Fix glmnet2

Author: elgabbas

DESCRIPTION

@@ -3,7 +3,7 @@ Package: IASDT.R
 Title: Modelling the Distribution of Invasive Alien Plant Species in
     Europe
 Version: 0.1.12
-Date: 2025-12-16
+Date: 2025-12-19
 Authors@R: 
     person("Ahmed", "El-Gabbas", , "ahmed.el-gabbas@ufz.de", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2225-088X"))

R/utils_helper_functions.R

@@ -16,8 +16,8 @@
   if (n_cores > max_cores) {
     warning(
       stringr::str_glue(
-        "`n_cores` exceeds available cores: {n_cores}. Using all available",
-        " cores: {max_cores}"),
+        "`n_cores` ({n_cores}) exceeds available cores. Using all available",
+        " cores ({max_cores})"),
       call. = FALSE)
     n_cores <- max_cores
   }

README.md

@@ -81,4 +81,4 @@ If you use the `IASDT.R` package, please cite it as:
 > <a href="https://biodt.eu" target="_blank">https://biodt.eu</a>.
 
 <span style="     color: grey !important;">Last update:
-2025-12-16</span>
+2025-12-19</span>

inst/glmnet2.R

@@ -22,13 +22,12 @@ methodInfo <- list(
     y <- sdm:::.getData.sdmY(formula, data)
 
     if (family == "binomial") {
-      m <- glmnet::cv.glmnet(
+      glmnet::cv.glmnet(
         x, y, family = "binomial", type.measure = "auc", ...)
     } else {
-      m <- glmnet::cv.glmnet(x, y, family = family, ...)
+      glmnet::cv.glmnet(x, y, family = family, ...)
     }
 
-    glmnet::glmnet(x = x, y = y, family = family, lambda = m$lambda.1se, ...)
   },
   settingRules = function(x = "sdmVariables", f = "fitSettings") {
     if (x@distribution %in% c("poisson", "multinomial")) {
@@ -45,8 +44,8 @@ methodInfo <- list(
     newx <- sdm:::.getData.sdmMatrix(
       formula, newx, normalize = TRUE, frame = v@varInfo$numeric)
     # Predict at the fitted lambda for safety (minimal change).
-    p <- predict(object, newx, type = type, s = object$lambda, ...)
+    p <- predict(object, newx, type = type, s = "lambda.1se", ...)
     if (is.matrix(p)) p <- p[, 1, drop = TRUE]
-    p
+    as.vector(p)
   }
 )