From a35b2c7c300a441ba87c85b4ad40afdb34e186f2 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Wed, 4 Sep 2024 10:33:25 -0400
Subject: [PATCH 01/16] derive an M matrix for IEF models #311

---
 R/ExternalImportFactors.R | 35 ++++++++++++++++++++++++++++++++++-
 man/deriveMMatrix.Rd      | 21 +++++++++++++++++++++
 2 files changed, 55 insertions(+), 1 deletion(-)
 create mode 100644 man/deriveMMatrix.Rd

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 5eb01866..28f43453 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -100,7 +100,7 @@ castImportFactors <- function(IFTable, model) {
 buildModelwithImportFactors <- function(model, configpaths = NULL) {
   # (see Palm et al. 2019)
 
-  logging::loginfo("Building Import A (A_m) accounting for ITA in Domestic FD.\n")
+  logging::loginfo("Building A_m (import requirements) accounting for international trade adjustment in domestic final demand.\n")
   # Re-derive import values in Use and final demand
   # _m denotes import-related structures
   model$UseTransactions_m <- model$UseTransactions - model$DomesticUseTransactions
@@ -126,5 +126,38 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
   
   model$M_m <- M_m
   
+  model$M <- deriveMMatrix(model)
+  
   return(model)
 }
+
+#' Derives an aggregate M matrix from M_d and M_m based on the Consumption demand vector and
+#' FINAL perspective. Results from this M matrix match those calculated using the Import Emission
+#' Factors when using the Consumption demand vector and FINAL perspective.
+#' @param model, An EEIO model object with model specs and crosswalk table loaded
+#' @return An M matrix of flows x sector
+deriveMMatrix <- function(model) {
+  y <- prepareDemandVectorForStandardResults(model, demand="Consumption",
+                                             location=model$specs$ModelRegionAcronyms[1],
+                                             use_domestic_requirements=FALSE)
+  y_d  <- prepareDemandVectorForStandardResults(model, demand="Consumption",
+                                                location=model$specs$ModelRegionAcronyms[1],
+                                                use_domestic_requirements=TRUE)
+  y_m <- prepareDemandVectorForImportResults(model, demand="Consumption",
+                                             location=model$specs$ModelRegionAcronyms[1])
+  if(!all.equal(y, y_d+y_m)) {
+    stop("Error in calculating demand for coupled model approach")
+  }
+  logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) consistent with the FINAL perspective ...")
+  result <- calculateResultsWithExternalFactors(model, demand="Consumption", perspective="FINAL",
+                                                location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
+  # Derive M by dividing the result by the final demand
+  M <- t(result) %*% solve(diag(as.vector(replace(y, y == 0 , 1))))
+  colnames(M) <- colnames(model$M_d)
+  result2 <- calculateFinalPerspectiveLCI(M, y)
+  if(!all.equal(result, result2)) {
+    stop("Error deriving M matrix for coupled model approach")
+  }
+
+  return(M)
+}
diff --git a/man/deriveMMatrix.Rd b/man/deriveMMatrix.Rd
new file mode 100644
index 00000000..69cfa82b
--- /dev/null
+++ b/man/deriveMMatrix.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ExternalImportFactors.R
+\name{deriveMMatrix}
+\alias{deriveMMatrix}
+\title{Derives an aggregate M matrix from M_d and M_m based on the Consumption demand vector and
+FINAL perspective. Results from this M matrix match those calculated using the Import Emission
+Factors when using the Consumption demand vector and FINAL perspective.}
+\usage{
+deriveMMatrix(model)
+}
+\arguments{
+\item{model, }{An EEIO model object with model specs and crosswalk table loaded}
+}
+\value{
+An M matrix of flows x sector
+}
+\description{
+Derives an aggregate M matrix from M_d and M_m based on the Consumption demand vector and
+FINAL perspective. Results from this M matrix match those calculated using the Import Emission
+Factors when using the Consumption demand vector and FINAL perspective.
+}

From 119ea9cfaa4a5d2e70e9e9c656d1cfacd6aa6ca6 Mon Sep 17 00:00:00 2001
From: Ben Young <Ben.Young@erg.com>
Date: Mon, 9 Sep 2024 21:20:28 -0400
Subject: [PATCH 02/16] use domestic production demand and import consumption
 demand to create ratios for M

