From 977427d27820fc05dc6c9f2f51598ea18bc2c69b Mon Sep 17 00:00:00 2001
From: Jeremy Coyle <jeremyrcoyle@gmail.com>
Date: Mon, 30 Oct 2023 13:31:32 -0700
Subject: [PATCH] * fix Matrix tests and other issues * bump version * update
 news

---
 .NEWS.md.swp              | Bin 0 -> 1024 bytes
 DESCRIPTION               |   4 ++--
 NEWS.md                   |   3 +++
 R/formula_hal9001.R       |   2 +-
 R/predict.R               |  22 ++++++++--------------
 man/formula_helpers.Rd    |  20 --------------------
 man/generate_all_rules.Rd |  14 ++++++++++++++
 7 files changed, 28 insertions(+), 37 deletions(-)
 create mode 100644 .NEWS.md.swp
 delete mode 100644 man/formula_helpers.Rd
 create mode 100644 man/generate_all_rules.Rd

diff --git a/.NEWS.md.swp b/.NEWS.md.swp
new file mode 100644
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GIT binary patch
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diff --git a/DESCRIPTION b/DESCRIPTION
index 21c99e4b..a57654b8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hal9001
 Title: The Scalable Highly Adaptive Lasso
-Version: 0.4.5
+Version: 0.4.6
 Authors@R: c(
   person("Jeremy", "Coyle", email = "jeremyrcoyle@gmail.com",
          role = c("aut", "cre"),
@@ -68,5 +68,5 @@ LinkingTo:
   Rcpp,
   RcppEigen
 VignetteBuilder: knitr
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
diff --git a/NEWS.md b/NEWS.md
index 777be02b..c04ae0c2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,6 @@
+# hal9001 0.4.6
+* Fixed predict method to address changes required by Matrix 1.6.2
+
 # hal9001 0.4.5
 * Added multivariate outcome prediction
 
diff --git a/R/formula_hal9001.R b/R/formula_hal9001.R
index f30f06e1..9d8e3d68 100644
--- a/R/formula_hal9001.R
+++ b/R/formula_hal9001.R
@@ -216,7 +216,7 @@ h <- function(..., k = NULL, s = NULL, pf = 1,
   })
 
 
-  basis_list_item <- hal9001:::make_basis_list(
+  basis_list_item <- make_basis_list(
     X[, col_index, drop = FALSE],
     col_index, rep(s, ncol(X))
   )
diff --git a/R/predict.R b/R/predict.R
index 3ef9f3ad..5767b4a9 100644
--- a/R/predict.R
+++ b/R/predict.R
@@ -80,16 +80,13 @@ predict.hal9001 <- function(object,
   # generate predictions
   if (!family %in% c("cox", "mgaussian")) {
     if (ncol(object$coefs) > 1) {
-      preds <- apply(object$coefs, 2, function(hal_coefs) {
-        as.vector(Matrix::tcrossprod(
-          x = pred_x_basis,
-          y = hal_coefs[-1]
-        ) + hal_coefs[1])
-      })
+      preds <- pred_x_basis%*%object$coefs[-1,]+
+        matrix(object$coefs[1,], nrow=nrow(pred_x_basis), 
+               ncol=ncol(object$coefs), byrow = TRUE)
     } else {
       preds <- as.vector(Matrix::tcrossprod(
         x = pred_x_basis,
-        y = object$coefs[-1]
+        y = matrix(object$coefs[-1],nrow=1)
       ) + object$coefs[1])
     }
   } else {
@@ -99,16 +96,13 @@ predict.hal9001 <- function(object,
       # Note: there is no intercept in the Cox model (built into the baseline
       #       hazard and would cancel in the partial likelihood).
       if (ncol(object$coefs) > 1) {
-        preds <- apply(object$coefs, 2, function(hal_coefs) {
-          as.vector(Matrix::tcrossprod(
-            x = pred_x_basis,
-            y = hal_coefs
-          ))
-        })
+        preds <- pred_x_basis%*%object$coefs[-1,]+
+          matrix(object$coefs[1,], nrow=nrow(pred_x_basis), 
+                 ncol=ncol(object$coefs), byrow = TRUE)
       } else {
         preds <- as.vector(Matrix::tcrossprod(
           x = pred_x_basis,
-          y = as.vector(object$coefs)
+          y = as.matrix(object$coefs,nrow = 1)
         ))
       }
     } else if (family == "mgaussian") {
diff --git a/man/formula_helpers.Rd b/man/formula_helpers.Rd
deleted file mode 100644
index 893a2de1..00000000
--- a/man/formula_helpers.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/formula_hal9001.R
-\name{formula_helpers}
-\alias{formula_helpers}
-\alias{fill_dots_helper}
-\alias{fill_dots}
-\title{Formula Helpers}
-\usage{
-fill_dots_helper(var_names, .)
-
-fill_dots(var_names, .)
-}
-\arguments{
-\item{var_names}{A \code{character} vector of variable names.}
-
-\item{.}{Specification of variables for use in the formula.}
-}
-\description{
-Formula Helpers
-}
diff --git a/man/generate_all_rules.Rd b/man/generate_all_rules.Rd
new file mode 100644
index 00000000..6fc2967a
--- /dev/null
+++ b/man/generate_all_rules.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/summary.R
+\name{generate_all_rules}
+\alias{generate_all_rules}
+\title{Generates rules based on knot points of the fitted HAL basis functions with
+non-zero coefficients.}
+\usage{
+generate_all_rules(basis_list, coefs, X_colnames)
+}
+\description{
+Generates rules based on knot points of the fitted HAL basis functions with
+non-zero coefficients.
+}
+\keyword{internal}