Last updated: 2019-06-15

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Knit directory: 2019-feature-selection/

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File Version Author Date Message
Rmd a036319 pat-s 2019-06-15 wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)

Datasets

VI

Overview

rows columns discrete_columns continuous_columns all_missing_columns total_missing_values complete_rows total_observations memory_usage
1759 90 0 90 0 0 1759 158310 1285080

Histograms

PCA

Corr

NRI

Overview

rows columns discrete_columns continuous_columns all_missing_columns total_missing_values complete_rows total_observations memory_usage
1759 7382 0 7382 0 0 1759 12984938 105368104

Histograms

No histograms for NRI -> too many features.

PCA

Corr

HR

Overview

rows columns discrete_columns continuous_columns all_missing_columns total_missing_values complete_rows total_observations memory_usage
1759 123 0 123 0 0 1759 216357 1754904

Histograms

PCA

Corr

Custom plots

Mean defoliation per plot

# A tibble: 4 x 2
  plot     `mean(defoliation)`
  <fct>                  <dbl>
1 Laukiz 1                56.0
2 Laukiz 2                13.5
3 Luiando                 68.4
4 Oiartzun                69.2

Coefficient of variation

# A tibble: 4 x 2
  plot     `(sd(defoliation)/mean(defoliation)) * 100`
  <fct>                                          <dbl>
1 Laukiz 1                                        35.4
2 Laukiz 2                                       125. 
3 Luiando                                         12.1
4 Oiartzun                                        19.9

sd / skewness

# A tibble: 4 x 2
  plot     `((sd(defoliation)/mean(defoliation)) * 100)/e1071::skewness(de~
  <fct>                                                               <dbl>
1 Laukiz 1                                                           -50.6 
2 Laukiz 2                                                            55.0 
3 Luiando                                                             -3.13
4 Oiartzun                                                           -21.3 
# A tibble: 4 x 2
  plot     `sd(defoliation)`
  <fct>                <dbl>
1 Laukiz 1             19.8 
2 Laukiz 2             16.9 
3 Luiando               8.28
4 Oiartzun             13.8 
Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Point density

In Meters.

$`Laukiz 1`
[1] 34.64678

$`Laukiz 2`
[1] 61.58605

$Luiando
[1] 33.14163

$Oiartzun
[1] 34.96409

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] C

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

other attached packages:
 [1] ggsci_2.9            DataExplorer_0.8.0   tidyselect_0.2.5    
 [4] mRMRe_2.0.9          igraph_1.2.4         survival_2.43-3     
 [7] praznik_5.0.0        workflowr_1.4.0      here_0.1            
[10] ggpubr_0.1.6         ggspatial_1.0.3      gdalUtils_2.0.1.7   
[13] getSpatialData_0.0.4 knitr_1.23           rgenoud_5.8-3.0     
[16] parallelMap_1.3      mlrMBO_1.1.2         smoof_1.5.1         
[19] checkmate_1.9.1      BBmisc_1.11          mapview_2.3.0       
[22] stringr_1.4.0        fs_1.2.6             curl_3.3            
[25] mlrCPO_0.3.4-2       mlr_2.14.0.9000      ParamHelpers_1.12   
[28] data.table_1.12.0    magrittr_1.5         future.apply_1.1.0  
[31] future.callr_0.4.0   furrr_0.1.0.9002     future_1.11.1.1     
[34] R.utils_2.8.0        R.oo_1.22.0          R.methodsS3_1.7.1   
[37] glue_1.3.0           purrr_0.3.0          sf_0.7-3            
[40] dplyr_0.8.0.1        hsdar_0.5.2          caret_6.0-81        
[43] ggplot2_3.1.0        lattice_0.20-38      signal_0.7-6        
[46] rootSolve_1.7        rgdal_1.4-3          raster_2.8-19       
[49] sp_1.3-1             drake_7.4.0         

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         lazyeval_0.2.1     splines_3.5.2     
  [7] storr_1.2.1        crosstalk_1.0.0    listenv_0.7.0     
 [10] leaflet_2.0.2      usethis_1.4.0      digest_0.6.18     
 [13] foreach_1.4.4      htmltools_0.3.6    fansi_0.4.0       
 [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] callr_3.1.1        crayon_1.3.4       jsonlite_1.6      
 [28] iterators_1.0.10   gtable_0.2.0       ipred_0.9-8       
 [31] webshot_0.5.1      pkgbuild_1.0.2     scales_1.0.0      
 [34] DBI_1.0.0          Rcpp_1.0.0         viridisLite_0.3.0 
 [37] xtable_1.8-3       units_0.6-2        stats4_3.5.2      
 [40] lava_1.6.5         prodlim_2018.04.18 htmlwidgets_1.3   
 [43] httr_1.4.0         RColorBrewer_1.1-2 pkgconfig_2.0.2   
 [46] nnet_7.3-12        utf8_1.1.4         RJSONIO_1.3-1.1   
 [49] labeling_0.3       rlang_0.3.4        reshape2_1.4.3    
 [52] later_0.8.0        munsell_0.5.0      tools_3.5.2       
 [55] cli_1.1.0          generics_0.0.2     devtools_2.0.1    
 [58] evaluate_0.13      yaml_2.2.0         ModelMetrics_1.2.2
 [61] processx_3.2.1     satellite_1.0.1    nlme_3.1-137      
 [64] whisker_0.3-2      mime_0.6           xml2_1.2.0        
 [67] compiler_3.5.2     plotly_4.8.0       png_0.1-7         
 [70] e1071_1.7-0.1      testthat_2.0.1     RPostgreSQL_0.6-2 
 [73] tibble_2.0.1       lhs_1.0.1          stringi_1.3.1     
 [76] highr_0.7          ps_1.3.0           desc_1.2.0        
 [79] plot3D_1.1.1       Matrix_1.2-15      classInt_0.3-1    
 [82] networkD3_0.4      pillar_1.3.1       httpuv_1.4.5.1    
 [85] R6_2.4.0           promises_1.0.1     gridExtra_2.3     
 [88] sessioninfo_1.1.1  codetools_0.2-16   MASS_7.3-51.1     
 [91] assertthat_0.2.0   pkgload_1.0.2      rprojroot_1.3-2   
 [94] withr_2.1.2        parallel_3.5.2     grid_3.5.2        
 [97] rpart_4.1-13       timeDate_3043.102  tidyr_0.8.2       
[100] class_7.3-15       rmarkdown_1.13     misc3d_0.8-4      
[103] mco_1.0-15.1       git2r_0.24.0       getPass_0.2-2     
[106] shiny_1.2.0        lubridate_1.7.4    base64enc_0.1-3