---
 R/ExternalImportFactors.R | 39 +++++++++++++++++++++++++--------------
 1 file changed, 25 insertions(+), 14 deletions(-)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 28f43453..1baf86a8 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -137,27 +137,38 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
 #' @param model, An EEIO model object with model specs and crosswalk table loaded
 #' @return An M matrix of flows x sector
 deriveMMatrix <- function(model) {
-  y <- prepareDemandVectorForStandardResults(model, demand="Consumption",
-                                             location=model$specs$ModelRegionAcronyms[1],
-                                             use_domestic_requirements=FALSE)
-  y_d  <- prepareDemandVectorForStandardResults(model, demand="Consumption",
+
+  # Domestic production demand
+  y_d  <- prepareDemandVectorForStandardResults(model, demand="Production",
                                                 location=model$specs$ModelRegionAcronyms[1],
                                                 use_domestic_requirements=TRUE)
+  # Import consumption
   y_m <- prepareDemandVectorForImportResults(model, demand="Consumption",
                                              location=model$specs$ModelRegionAcronyms[1])
-  if(!all.equal(y, y_d+y_m)) {
-    stop("Error in calculating demand for coupled model approach")
-  }
-  logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) consistent with the FINAL perspective ...")
+
+  y <- y_m + y_d
+  y_mr <- pmax(pmin(y_m / y, 1), 0)
+  y_dr <- pmin(pmax(y_d / y, 0), 1)
+
+  r1 <- model$M_d %*% diag(as.vector(y_dr))
+  r2 <- model$M_m %*% model$A_m %*% model$L_d %*% diag(as.vector(y_dr))
+  r3 <- model$M_m %*% diag(as.vector(y_mr))
+  M <- r1 + r2 + r3
+  colnames(M) <- colnames(model$M_d)
+  
+  # logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) consistent with the FINAL perspective ...")
   result <- calculateResultsWithExternalFactors(model, demand="Consumption", perspective="FINAL",
                                                 location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
   # Derive M by dividing the result by the final demand
-  M <- t(result) %*% solve(diag(as.vector(replace(y, y == 0 , 1))))
-  colnames(M) <- colnames(model$M_d)
-  result2 <- calculateFinalPerspectiveLCI(M, y)
-  if(!all.equal(result, result2)) {
-    stop("Error deriving M matrix for coupled model approach")
-  }
+  # M <- t(result) %*% solve(diag(as.vector(replace(y, y == 0 , 1))))
+  # colnames(M) <- colnames(model$M_d)
+  y_cons <- prepareDemandVectorForStandardResults(model, demand="Consumption",
+                                             location=model$specs$ModelRegionAcronyms[1],
+                                             use_domestic_requirements=FALSE)
+  result2 <- calculateFinalPerspectiveLCI(M, y_cons)
+  # if(!all.equal(result, result2)) {
+  #   stop("Error deriving M matrix for coupled model approach")
+  # }
 
   return(M)
 }

From 04b7a8ecfd460ceac4a6958a6cfac59d1e146f17 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Tue, 10 Sep 2024 14:13:35 -0400
Subject: [PATCH 03/16] revise approach for deriving M to use q and y_m

---
 R/ExternalImportFactors.R | 51 ++++++++++++++-------------------------
 man/deriveMMatrix.Rd      |  8 ++----
 2 files changed, 20 insertions(+), 39 deletions(-)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 1baf86a8..6c7d6468 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -131,44 +131,29 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
   return(model)
 }
 
-#' Derives an aggregate M matrix from M_d and M_m based on the Consumption demand vector and
-#' FINAL perspective. Results from this M matrix match those calculated using the Import Emission
-#' Factors when using the Consumption demand vector and FINAL perspective.
+#' Derives an aggregate M matrix from M_d and M_m based on the ratio of commodity output to total imports.
 #' @param model, An EEIO model object with model specs and crosswalk table loaded
 #' @return An M matrix of flows x sector
 deriveMMatrix <- function(model) {
-
-  # Domestic production demand
-  y_d  <- prepareDemandVectorForStandardResults(model, demand="Production",
-                                                location=model$specs$ModelRegionAcronyms[1],
-                                                use_domestic_requirements=TRUE)
-  # Import consumption
-  y_m <- prepareDemandVectorForImportResults(model, demand="Consumption",
-                                             location=model$specs$ModelRegionAcronyms[1])
-
-  y <- y_m + y_d
-  y_mr <- pmax(pmin(y_m / y, 1), 0)
-  y_dr <- pmin(pmax(y_d / y, 0), 1)
-
-  r1 <- model$M_d %*% diag(as.vector(y_dr))
-  r2 <- model$M_m %*% model$A_m %*% model$L_d %*% diag(as.vector(y_dr))
-  r3 <- model$M_m %*% diag(as.vector(y_mr))
-  M <- r1 + r2 + r3
+  # logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) ...")
+  q <- model$q
+  loc <- grepl(model$specs$ModelRegionAcronyms[1], model$FinalDemandMeta$Code_Loc)
+  import_code <- model$FinalDemandMeta[model$FinalDemandMeta$Group=="Import" & loc, "Code_Loc"]
+  y_m <- sumDemandCols(model$FinalDemand, import_code)
+  
+  dr <- q / (q + abs(y_m))
+  mr <- 1 - dr
+  # Derive M by taking the ratio of domestic vs imported goods
+  M <- model$M_d %*% diag(as.vector(dr)) + model$M_m %*% diag(as.vector(mr))
   colnames(M) <- colnames(model$M_d)
   
-  # logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) consistent with the FINAL perspective ...")
-  result <- calculateResultsWithExternalFactors(model, demand="Consumption", perspective="FINAL",
-                                                location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
-  # Derive M by dividing the result by the final demand
-  # M <- t(result) %*% solve(diag(as.vector(replace(y, y == 0 , 1))))
-  # colnames(M) <- colnames(model$M_d)
-  y_cons <- prepareDemandVectorForStandardResults(model, demand="Consumption",
-                                             location=model$specs$ModelRegionAcronyms[1],
-                                             use_domestic_requirements=FALSE)
-  result2 <- calculateFinalPerspectiveLCI(M, y_cons)
-  # if(!all.equal(result, result2)) {
-  #   stop("Error deriving M matrix for coupled model approach")
-  # }
+  # result <- calculateResultsWithExternalFactors(model, demand="Consumption", perspective="FINAL",
+  #                                               location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
+  # model2 <- model
+  # model2$M <- M
+  # model2$N <- model$C %*% M
+  # result2 <- calculateStandardResults(model2, demand="Consumption", perspective="FINAL",
+  #                                     location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
 
