From 9de329dd30acc9d50d44fbe1629af3c555add6e5 Mon Sep 17 00:00:00 2001
From: Jim Thorson <James.T.Thorson@gmail.com>
Date: Fri, 6 Sep 2024 14:09:30 -0700
Subject: [PATCH] add abundance-expanded option

---
 DESCRIPTION             |  2 +-
 R/predict.R             | 11 +++++++++--
 man/integrate_output.Rd |  9 ++++++++-
 src/tinyVAST.cpp        |  4 ++++
 4 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9932334..2558ce9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -60,6 +60,6 @@ Config/testthat/parallel: true
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://vast-lib.github.io/tinyVAST/
 BugReports: https://github.com/vast-lib/tinyVAST/issues
diff --git a/R/predict.R b/R/predict.R
index 9b143d6..7f9b57b 100644
--- a/R/predict.R
+++ b/R/predict.R
@@ -93,8 +93,13 @@ function( object,
 #'   \item{\code{type=3}}{Abundance-weighted variable: weight predictor by 
 #'   proportion of total in a prior row of `newdata`. 
 #'   This option is used to weight a prediction for 
-#'   one category based on predicted density of another category, e.g., 
+#'   one category based on predicted proportional density of another category, e.g.,
 #'   to calculate abundance-weighted condition in a bivariate model.}
+#'   \item{\code{type=4}}{Abundance-expanded variable: weight predictor by
+#'   density in a prior row of `newdata`.
+#'   This option is used to weight a prediction for
+#'   one category based on predicted density of another category, e.g.,
+#'   to calculate abundance-expanded consumption in a bivariate model.}
 #'   \item{\code{type=0}}{Exclude from weighting: give weight of zero for
 #'   a given row of `newdata`. Including a row of `newdata` with 
 #'   \code{type=0} is useful, e.g., when calculating abundance at that 
@@ -169,6 +174,8 @@ function( object,
 #'  
 #' If \eqn{type_g = 3} then \eqn{\phi_g = \frac{\nu_{h_g}}{\nu^*} \mu_g }
 #'  
+#' If \eqn{type_g = 4} then \eqn{\phi_g = \nu_{h_g} \mu_g }
+#'
 #' Finally, the total value from this second pass is calculated as:
 #'
 #' \deqn{ \phi^* = \sum_{g=0}^{G-1} \phi_g }
@@ -221,7 +228,7 @@ function( object,
   }else if(length(type)==1){
     type = rep(type, nrow(type))
   }  
-  checkInteger( type, lower=0, upper=3, len=nrow(newdata), any.missing=FALSE )
+  checkInteger( type, lower=0, upper=4, len=nrow(newdata), any.missing=FALSE )
   
   # Index for variable-weighted value
   if(missing(weighting_index)){
diff --git a/man/integrate_output.Rd b/man/integrate_output.Rd
index ea7c150..08b5d72 100644
--- a/man/integrate_output.Rd
+++ b/man/integrate_output.Rd
@@ -40,8 +40,13 @@ proportion of total in each row of \code{newdata}}
 \item{\code{type=3}}{Abundance-weighted variable: weight predictor by
 proportion of total in a prior row of \code{newdata}.
 This option is used to weight a prediction for
-one category based on predicted density of another category, e.g.,
+one category based on predicted proportional density of another category, e.g.,
 to calculate abundance-weighted condition in a bivariate model.}
+\item{\code{type=4}}{Abundance-expanded variable: weight predictor by
+density in a prior row of \code{newdata}.
+This option is used to weight a prediction for
+one category based on predicted density of another category, e.g.,
+to calculate abundance-expanded consumption in a bivariate model.}
 \item{\code{type=0}}{Exclude from weighting: give weight of zero for
 a given row of \code{newdata}. Including a row of \code{newdata} with
 \code{type=0} is useful, e.g., when calculating abundance at that
@@ -128,6 +133,8 @@ If \eqn{type_g = 2} then \eqn{\phi_g = x_g \frac{\nu_g}{\nu^*} }
 
 If \eqn{type_g = 3} then \eqn{\phi_g = \frac{\nu_{h_g}}{\nu^*} \mu_g }
 
+If \eqn{type_g = 4} then \eqn{\phi_g = \nu_{h_g} \mu_g }
+
 Finally, the total value from this second pass is calculated as:
 
 \deqn{ \phi^* = \sum_{g=0}^{G-1} \phi_g }
diff --git a/src/tinyVAST.cpp b/src/tinyVAST.cpp
index 6da9e83..0d41e84 100644
--- a/src/tinyVAST.cpp
+++ b/src/tinyVAST.cpp
@@ -868,6 +868,10 @@ Type objective_function<Type>::operator() (){
           // density-weighted average of prediction
           phi_g(g) = (phi0_g(V_gz(g,1)) / sumphi0) * mu_g(g);
         }
+        if( (V_gz(g,0)==4) && (V_gz(g,1)>=0) && (V_gz(g,1)<=g) ){
+          // density-weighted total of prediction
+          phi_g(g) = phi0_g(V_gz(g,1)) * mu_g(g);
+        }
       }
       //Type Metric = sum(phi_g);
       Type Metric = newton::Tag( sum(phi_g) ); // Set lowrank tag on Metric = sum(exp(x))