rand_forest() models

[EmilHvitfeldt]

• party time
• party survival
• randomForestSRC time
• party parameters
• randomForestSRC parameters

library(party)
#> Loading required package: grid
#> Loading required package: mvtnorm
#> Loading required package: modeltools
#> Loading required package: stats4
#> Loading required package: strucchange
#> Loading required package: zoo
#> 
#> Attaching package: 'zoo'
#> The following objects are masked from 'package:base':
#> 
#>     as.Date, as.Date.numeric
#> Loading required package: sandwich
library(survival)
library(pec)
#> Loading required package: prodlim

set.seed(342)
cforest_mod <-
  cforest(Surv(time, status) ~ age + ph.ecog, data = lung,
          controls = cforest_unbiased(ntree = 100, mtry = 1))

# time
predict(cforest_mod, newdata = lung)
#>   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20 
#> 306 353 428 306 558 306 288 222 286 177 306 288 371 305 306 283 345 222 180 306 
#>  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40 
#> 283 371 305 433 350 345 558 239 286 208 371 199 199 177 177 177 285 283 208 345 
#>  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 
#> 345 199 433 177 371 201 350 345 350 305 301 477 353 433 345 455 350 177 348 345 
#>  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80 
#> 208 305 285 283 371 288 285 433 353 283 477 305 208 353 286 310 371 363 303 320 
#>  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 100 
#> 433 363 353 353 353 310 310 455 353 201 477 345 283 306 353 201 371 310 345 353 
#> 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 
#> 433 371 363 345 177 283 363 283 363 208 353 353 283 348 363 201 199 288 285 283 
#> 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 
#> 348 177 371 201 353 283 305 345 201 371 345 286 371 363 350 208 348 180 363 428 
#> 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 
#> 199 306 201 283 306 286 353 363 303 433 345 558 455 286 180 288 371 177 345 363 
#> 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 
#> 455 353 288 345 345 394 301 371 301 350 301 433 363 433 286 345 180 363 286 350 
#> 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 
#> 558 433 350 283 371 428 201 433 345 371 301 180 305 345 310 353 345 345 371 301 
#> 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 
#> 345 285 477 371 477 177 394 199 371 345 558 283 371 285 283 283 353 201 239 394 
#> 221 222 223 224 225 226 227 228 
#> 283 310 283 283 433 208 283 348

# survival
set.seed(342)
pec_cforest_mod <-
  pecCforest(Surv(time, status) ~ age + ph.ecog, data = lung,
             controls = cforest_unbiased(ntree = 100, mtry = 1))

str(predictSurvProb(pec_cforest_mod, newdata = lung, times = c(100, 200)))
#>  num [1:228, 1:2] 0.869 0.839 0.936 0.895 0.93 ...

^{Created on 2020-08-06 by the reprex package (v0.3.0)}

randomForestSRC

library(randomForestSRC)
#> 
#>  randomForestSRC 2.9.3 
#>  
#>  Type rfsrc.news() to see new features, changes, and bug fixes. 
#> 
library(survival)
library(pec)
#> Loading required package: prodlim

rfsrce_mod <- rfsrc(Surv(time, status) ~ age + ph.ecog, data = lung, ntree = 1000)
# The predict function generates an object with classes "rfsrc", "predict", and "surv". It is unclear what is being predicted:

# time?
str(predict(rfsrce_mod, lung)$predicted)
#>  num [1:227, 1:2] 163 145 344 170 328 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ : NULL
#>   ..$ : chr [1:2] "event.1" "event.2"

^{Created on 2020-08-06 by the reprex package (v0.3.0)}

[hfrick]

Party parameters were added to dials in tidymodels/dials#162

[hfrick]

closing in favour of #130

[github-actions]

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