   return(M)
 }
diff --git a/man/deriveMMatrix.Rd b/man/deriveMMatrix.Rd
index 69cfa82b..c56ac74e 100644
--- a/man/deriveMMatrix.Rd
+++ b/man/deriveMMatrix.Rd
@@ -2,9 +2,7 @@
 % Please edit documentation in R/ExternalImportFactors.R
 \name{deriveMMatrix}
 \alias{deriveMMatrix}
-\title{Derives an aggregate M matrix from M_d and M_m based on the Consumption demand vector and
-FINAL perspective. Results from this M matrix match those calculated using the Import Emission
-Factors when using the Consumption demand vector and FINAL perspective.}
+\title{Derives an aggregate M matrix from M_d and M_m based on the ratio of commodity output to total imports.}
 \usage{
 deriveMMatrix(model)
 }
@@ -15,7 +13,5 @@ deriveMMatrix(model)
 An M matrix of flows x sector
 }
 \description{
-Derives an aggregate M matrix from M_d and M_m based on the Consumption demand vector and
-FINAL perspective. Results from this M matrix match those calculated using the Import Emission
-Factors when using the Consumption demand vector and FINAL perspective.
+Derives an aggregate M matrix from M_d and M_m based on the ratio of commodity output to total imports.
 }

From 7c7f8550e6a2cd4c37ab276a0ce4936a2c04c509 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Tue, 10 Sep 2024 15:18:31 -0400
Subject: [PATCH 04/16] derive m from use table

---
 R/ExternalImportFactors.R | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 6c7d6468..c026d602 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -139,21 +139,16 @@ deriveMMatrix <- function(model) {
   q <- model$q
   loc <- grepl(model$specs$ModelRegionAcronyms[1], model$FinalDemandMeta$Code_Loc)
   import_code <- model$FinalDemandMeta[model$FinalDemandMeta$Group=="Import" & loc, "Code_Loc"]
-  y_m <- sumDemandCols(model$FinalDemand, import_code)
+  # derive total imports (m) from the Use table
+  U_m <- model$U - model$U_d
+  # Exclude imports col when calculating total imports
+  m <- head(rowSums(U_m[, !(colnames(U_m) %in% import_code)]), -3) # drop VA
   
-  dr <- q / (q + abs(y_m))
+  dr <- q / (q + m)
   mr <- 1 - dr
   # Derive M by taking the ratio of domestic vs imported goods
   M <- model$M_d %*% diag(as.vector(dr)) + model$M_m %*% diag(as.vector(mr))
   colnames(M) <- colnames(model$M_d)
-  
-  # result <- calculateResultsWithExternalFactors(model, demand="Consumption", perspective="FINAL",
-  #                                               location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
-  # model2 <- model
-  # model2$M <- M
-  # model2$N <- model$C %*% M
-  # result2 <- calculateStandardResults(model2, demand="Consumption", perspective="FINAL",
-  #                                     location=model$specs$ModelRegionAcronyms[1])[["LCI_f"]]
 
   return(M)
 }

From adb2dafbf6b1af2f66223d939d2898556d78142b Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Tue, 10 Sep 2024 15:37:23 -0400
Subject: [PATCH 05/16] fix error in deriving M matrix for 2R models

---
 R/ExternalImportFactors.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index c026d602..83fbdbbc 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -135,14 +135,14 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
 #' @param model, An EEIO model object with model specs and crosswalk table loaded
 #' @return An M matrix of flows x sector
 deriveMMatrix <- function(model) {
-  # logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) ...")
+  logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) ...")
   q <- model$q
   loc <- grepl(model$specs$ModelRegionAcronyms[1], model$FinalDemandMeta$Code_Loc)
   import_code <- model$FinalDemandMeta[model$FinalDemandMeta$Group=="Import" & loc, "Code_Loc"]
   # derive total imports (m) from the Use table
   U_m <- model$U - model$U_d
   # Exclude imports col when calculating total imports
-  m <- head(rowSums(U_m[, !(colnames(U_m) %in% import_code)]), -3) # drop VA
+  m <- rowSums(U_m[model$Commodities$Code_Loc, !(colnames(U_m) %in% import_code)]) # drop VA
   
   dr <- q / (q + m)
   mr <- 1 - dr

From b80c38b261c3810c1d7db08584053f9c7e22a87f Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Tue, 10 Sep 2024 16:03:31 -0400
Subject: [PATCH 06/16] ignore location when removing imports

---
 R/ExternalImportFactors.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 83fbdbbc..6aedcb77 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -137,8 +137,7 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
 deriveMMatrix <- function(model) {
   logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) ...")
   q <- model$q
-  loc <- grepl(model$specs$ModelRegionAcronyms[1], model$FinalDemandMeta$Code_Loc)
-  import_code <- model$FinalDemandMeta[model$FinalDemandMeta$Group=="Import" & loc, "Code_Loc"]
+  import_code <- model$FinalDemandMeta[model$FinalDemandMeta$Group=="Import", "Code_Loc"]
   # derive total imports (m) from the Use table
   U_m <- model$U - model$U_d
   # Exclude imports col when calculating total imports

From c9762f422fcca422a3e6ee4a938e4d5ea22e9df0 Mon Sep 17 00:00:00 2001
From: Ben Young <Ben.Young@erg.com>
Date: Wed, 11 Sep 2024 18:41:32 -0400
Subject: [PATCH 07/16] validate that M is between M_m and M_d

