From 7c350e66f717a5de15e403d53e04ee926813c543 Mon Sep 17 00:00:00 2001
From: "Behrus Puladi, MD DMD" <44176896+bpuladi@users.noreply.github.com>
Date: Fri, 10 May 2024 19:16:27 +0200
Subject: [PATCH 1/3] Update avNNet.R - Correct the linout parameter

Correct the linout parameter for avNNet. This is required for regression. If not set, regression performance metrics will be wrong.
---
 models/files/avNNet.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/models/files/avNNet.R b/models/files/avNNet.R
index 213b19a83..08ba3dc1d 100644
--- a/models/files/avNNet.R
+++ b/models/files/avNNet.R
@@ -19,7 +19,8 @@ modelInfo <- list(label = "Model Averaged Neural Network",
                   },
                   fit = function(x, y, wts, param, lev, last, classProbs, ...) {
                     dat <- if(is.data.frame(x)) x else as.data.frame(x, stringsAsFactors = TRUE)
-                    dat$.outcome <- y
+                    dat$.outcome <- y                    
+                    lt <- ifelse(is.factor(y),FALSE,TRUE)
                     if(!is.null(wts)) {
                       out <- caret::avNNet(.outcome ~ .,
                                     data = dat,
@@ -27,12 +28,14 @@ modelInfo <- list(label = "Model Averaged Neural Network",
                                     size = param$size,
                                     decay = param$decay,
                                     bag = param$bag,
+                                    linout = lt,
                                     ...)
                     } else out <- caret::avNNet(.outcome ~ .,
                                          data = dat,
                                          size = param$size,
                                          decay = param$decay,
                                          bag = param$bag,
+                                         linout = lt,                                                
                                          ...)
                     out
                   },

From 0b8cf1b5a688716b2e9a883561da6039da1496ea Mon Sep 17 00:00:00 2001
From: "Behrus Puladi, MD DMD" <44176896+bpuladi@users.noreply.github.com>
Date: Fri, 10 May 2024 19:17:48 +0200
Subject: [PATCH 2/3] Update pcaNNet.R - Correct the linout parameter

Correct the linout parameter for pcaNNet. This is required for regression. If not set, regression performance metrics will be wrong.
---
 models/files/pcaNNet.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/models/files/pcaNNet.R b/models/files/pcaNNet.R
index 78ea3a6f3..183e1f96f 100644
--- a/models/files/pcaNNet.R
+++ b/models/files/pcaNNet.R
@@ -18,6 +18,7 @@ modelInfo <- list(label = "Neural Networks with Feature Extraction",
                   fit = function(x, y, wts, param, lev, last, classProbs, ...) {
                     dat <- if(is.data.frame(x)) x else as.data.frame(x, stringsAsFactors = TRUE)
                     dat$.outcome <- y
+                    lt <- ifelse(is.factor(y),FALSE,TRUE)                    
                     if(!is.null(wts))
                     {
                       out <- caret::pcaNNet(.outcome ~ .,
@@ -25,11 +26,13 @@ modelInfo <- list(label = "Neural Networks with Feature Extraction",
                                           weights = wts,
                                           size = param$size,
                                           decay = param$decay,
+                                          linout = lt,
                                           ...)
                     } else out <- caret::pcaNNet(.outcome ~ .,
                                                 data = dat,
                                                 size = param$size,
                                                 decay = param$decay,
+                                                linout = lt,
                                                 ...)
                     out
                   },

From 2de0a80b1e4346bbddf1fa1de353cacafcb76da9 Mon Sep 17 00:00:00 2001
From: "Behrus Puladi, MD DMD" <44176896+bpuladi@users.noreply.github.com>
Date: Fri, 10 May 2024 19:21:04 +0200
Subject: [PATCH 3/3] Update nnet.R - Correct the linout parameter

Correct the linout parameter for nnet. This is required for regression. If not set, regression performance metrics will be wrong.
---
 models/files/nnet.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/models/files/nnet.R b/models/files/nnet.R
index 978a7dece..36a53e4fa 100644
--- a/models/files/nnet.R
+++ b/models/files/nnet.R
@@ -18,17 +18,20 @@ modelInfo <- list(label = "Neural Network",
                   fit = function(x, y, wts, param, lev, last, classProbs, ...) {
                     dat <- if(is.data.frame(x)) x else as.data.frame(x, stringsAsFactors = TRUE)
                     dat$.outcome <- y
+                    lt <- ifelse(is.factor(y),FALSE,TRUE)
                     if(!is.null(wts)) {
                       out <- nnet::nnet(.outcome ~ .,
                                         data = dat,
                                         weights = wts,
                                         size = param$size,
                                         decay = param$decay,
+                                        linout = lt,
                                         ...)
                     } else out <- nnet::nnet(.outcome ~ .,
                                              data = dat,
                                              size = param$size,
                                              decay = param$decay,
+                                             linout = lt,
                                              ...)
                     out
                   },