Adds support for flexsurvspline engine for survival_reg model spec

NAMESPACE

@@ -283,6 +283,7 @@ export(svm_rbf)
 export(tidy)
 export(translate)
 export(translate.default)
+export(tunable.survival_reg)
 export(tune)
 export(update_dot_check)
 export(update_engine_parameters)

NEWS.md

@@ -1,5 +1,7 @@
 # parsnip (development version)
 
+* Adds support for `flexsurvspline` engine for the `survival_reg()` model specification from the `censored` package (#831)
+
 * The matrix interface for fitting `fit_xy()` now works for the `"censored regression"` mode (#829).
 
 # parsnip 1.0.2

R/survival_reg_flexsurvspline.R

@@ -0,0 +1,11 @@
+#' Flexible parametric survival regression
+#'
+#' [flexsurv::flexsurvspline()] fits a flexible parametric survival model.
+#'
+#' @includeRmd man/rmd/survival_reg_flexsurvspline.md details
+#'
+#' @name details_survival_reg_flexsurvspline
+#' @keywords internal
+NULL
+
+# See inst/README-DOCS.md for a description of how these files are processed

R/tunable.R

@@ -190,6 +190,17 @@ brulee_multinomial_engine_args <-
   brulee_mlp_engine_args %>%
   dplyr::filter(name %in% c("momentum", "batch_size", "stop_iter", "class_weights"))
 
+flexsurvspline_engine_args <-
+  tibble::tibble(
+    name = c("k"),
+    call_info = list(
+      list(pkg = "dials", fun = "num_knots")
+    ),
+    source = "model_spec",
+    component = "survival_reg",
+    component_id = "engine"
+  )
+
 # ------------------------------------------------------------------------------
 
 # Lazily registered in .onLoad()
@@ -310,5 +321,14 @@ tunable_mlp <- function(x, ...) {
   res
 }
 
+#' @export
+tunable.survival_reg <- function(x, ...) {
+  res <- NextMethod()
+  if (x$engine == "flexsurvspline") {
+    res <- add_engine_parameters(res, flexsurvspline_engine_args)
+  }
+  res
+}
+
 # nocov end
 

inst/models.tsv

@@ -123,6 +123,7 @@
 "surv_reg"	"regression"	"flexsurv"	NA
 "surv_reg"	"regression"	"survival"	NA
 "survival_reg"	"censored regression"	"flexsurv"	"censored"
+"survival_reg"	"censored regression"	"flexsurvspline"	"censored"
 "survival_reg"	"censored regression"	"survival"	"censored"
 "svm_linear"	"classification"	"kernlab"	NA
 "svm_linear"	"classification"	"LiblineaR"	NA

man/rmd/survival_reg_flexsurvspline.Rmd

@@ -0,0 +1,42 @@
+```{r, child = "aaa.Rmd", include = FALSE}
+```
+
+`r descr_models("survival_reg", "flexsurvspline")`
+
+## Tuning Parameters
+
+This model has one engine-specific tuning parameter:
+
+ * `k`: Number of knots in the spline. The default is `k = 0`.
+
+## Translation from parsnip to the original package
+
+`r uses_extension("survival_reg", "flexsurvspline", "censored regression")`
+
+```{r flexsurvspline-creg}
+library(censored)
+
+survival_reg() %>% 
+  set_engine("flexsurvspline", k = 1L) %>% 
+  set_mode("censored regression") %>% 
+  translate()
+```
+
+## Other details
+
+The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
+
+For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvspline()] for alternative specifications.
+
+```{r child = "template-survival-mean.Rmd"}
+```
+
+## Saving fitted model objects
+
+```{r child = "template-butcher.Rmd"}
+```
+
+
+## References
+
+- Jackson, C. 2016. `flexsurv`: A Platform for Parametric Survival  Modeling in R. _Journal of Statistical Software_, 70(8), 1 - 33.

man/rmd/survival_reg_flexsurvspline.md

@@ -0,0 +1,57 @@
+
+
+
+For this engine, there is a single mode: censored regression
+
+## Tuning Parameters
+
+This model has one engine-specific tuning parameter:
+
+ * `k`: Number of knots in the spline. The default is `k = 0`.
+
+## Translation from parsnip to the original package
+
+The **censored** extension package is required to fit this model.
+
+
+```r
+library(censored)
+
+survival_reg() %>% 
+  set_engine("flexsurvspline", k = 1L) %>% 
+  set_mode("censored regression") %>% 
+  translate()
+```
+
+```
+## Parametric Survival Regression Model Specification (censored regression)
+## 
+## Engine-Specific Arguments:
+##   k = 1
+## 
+## Computational engine: flexsurvspline 
+## 
+## Model fit template:
+## flexsurv::flexsurvspline(formula = missing_arg(), data = missing_arg(), 
+##     weights = missing_arg(), k = 1L)
+```
+
+## Other details
+
+The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
+
+For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvspline()] for alternative specifications.
+
+
+
+Predictions of type `"time"` are predictions of the mean survival time.
+
+## Saving fitted model objects
+
+
+This model object contains data that are not required to make predictions. When saving the model for the purpose of prediction, the size of the saved object might be substantially reduced by using functions from the [butcher](https://butcher.tidymodels.org) package.
+
+
+## References
+
+- Jackson, C. 2016. `flexsurv`: A Platform for Parametric Survival  Modeling in R. _Journal of Statistical Software_, 70(8), 1 - 33.