7.3-51.1     
 [94] assertthat_0.2.0   pkgload_1.0.2      rprojroot_1.3-2   
 [97] withr_2.1.2        parallel_3.5.2     rpart_4.1-13      
[100] timeDate_3043.102  tidyr_0.8.2        class_7.3-15      
[103] rmarkdown_1.11     misc3d_0.8-4       mco_1.0-15.1      
[106] git2r_0.24.0       getPass_0.2-2      shiny_1.2.0       
[109] lubridate_1.7.4    base64enc_0.1-3