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updated random forest metric, model and simulate_wrappers for survival
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| @@ -149,16 +149,34 @@ predict_custom <- function(x, y = NULL, fit, model, type = "response") { | |||
| } | |||
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| # Survival: ranger returns a matrix of survival probabilities by timepoint | ||
| if (is.matrix(preds) && inherits(fit, "ranger") && fit$treetype == "Surv") { | ||
| # If user asks for survival probabilities, return the matrix | ||
| if (is.matrix(pr$survival) && inherits(fit, "ranger") && fit$treetype == "Survival") { |
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| if (is.matrix(pr$survival) && inherits(fit, "ranger") && fit$treetype == "Survival") { | |
| if ( | |
| is.matrix(pr$survival) && | |
| inherits(fit, "ranger") && | |
| fit$treetype == "Survival" | |
| ) { |
| # If user asks for survival probabilities, return the survival matrix | ||
| if (type == "survival") { | ||
| return(preds) | ||
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| times <- pr$unique.death.times | ||
| surv_matrix <- pr$survival | ||
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| if (type == "lp") { | ||
| lp <- -rowMeans(preds, na.rm = TRUE) | ||
| return(as.numeric(lp)) | ||
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| ) | ||
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| }, | ||
| xgboost = function(d, nrounds = 100, params = list(objective = "binary:logistic", eval_metric = "logloss")) { |
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| xgboost = function(d, nrounds = 100, params = list(objective = "binary:logistic", eval_metric = "logloss")) { | |
| xgboost = function( | |
| d, | |
| nrounds = 100, | |
| params = list(objective = "binary:logistic", eval_metric = "logloss") | |
| ) { |
| @@ -141,7 +157,7 @@ default_models <- list( | |||
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| stopifnot(all(c("time", "event") %in% colnames(d))) | ||
| formula <- stats::as.formula("survival::Surv(time, event) ~ .") | ||
| ranger::ranger(formula, data = d, num.threads = nthreads) | ||
| ranger::ranger(formula, data = d, num.trees = 300, num.threads = nthreads) |
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| ranger::ranger(formula, data = d, num.trees = 300, num.threads = nthreads) | |
| ranger::ranger(formula, data = d, num.trees = 300, num.threads = nthreads) |
| ranger::ranger(formula, data = d, num.threads = nthreads) | ||
| ranger::ranger(formula, data = d, num.trees = 300, num.threads = nthreads) | ||
| }, | ||
| xgboost = function(d, nrounds = 100, params = list(objective = "survival:cox", eval_metric = "cox-nloglik")) { |
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| xgboost = function(d, nrounds = 100, params = list(objective = "survival:cox", eval_metric = "cox-nloglik")) { | |
| xgboost = function( | |
| d, | |
| nrounds = 100, | |
| params = list(objective = "survival:cox", eval_metric = "cox-nloglik") | |
| ) { |
| @@ -364,7 +364,7 @@ simulate_survival <- function( | |||
| ) | |||
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