---
 R/ExternalImportFactors.R | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 6aedcb77..552b44b1 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -149,5 +149,14 @@ deriveMMatrix <- function(model) {
   M <- model$M_d %*% diag(as.vector(dr)) + model$M_m %*% diag(as.vector(mr))
   colnames(M) <- colnames(model$M_d)
 
+  # Validate that M is between M_m and M_d
+  a <- signif(model$M_m, 6)
+  b <- signif(M, 6)
+  c <- signif(model$M_d, 6)
+  z <- ((b > a) & (b > c)) | ((b < a) & (b < c))
+  if(sum(z) > 0) {
+    stop("Error in deriving M matrix")
+  }
+  
   return(M)
 }

From e232ca115ee63a513b644950a04f533542888407 Mon Sep 17 00:00:00 2001
From: Ben Young <Ben.Young@erg.com>
Date: Thu, 12 Sep 2024 21:10:13 -0400
Subject: [PATCH 08/16] move M matrix test to validation and print any failures

---
 R/ExternalImportFactors.R |  9 ---------
 R/ValidateModel.R         | 13 +++++++++++++
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 552b44b1..6aedcb77 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -149,14 +149,5 @@ deriveMMatrix <- function(model) {
   M <- model$M_d %*% diag(as.vector(dr)) + model$M_m %*% diag(as.vector(mr))
   colnames(M) <- colnames(model$M_d)
 
-  # Validate that M is between M_m and M_d
-  a <- signif(model$M_m, 6)
-  b <- signif(M, 6)
-  c <- signif(model$M_d, 6)
-  z <- ((b > a) & (b > c)) | ((b < a) & (b < c))
-  if(sum(z) > 0) {
-    stop("Error in deriving M matrix")
-  }
-  
   return(M)
 }
diff --git a/R/ValidateModel.R b/R/ValidateModel.R
index 4b41c142..2c95753c 100644
--- a/R/ValidateModel.R
+++ b/R/ValidateModel.R
@@ -474,6 +474,19 @@ validateImportFactorsApproach <- function(model, demand = "Consumption"){
   cat("assuming model$M = model$M_m.\n")
   print(all.equal(LCIA_dm, LCIA))
   
+  cat("\nValidating that the derived M matrix has all values between M_d and M_m\n")
+
+  # Validate that M is between M_m and M_d
+  a <- signif(model$M_m, 6)
+  b <- signif(model$M, 6)
+  c <- signif(model$M_d, 6)
+  z <- ((b > a) & (b > c)) | ((b < a) & (b < c))
+  if(sum(z) == 0) {
+    print(TRUE)
+  } else {
+    comm <- colSums(z) > 0
+    print(paste0("Failures: ", names(comm)[comm == TRUE]))
+  }
 }
 
 #' Validate the calculation of household_emissions

From e9256a8f5f2b48a45e0dad4ff1d849e4a32d685b Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Thu, 31 Oct 2024 09:33:39 -0400
Subject: [PATCH 09/16] move two region model spec (v1.0) out of tests

---
 {tests => inst/extdata}/modelspecs/GAEEIOv1.0-GHG-19.yml | 0
 tests/test_model_build.R                                 | 5 ++---
 2 files changed, 2 insertions(+), 3 deletions(-)
 rename {tests => inst/extdata}/modelspecs/GAEEIOv1.0-GHG-19.yml (100%)

diff --git a/tests/modelspecs/GAEEIOv1.0-GHG-19.yml b/inst/extdata/modelspecs/GAEEIOv1.0-GHG-19.yml
similarity index 100%
rename from tests/modelspecs/GAEEIOv1.0-GHG-19.yml
rename to inst/extdata/modelspecs/GAEEIOv1.0-GHG-19.yml
diff --git a/tests/test_model_build.R b/tests/test_model_build.R
index a0af581b..bab449ff 100644
--- a/tests/test_model_build.R
+++ b/tests/test_model_build.R
@@ -131,13 +131,12 @@ printValidationResults(model)
 
 ## StateEEIOv1.0 Two-region Summary model
 m <- "GAEEIOv1.0-GHG-19"
-cfg <- paste0("modelspecs/", m, ".yml")
-model <- buildModel(m, configpaths = file.path(cfg))
+model <- buildModel(m)
 printValidationResults(model)
 writeModeltoXLSX(model, ".")
 
 ## StateEEIOv1.0 Two-region Summary model (Economic only)
-model <- buildIOModel(m, configpaths = file.path(cfg))
+model <- buildIOModel(m)
 printValidationResults(model)
 writeModeltoXLSX(model, ".")
 

