export assess_2d() and remove glmnet suggest

lgessl · Feb 19, 2024 · b3a4ca8 · b3a4ca8
1 parent ae66101
commit b3a4ca8
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Showing 5 changed files with 5 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,8 +17,7 @@ Suggests:
     testthat (>= 3.0.0),
     withr (>= 2.5.2),
     tibble (>= 3.0.0),
-    zeroSum (>= 2.0.6),
-    glmnet(>= 4.1.8)
+    zeroSum (>= 2.0.6)
 Imports:
     dplyr (>= 1.1.3),
     readr (>= 2.1.4),

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(DataSpec)
 export(ModelSpec)
 export(assess_0d)
 export(assess_0d_center)
+export(assess_2d)
 export(assess_2d_center)
 export(discretize_tbl_cols)
 export(ensure_patients_match)

diff --git a/R/asssess_2d.R b/R/asssess_2d.R
@@ -25,6 +25,7 @@
 #' @details The AssSpec2d class is tailored for this function, so see its constructor 
 #' [`AssSpec2d()`] for details.
 #' @param msg_prefix string. Prefix for messages. Default is `""`.
+#' @export
 assess_2d <- function(
     expr_mat,
     pheno_tbl,

diff --git a/R/prepare_and_predict.R b/R/prepare_and_predict.R
@@ -14,7 +14,7 @@
 #' @param lambda string or numeric. The lambda regularization parameter of the model
 #' to predict with. Technically, we will pass it to the `s` parameter of the `predict()`
 #' method of the object returned by the `fitter` attribute of the `ModelSpec` object.
-#' See, e.g., [glmnet::predict.cv.glmnet()] or [zeroSum::predict.zeroSum()].
+#' See, e.g., [zeroSum::predict.zeroSum()].
 #' @param pivot_time_cutoff numeric. Time-to-event threshold that divides samples into a
 #' high/low-risk (time to event below/above `pivot_time_cutoff`) group. See return value 
 #' below.

diff --git a/man/prepare_and_predict.Rd b/man/prepare_and_predict.Rd