* fix Matrix tests and other issues

* bump version * update news
tlverse · Oct 30, 2023 · 977427d · 977427d
1 parent 48f41e5
commit 977427d
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Showing 7 changed files with 28 additions and 37 deletions.
diff --git a/.NEWS.md.swp b/.NEWS.md.swp
diff --git 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
@@ -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
@@ -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
@@ -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
diff --git a/man/generate_all_rules.Rd b/man/generate_all_rules.Rd