From 5c5c18e0fd20299c3777d92f62bdbe2380e513f4 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Thu, 31 Oct 2024 09:56:37 -0400
Subject: [PATCH 10/16] include additional warnings for functions that don't
 work for specific model types

---
 R/AdjustPrice.R            | 8 ++++++--
 R/VisualizationFunctions.R | 3 +++
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/R/AdjustPrice.R b/R/AdjustPrice.R
index 3170f08a..8a473a84 100644
--- a/R/AdjustPrice.R
+++ b/R/AdjustPrice.R
@@ -19,8 +19,12 @@ adjustResultMatrixPrice <- function(matrix_name, currency_year, purchaser_price=
   }
   # Adjust price type of multiplier
   if (purchaser_price) {
-    logging::loginfo(paste("Adjusting", matrix_name, "matrix from producer to purchaser price..."))
-    mat <- adjustMultiplierPriceType(mat, currency_year, model)
+    if(is.null(model$Phi)) {
+      logging::logwarn("Model does not contain margins, purchaser price can not be calculated")
+    } else {
+      logging::loginfo(paste("Adjusting", matrix_name, "matrix from producer to purchaser price..."))
+      mat <- adjustMultiplierPriceType(mat, currency_year, model)
+    }
   } else {
     logging::loginfo(paste("Keeping", matrix_name, "matrix in producer price..."))
   }
diff --git a/R/VisualizationFunctions.R b/R/VisualizationFunctions.R
index 7a2df283..cb757585 100644
--- a/R/VisualizationFunctions.R
+++ b/R/VisualizationFunctions.R
@@ -237,6 +237,9 @@ heatmapSatelliteTableCoverage <- function(model, form="Commodity") {
 #' @export
 heatmapSectorRanking <- function(model, matrix, indicators, sector_to_remove, N_sector, x_title = NULL,
                                  use_codes = TRUE) {
+  if(model$specs$IODataSource == "stateior") {
+    stop("heatmapSectorRanking not available for two-region models.")
+  }
   # Generate BEA sector color mapping
   mapping <- getBEASectorColorMapping(model)
   mapping$GroupName <- mapping$SectorName

From bea22ec94299b9598fef416293f55d42d434a739 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Thu, 31 Oct 2024 10:12:48 -0400
Subject: [PATCH 11/16] adds result and visualization tests to a number of
 models, #320

---
 R/ValidateModel.R                 | 88 +++++++++++++++++++++++++++++++
 man/testCalculationFunctions.Rd   | 24 +++++++++
 man/testVisualizationFunctions.Rd | 20 +++++++
 tests/test_model_build.R          | 12 +++--
 4 files changed, 141 insertions(+), 3 deletions(-)
 create mode 100644 man/testCalculationFunctions.Rd
 create mode 100644 man/testVisualizationFunctions.Rd

