The survivalmodels package implements neural networks from the Python packages pycox. Importantly, this a lighter but CRAN-compatible version of the ‘survivalmodels’ package proposed by Raphael Sonabend based on the version 0.1.19. The complete and updated version is available at this link.
# load dependencies
library(survival)
train <- simsurvdata(200)
# Fit the survival neural network
fit <- deepsurv(Surv(time, status) ~ ., data = train, frac = 0.3, activation = "relu",
num_nodes = c(4L, 8L, 4L, 2L), dropout = 0.1, early_stopping = TRUE, epochs = 100L,
batch_size = 32L)
# Return survivals for two independent individuals
test <- simsurvdata(1)
predict(fit, newdata = test)
#> 3.33999991416931 3.34299993515015 3.38000011444092 3.38899993896484
#> 0 0.9929 0.9858 0.9786 0.9715
#> 3.43600010871887 3.45600008964539 3.47300004959106 3.48600006103516
#> 0 0.9644 0.9573 0.9502 0.9431
#> 3.49499988555908 3.49900007247925 3.50300002098083 3.50799989700317
#> 0 0.9359 0.9218 0.9146 0.9075
#> 3.52600002288818 3.53500008583069 3.53699994087219 3.54699993133545
#> 0 0.9004 0.8933 0.8862 0.8791
#> 3.58899998664856 4.65999984741211 4.68200016021729 4.79400014877319
#> 0 0.8719 0.8648 0.8577 0.8506
#> 4.84000015258789 4.89699983596802 4.93200016021729 4.93699979782104
#> 0 0.8435 0.8363 0.8292 0.8221
#> 4.94500017166138 4.95900011062622 4.96199989318848 4.98600006103516
#> 0 0.815 0.8079 0.8008 0.7936
#> 4.98899984359741 4.99499988555908 4.99700021743774 5.00400018692017
#> 0 0.7865 0.7794 0.7723 0.7652
#> 5.00799989700317 5.01000022888184 5.02299976348877 5.02600002288818
#> 0 0.7581 0.7439 0.7368 0.7296
#> 5.02799987792969 5.07200002670288 5.18400001525879 5.30700016021729
#> 0 0.7225 0.7154 0.7083 0.7012
#> 5.34200000762939 5.35099983215332 5.35500001907349 5.3600001335144
#> 0 0.6941 0.6869 0.6798 0.6727
#> 5.36100006103516 5.38600015640259 5.39599990844727 5.40999984741211
#> 0 0.6656 0.6585 0.6513 0.6442
#> 5.41300010681152 5.42700004577637 5.42899990081787 5.43400001525879
#> 0 0.6371 0.63 0.6229 0.6158
#> 5.43699979782104 5.44700002670288 5.46700000762939 5.46799993515015
#> 0 0.6086 0.6015 0.5944 0.5733
#> 5.47100019454956 5.47499990463257 5.47700023651123 5.48699998855591
#> 0 0.5662 0.5591 0.5519 0.5378
#> 5.49300003051758 5.49399995803833 5.49499988555908 5.4980001449585
#> 0 0.5307 0.5235 0.5164 0.5093
#> 5.51300001144409 5.53599977493286 5.53800010681152 5.54099988937378
#> 0 0.5022 0.495 0.4809 0.4738
#> 5.54699993133545 5.55000019073486 5.55900001525879 5.56099987030029
#> 0 0.4667 0.4595 0.4524 0.4453
#> 5.56199979782104 5.56400012969971 5.56699991226196 5.57800006866455
#> 0 0.4382 0.431 0.4239 0.4168
#> 5.58500003814697 5.58799982070923 5.59600019454956 5.59700012207031
#> 0 0.4097 0.4025 0.3954 0.3883
#> 6.66099977493286 6.67500019073486 6.69000005722046 6.69099998474121
#> 0 0.3812 0.367 0.3599 0.3528
#> 6.74100017547607 6.77400016784668 6.77600002288818 6.78299999237061
#> 0 0.3457 0.3385 0.3314 0.3243
#> 6.80200004577637 6.80800008773804 6.80999994277954 6.81899976730347
#> 0 0.3172 0.31 0.3029 0.2958
#> 6.86899995803833 6.8769998550415
#> 0 0.2886 0.2886The survivalmodels package implements models from Python using reticulate. In order to use these models, the required Python packages must be installed following with reticulate::py_install. survivalmodels includes a helper function to install the required pycox function (with pytorch if also required). Before running any models in this package, if you have not already installed pycox please run.
Install the latest release from CRAN:
Install the development version from GitHub: