Install packages
#install.packages('sp')
#install.packages('raster')
#install.packages('rpart')
#install.packages("knitr")
#install.packages("leaflet")
#install.packages("DT")Load packages
library(sp)
library(raster)
library(rpart)
library(knitr)
library(leaflet)
library(DT)Load data
load("C:/Users/Linde/Desktop/Scriptie/Schrijven begin/Textuele conceptversie/Final Conceptversion MSc Linde Berbers/Supplementary Information/Supplementary Data 2. RStudio Data/Script Data/EurekaFirst_Brick_df.RData")Rpart.Choose <- rpart(HigherThan1km ~ Land + GeoMean + Lithology + Temp + DistTrans + DistFault + Faults + DistPlateBound + Precip + DistTrench + DistVolc + Volc + Trans + Trench + PlateBound + SeaSedThick + SeaFloorAge + Ophiolites + Ridge, data=EurekaFirst_Brick_df, method="class", cp=0.0001)
printcp(Rpart.Choose)##
## Classification tree:
## rpart(formula = HigherThan1km ~ Land + GeoMean + Lithology +
## Temp + DistTrans + DistFault + Faults + DistPlateBound +
## Precip + DistTrench + DistVolc + Volc + Trans + Trench +
## PlateBound + SeaSedThick + SeaFloorAge + Ophiolites + Ridge,
## data = EurekaFirst_Brick_df, method = "class", cp = 1e-04)
##
## Variables actually used in tree construction:
## [1] DistFault DistPlateBound DistTrans DistTrench DistVolc
## [6] GeoMean Lithology Precip Temp
##
## Root node error: 4363/180000 = 0.024239
##
## n= 180000
##
## CP nsplit rel error xerror xstd
## 1 0.73458629 0 1.000000 1.00000 0.0149547
## 2 0.03082741 1 0.265414 0.26679 0.0077944
## 3 0.01822141 3 0.203759 0.20766 0.0068815
## 4 0.00389640 5 0.167316 0.17671 0.0063505
## 5 0.00297960 6 0.163420 0.17396 0.0063011
## 6 0.00229200 8 0.157460 0.17121 0.0062513
## 7 0.00194820 10 0.152876 0.17121 0.0062513
## 8 0.00183360 12 0.148980 0.16686 0.0061716
## 9 0.00143250 14 0.145313 0.16319 0.0061037
## 10 0.00137520 21 0.133624 0.16250 0.0060909
## 11 0.00126060 24 0.129498 0.16159 0.0060738
## 12 0.00114600 26 0.126977 0.15815 0.0060090
## 13 0.00091680 30 0.121705 0.15884 0.0060220
## 14 0.00080220 38 0.114371 0.15609 0.0059699
## 15 0.00076400 40 0.112766 0.15242 0.0058996
## 16 0.00075309 43 0.110474 0.14898 0.0058329
## 17 0.00068760 52 0.103598 0.14898 0.0058329
## 18 0.00061120 54 0.102223 0.14852 0.0058240
## 19 0.00057300 57 0.100390 0.14852 0.0058240
## 20 0.00045840 62 0.097410 0.14852 0.0058240
## 21 0.00022920 66 0.095576 0.14852 0.0058240
## 22 0.00015280 76 0.093055 0.15150 0.0058819
## 23 0.00010000 79 0.092597 0.14990 0.0058508Rpart.Choose.cp <- rpart(HigherThan1km ~ Land + GeoMean + Lithology + Temp + DistTrans + DistFault + Faults + DistPlateBound + Precip + DistTrench + DistVolc + Volc + Trans + Trench + PlateBound + SeaSedThick + SeaFloorAge + Ophiolites + Ridge, data=EurekaFirst_Brick_df, method="class", cp=0.00091680)
printcp(Rpart.Choose.cp)##
## Classification tree:
## rpart(formula = HigherThan1km ~ Land + GeoMean + Lithology +
## Temp + DistTrans + DistFault + Faults + DistPlateBound +
## Precip + DistTrench + DistVolc + Volc + Trans + Trench +
## PlateBound + SeaSedThick + SeaFloorAge + Ophiolites + Ridge,
## data = EurekaFirst_Brick_df, method = "class", cp = 0.0009168)
##
## Variables actually used in tree construction:
## [1] DistFault DistPlateBound DistTrans DistTrench DistVolc
## [6] GeoMean Lithology Precip Temp
##
## Root node error: 4363/180000 = 0.024239
##
## n= 180000
##
## CP nsplit rel error xerror xstd
## 1 0.7345863 0 1.00000 1.00000 0.0149547
## 2 0.0308274 1 0.26541 0.26679 0.0077944
## 3 0.0182214 3 0.20376 0.20766 0.0068815
## 4 0.0038964 5 0.16732 0.17511 0.0063218
## 5 0.0029796 6 0.16342 0.17121 0.0062513
## 6 0.0022920 8 0.15746 0.16961 0.0062221
## 7 0.0019482 10 0.15288 0.16594 0.0061547
## 8 0.0018336 12 0.14898 0.16457 0.0061293
## 9 0.0014325 14 0.14531 0.16136 0.0060695
## 10 0.0013752 21 0.13362 0.15952 0.0060350
## 11 0.0012606 24 0.12950 0.15769 0.0060004
## 12 0.0011460 26 0.12698 0.15654 0.0059786
## 13 0.0009168 30 0.12171 0.15333 0.0059172
## 14 0.0009168 38 0.11437 0.15219 0.0058952