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remove print._coxnet() #313

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merged 3 commits into from
Apr 15, 2024
Merged

remove print._coxnet() #313

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881d8c3
remove print._coxnet()
EmilHvitfeldt Apr 10, 2024
244caa8
bring back print._coxnet
EmilHvitfeldt Apr 12, 2024
51ab312
slim down print method a little further
hfrick Apr 15, 2024
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3 changes: 1 addition & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,6 @@ Imports:
hardhat (>= 1.1.0),
lifecycle,
mboost,
prettyunits,
prodlim (>= 2023.03.31),
purrr,
rlang (>= 1.0.0),
Expand All @@ -56,4 +55,4 @@ Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
RoxygenNote: 7.3.1
16 changes: 4 additions & 12 deletions R/proportional_hazards-glmnet.R
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Expand Up @@ -187,19 +187,11 @@ check_dots_coxnet <- function(x, call = caller_env()) {

#' @export
print._coxnet <- function(x, ...) {
cat("parsnip model object\n\n")
cat("Fit time: ", prettyunits::pretty_sec(x$elapsed[["elapsed"]]), "\n")

if (inherits(x$fit, "try-error")) {
cat("Model fit failed with error:\n", x$fit, "\n")
} else {
print(x$fit, ...)
cat("The training data has been saved for prediction.\n")
}
NextMethod(print, x)
cat("The training data has been saved for prediction.\n")
invisible(x)
}


# prediction --------------------------------------------------------------

coxnet_prepare_x <- function(new_data, object) {
Expand Down Expand Up @@ -462,7 +454,7 @@ multi_predict_coxnet_linear_pred <- function(object, new_data, opts, penalty) {
# prediction: time --------------------------------------------------------

#' A wrapper for survival times with coxnet models
#' @param object A parsnip `model_fit` object resulting from
#' @param object A parsnip `model_fit` object resulting from
#' [proportional_hazards() with engine = "glmnet"][parsnip::details_proportional_hazards_glmnet].
#' @param new_data Data for prediction.
#' @param penalty Penalty value(s).
Expand Down Expand Up @@ -584,7 +576,7 @@ get_missings_coxnet <- function(new_x, new_strata) {


#' A wrapper for survival probabilities with coxnet models
#' @param object A parsnip `model_fit` object resulting from
#' @param object A parsnip `model_fit` object resulting from
#' [proportional_hazards() with engine = "glmnet"][parsnip::details_proportional_hazards_glmnet].
#' @param new_data Data for prediction.
#' @param eval_time A vector of integers for prediction times.
Expand Down
1 change: 0 additions & 1 deletion tests/testthat/_snaps/proportional_hazards-glmnet.md
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Expand Up @@ -5,7 +5,6 @@
Output
parsnip model object

Fit time: NA

Call: glmnet::glmnet(x = data_obj$x, y = data_obj$y, family = "cox", weights = weights, alpha = alpha, lambda = lambda)

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