diff --git a/R/ValidateModel.R b/R/ValidateModel.R
index 2c95753c..8aa2a445 100644
--- a/R/ValidateModel.R
+++ b/R/ValidateModel.R
@@ -507,3 +507,91 @@ validateHouseholdEmissions <- function(model) {
   result <- r$LCI_f[codes, names(flows)]
   all.equal(flows, result)
 }
+
+#' Test that model calculation functions are successful
+#' Includes tests for the following functions:
+#' adjustResultMatrixPrice, calculateFlowContributiontoImpact,
+#' calculateSectorContributiontoImpact, disaggregateTotalToDirectAndTier1,
+#' calculateSectorPurchasedbySectorSourcedImpact, aggregateResultMatrix,
+#' calculateMarginSectorImpacts
+#' 
+#' @param model, A fully built EEIO model object
+testCalculationFunctions <- function(model) {
+  target_year <- ifelse(model$specs$IOYear != 2019, 2019, 2020)
+  sector <- model$Commodities$Code_Loc[[10]]
+  indicator <- model$Indicators$meta$Name[[1]]
+  
+  matrix <- adjustResultMatrixPrice(matrix_name = "N",
+                                    currency_year = target_year,
+                                    purchaser_price = TRUE,
+                                    model)
+  if(!all(dim(model$N) == dim(matrix)) && !all(model$N == matrix)) {
+    print("Error in adjustResultMatrixPrice()")
+  }
+  
+  flow_contrib <- calculateFlowContributiontoImpact(model, sector, indicator)
+  if(!all.equal(sum(flow_contrib$contribution), 1)) {
+    print("Error in calculateFlowContributiontoImpact()")
+  }
+  
+  sector_contrib <- calculateSectorContributiontoImpact(model, sector, indicator)
+  if(!all.equal(sum(sector_contrib$contribution), 1)) {
+    print("Error in calculateSectorContributiontoImpact()")
+  }
+  
+  demand = model$DemandVectors$vectors[[1]]
+  result <- calculateSectorPurchasedbySectorSourcedImpact(y=demand, model, indicator)
+  if(model$specs$IODataSource != "stateior") {
+    # not working for 2R mode
+    agg_result <- aggregateResultMatrix(result, "Sector", model$crosswalk)
+  }
+  
+  result <- disaggregateTotalToDirectAndTier1(model, indicator)
+  
+  if(model$specs$IODataSource != "stateior") {
+    margins <- calculateMarginSectorImpacts(model)
+  }
+
+}
+
+#' Test that visualization functions are successful
+#' Includes tests for the following functions:
+#' barplotFloworImpactFractionbyRegion, barplotIndicatorScoresbySector, 
+#' heatmapSatelliteTableCoverage, heatmapSectorRanking, plotMatrixCoefficient
+#' 
+#' @param model, A fully built EEIO model object
+testVisualizationFunctions <- function(model) {
+  model_list <- list("model" = model)
+  loc <- model$specs$ModelRegionAcronyms[[1]]
+  indicator <- model$Indicators$meta$Name[[1]]
+  
+  fullcons <- calculateEEIOModel(model, perspective='DIRECT', demand="Consumption",
+                                 location = loc)
+  domcons <- calculateEEIOModel(model, perspective='DIRECT', demand="Consumption",
+                                location = loc,  use_domestic_requirements = TRUE)
+  barplotFloworImpactFractionbyRegion(domcons$LCIA_d,
+                                      fullcons$LCIA_d,
+                                      "Domestic Proportion of Impact")
+  ## ^^ This may not be working correctly for 2R models
+  
+  barplotIndicatorScoresbySector(model_list,
+                                 totals_by_sector_name = "GHG",
+                                 indicator_name = "Greenhouse Gases",
+                                 sector = FALSE, y_title = "")
+  
+  heatmapSatelliteTableCoverage(model, form = "Industry")
+  # ^^ not working for form = "Commodity"
+  
+  indicators <- model$Indicators$meta$Code[1:min(5, length(model$Indicators$meta$Code))]
+  
+  if(model$specs$IODataSource != "stateior") {
+    # not working for 2R models
+    heatmapSectorRanking(model, matrix = fullcons$LCIA_d, indicators,
+                         sector_to_remove = "", N_sector = 20)
+  }
+  
+  plotMatrixCoefficient(model_list, matrix_name = "D",
+                        coefficient_name = indicator,
+                        sector_to_remove = "", y_title = indicator,
+                        y_label = "Name")
+}
diff --git a/man/testCalculationFunctions.Rd b/man/testCalculationFunctions.Rd
new file mode 100644
index 00000000..b33dc432
--- /dev/null
+++ b/man/testCalculationFunctions.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ValidateModel.R
+\name{testCalculationFunctions}
+\alias{testCalculationFunctions}
+\title{Test that model calculation functions are successful
+Includes tests for the following functions:
+adjustResultMatrixPrice, calculateFlowContributiontoImpact,
+calculateSectorContributiontoImpact, disaggregateTotalToDirectAndTier1,
+calculateSectorPurchasedbySectorSourcedImpact, aggregateResultMatrix,
+calculateMarginSectorImpacts}
+\usage{
+testCalculationFunctions(model)
+}
+\arguments{
+\item{model, }{A fully built EEIO model object}
+}
+\description{
+Test that model calculation functions are successful
+Includes tests for the following functions:
+adjustResultMatrixPrice, calculateFlowContributiontoImpact,
+calculateSectorContributiontoImpact, disaggregateTotalToDirectAndTier1,
+calculateSectorPurchasedbySectorSourcedImpact, aggregateResultMatrix,
+calculateMarginSectorImpacts
+}
diff --git a/man/testVisualizationFunctions.Rd b/man/testVisualizationFunctions.Rd
new file mode 100644
index 00000000..4de6fbe3
--- /dev/null
+++ b/man/testVisualizationFunctions.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ValidateModel.R
+\name{testVisualizationFunctions}
+\alias{testVisualizationFunctions}
+\title{Test that visualization functions are successful
+Includes tests for the following functions:
+barplotFloworImpactFractionbyRegion, barplotIndicatorScoresbySector, 
+heatmapSatelliteTableCoverage, heatmapSectorRanking, plotMatrixCoefficient}
+\usage{
+testVisualizationFunctions(model)
+}
+\arguments{
+\item{model, }{A fully built EEIO model object}
+}
+\description{
+Test that visualization functions are successful
+Includes tests for the following functions:
+barplotFloworImpactFractionbyRegion, barplotIndicatorScoresbySector, 
+heatmapSatelliteTableCoverage, heatmapSectorRanking, plotMatrixCoefficient
+}
diff --git a/tests/test_model_build.R b/tests/test_model_build.R
index bab449ff..a441fa38 100644
--- a/tests/test_model_build.R
+++ b/tests/test_model_build.R
@@ -10,6 +10,8 @@ if (!interactive()) options(warn=2, error = function() { sink(stderr()) ; traceb
 m <- "USEEIOv2.0.1-411"
 model <- buildModel(m)
 printValidationResults(model)
+testCalculationFunctions(model)
+testVisualizationFunctions(model)
 
 ## USEEIOv2.0.1-411 Detail model with waste disaggregation (Economic only)
 m <- "USEEIOv2.0.1-411"
@@ -128,12 +130,16 @@ writeModeltoXLSX(model, ".")
 m <- "USEEIOv2.3-s-GHG-19"
 model <- buildModel(m)
 printValidationResults(model)
+testCalculationFunctions(model)
+testVisualizationFunctions(model)
 
 ## StateEEIOv1.0 Two-region Summary model
 m <- "GAEEIOv1.0-GHG-19"
 model <- buildModel(m)
 printValidationResults(model)
 writeModeltoXLSX(model, ".")
+testCalculationFunctions(model)
+testVisualizationFunctions(model)
 
 ## StateEEIOv1.0 Two-region Summary model (Economic only)
 model <- buildIOModel(m)
@@ -141,9 +147,7 @@ printValidationResults(model)
 writeModeltoXLSX(model, ".")
 
