Last updated: 2019-05-24
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Knit directory: 2019-feature-selection/
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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:
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 39.47527Some more details on the optimization path are presented below:
| Version | Author | Date |
|---|---|---|
| 39ea046 | pat-s | 2019-05-22 |
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.
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