 ## StateEEIOv1.1 Two-region Summary model with Import Factors
-cfg <- c(paste0("modelspecs/", m, ".yml"),
-         "US_summary_import_factors_exio_2019_12sch.csv"
-         )
+cfg <- c("US_summary_import_factors_exio_2019_12sch.csv")
 model <- useeior:::initializeModel(m, configpaths = file.path(cfg))
 model$specs$Model <- "GAEEIOv1.1-GHG-19-IF"
 model$specs$ExternalImportFactors <- TRUE
@@ -156,6 +160,8 @@ model <- useeior:::loadandbuildIndicators(model)
 model <- useeior:::loadDemandVectors(model)
 model <- useeior:::constructEEIOMatrices(model, file.path(cfg))
 printValidationResults(model)
+testCalculationFunctions(model)
+testVisualizationFunctions(model)
 
 # ## StateEEIOv1.0 Two-region Summary model with Utility disaggregation
 # model <- useeior:::initializeModel(m, configpaths = file.path(cfg))

From 87a0d0b2decc71327b16a18408cd475e5db548e0 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Thu, 31 Oct 2024 10:19:49 -0400
Subject: [PATCH 12/16] export validation functions

---
 NAMESPACE         | 2 ++
 R/ValidateModel.R | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 7f42189c..c504c06d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -22,6 +22,8 @@ export(normalizeResultMatrixByTotalImpacts)
 export(plotMatrixCoefficient)
 export(printValidationResults)
 export(seeAvailableModels)
+export(testCalculationFunctions)
+export(testVisualizationFunctions)
 export(writeModelMatrices)
 export(writeModelforAPI)
 export(writeModeltoXLSX)
diff --git a/R/ValidateModel.R b/R/ValidateModel.R
index 8aa2a445..caac8648 100644
--- a/R/ValidateModel.R
+++ b/R/ValidateModel.R
@@ -516,6 +516,7 @@ validateHouseholdEmissions <- function(model) {
 #' calculateMarginSectorImpacts
 #' 
 #' @param model, A fully built EEIO model object
+#' @export
 testCalculationFunctions <- function(model) {
   target_year <- ifelse(model$specs$IOYear != 2019, 2019, 2020)
   sector <- model$Commodities$Code_Loc[[10]]
@@ -560,6 +561,7 @@ testCalculationFunctions <- function(model) {
 #' heatmapSatelliteTableCoverage, heatmapSectorRanking, plotMatrixCoefficient
 #' 
 #' @param model, A fully built EEIO model object
+#' @export
 testVisualizationFunctions <- function(model) {
   model_list <- list("model" = model)
   loc <- model$specs$ModelRegionAcronyms[[1]]

From 13d78eb905997a2757049e95d489b22b3749e5c1 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Thu, 31 Oct 2024 10:50:14 -0400
Subject: [PATCH 13/16] warnings not converted to errors

---
 tests/test_model_build.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_model_build.R b/tests/test_model_build.R
index a441fa38..8f36d433 100644
--- a/tests/test_model_build.R
+++ b/tests/test_model_build.R
@@ -4,7 +4,7 @@
 # setwd("tests")
 library(useeior)
 # library(unittest, quietly = TRUE)
-if (!interactive()) options(warn=2, error = function() { sink(stderr()) ; traceback(3) ; q(status = 1) })
+if (!interactive()) options(warn=1, error = function() { sink(stderr()) ; traceback(3) ; q(status = 1) })
 
 ## USEEIOv2.0.1-411 Detail model with waste disaggregation
 m <- "USEEIOv2.0.1-411"

From 031e992e15b8c3d452d23a3c0a386a628c17d6a9 Mon Sep 17 00:00:00 2001
From: Wesley Ingwersen <ingwersen.wesley@epa.gov>
Date: Fri, 1 Nov 2024 08:39:17 -0400
Subject: [PATCH 14/16] Revert "derive an M matrix for IEF models"

---
 R/ExternalImportFactors.R | 25 +------------------------
 R/ValidateModel.R         | 13 -------------
 man/deriveMMatrix.Rd      | 17 -----------------
 3 files changed, 1 insertion(+), 54 deletions(-)
 delete mode 100644 man/deriveMMatrix.Rd

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 6aedcb77..5eb01866 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -100,7 +100,7 @@ castImportFactors <- function(IFTable, model) {
 buildModelwithImportFactors <- function(model, configpaths = NULL) {
   # (see Palm et al. 2019)
 
-  logging::loginfo("Building A_m (import requirements) accounting for international trade adjustment in domestic final demand.\n")
+  logging::loginfo("Building Import A (A_m) accounting for ITA in Domestic FD.\n")
   # Re-derive import values in Use and final demand
   # _m denotes import-related structures
   model$UseTransactions_m <- model$UseTransactions - model$DomesticUseTransactions
@@ -126,28 +126,5 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
   
   model$M_m <- M_m
   
-  model$M <- deriveMMatrix(model)
-  
   return(model)
 }
-
-#' Derives an aggregate M matrix from M_d and M_m based on the ratio of commodity output to total imports.
-#' @param model, An EEIO model object with model specs and crosswalk table loaded
-#' @return An M matrix of flows x sector
-deriveMMatrix <- function(model) {
-  logging::loginfo("Deriving M matrix (total emissions and resource use per dollar) ...")
-  q <- model$q
-  import_code <- model$FinalDemandMeta[model$FinalDemandMeta$Group=="Import", "Code_Loc"]
-  # derive total imports (m) from the Use table
-  U_m <- model$U - model$U_d
-  # Exclude imports col when calculating total imports
-  m <- rowSums(U_m[model$Commodities$Code_Loc, !(colnames(U_m) %in% import_code)]) # drop VA
-  
-  dr <- q / (q + m)
-  mr <- 1 - dr
-  # Derive M by taking the ratio of domestic vs imported goods
-  M <- model$M_d %*% diag(as.vector(dr)) + model$M_m %*% diag(as.vector(mr))
-  colnames(M) <- colnames(model$M_d)
-
-  return(M)
-}
diff --git a/R/ValidateModel.R b/R/ValidateModel.R
index 2c95753c..4b41c142 100644
--- a/R/ValidateModel.R
+++ b/R/ValidateModel.R
@@ -474,19 +474,6 @@ validateImportFactorsApproach <- function(model, demand = "Consumption"){
   cat("assuming model$M = model$M_m.\n")
   print(all.equal(LCIA_dm, LCIA))
   
-  cat("\nValidating that the derived M matrix has all values between M_d and M_m\n")
-
-  # Validate that M is between M_m and M_d
-  a <- signif(model$M_m, 6)
-  b <- signif(model$M, 6)
-  c <- signif(model$M_d, 6)
-  z <- ((b > a) & (b > c)) | ((b < a) & (b < c))
-  if(sum(z) == 0) {
-    print(TRUE)
-  } else {
-    comm <- colSums(z) > 0
-    print(paste0("Failures: ", names(comm)[comm == TRUE]))
-  }
 }
 
 #' Validate the calculation of household_emissions
diff --git a/man/deriveMMatrix.Rd b/man/deriveMMatrix.Rd
deleted file mode 100644
index c56ac74e..00000000
--- a/man/deriveMMatrix.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ExternalImportFactors.R
-\name{deriveMMatrix}
-\alias{deriveMMatrix}
-\title{Derives an aggregate M matrix from M_d and M_m based on the ratio of commodity output to total imports.}
-\usage{
-deriveMMatrix(model)
-}
-\arguments{
-\item{model, }{An EEIO model object with model specs and crosswalk table loaded}
-}
-\value{
-An M matrix of flows x sector
-}
-\description{
-Derives an aggregate M matrix from M_d and M_m based on the ratio of commodity output to total imports.
-}

From 70ea6d4906557506ad1d7c3936fe0664e5c5a888 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Fri, 1 Nov 2024 09:41:13 -0400
Subject: [PATCH 15/16] add new calculation for M matrix with IEFs, #311

---
 R/ExternalImportFactors.R          | 18 +++++++++++++++++-
 man/calculateMwithImportFactors.Rd | 17 +++++++++++++++++
 2 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 man/calculateMwithImportFactors.Rd

diff --git a/R/ExternalImportFactors.R b/R/ExternalImportFactors.R
index 5eb01866..2a8f8b73 100644
--- a/R/ExternalImportFactors.R
+++ b/R/ExternalImportFactors.R
@@ -100,7 +100,7 @@ castImportFactors <- function(IFTable, model) {
 buildModelwithImportFactors <- function(model, configpaths = NULL) {
   # (see Palm et al. 2019)
 
-  logging::loginfo("Building Import A (A_m) accounting for ITA in Domestic FD.\n")
+  logging::loginfo("Building A_m (import requirements) accounting for international trade adjustment in domestic final demand.\n")
   # Re-derive import values in Use and final demand
   # _m denotes import-related structures
   model$UseTransactions_m <- model$UseTransactions - model$DomesticUseTransactions
@@ -126,5 +126,21 @@ buildModelwithImportFactors <- function(model, configpaths = NULL) {
   
   model$M_m <- M_m
   
+  model$M <- calculateMwithImportFactors(model)
+  
   return(model)
 }
+
+#' Derives an M matrix for total embodied flows from domestic and imported supply chains.
+#' @param model, An EEIO model object with model specs and crosswalk table loaded
+#' @return An M matrix of flows x sector
+calculateMwithImportFactors <- function(model) {
+  logging::loginfo("Calculating M matrix (total emissions and resource use per dollar) ...")
+  
+  # embodied flows from the use of imports by industries to make their commodities
+  # both directly (from A_m) and indirectly (by scaling it to total requirements using L_d)
+  M_mi <- model$M_m %*% model$A_m %*% model$L_d
+  
+  M <- model$M_d + M_mi
+  return(M)
+}
diff --git a/man/calculateMwithImportFactors.Rd b/man/calculateMwithImportFactors.Rd
new file mode 100644
index 00000000..d6725db0
--- /dev/null
+++ b/man/calculateMwithImportFactors.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ExternalImportFactors.R
+\name{calculateMwithImportFactors}
+\alias{calculateMwithImportFactors}
+\title{Derives an M matrix for total embodied flows from domestic and imported supply chains.}
+\usage{
+calculateMwithImportFactors(model)
+}
+\arguments{
+\item{model, }{An EEIO model object with model specs and crosswalk table loaded}
+}
+\value{
+An M matrix of flows x sector
+}
+\description{
+Derives an M matrix for total embodied flows from domestic and imported supply chains.
+}

From 13854b4a8a4c8965fe15bcb0907d9758337914d5 Mon Sep 17 00:00:00 2001
From: Ben Young <ben.young@erg.com>
Date: Mon, 4 Nov 2024 13:56:51 -0500
Subject: [PATCH 16/16] :bookmark: bump to v1.6.1

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 42bbf678..b703a37c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: useeior
 Type: Package
 Title: USEEIO R modeling software
-Version: 1.6.0
-Date: 2024-8-6
+Version: 1.6.1
+Date: 2024-11-4
 Authors@R: c(
   person("Ben","Young", email="ben.young@erg.com", role="aut"),
   person("Jorge","Vendries", email="jvendries@gmail.com", role="aut"),