Updates to demo data

gemmagerber · Jun 29, 2023 · 197af2d · 197af2d
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commit 197af2d
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Showing 11 changed files with 84 additions and 98 deletions.
diff --git a/inst/example_input_csv/winter_demo_net_input.csv b/inst/example_input_csv/winter_demo_net_input.csv
@@ -1,5 +1,5 @@
 Compartment,Biomass,Consumption_lower,Consumption_upper,Production_lower,Production_upper,Respiration_lower,Respiration_upper,Unused_energy_lower,Unused_energy_upper,Imports_lower,Imports_upper,Exports_lower,Exports_upper
-Det,7111,,,,,,,,,200,1200,180,380
-Plant,500,700,1000,,,,,,,700,1300,300,1300
-Invert,822,,,,,,,,,1,,,
-Vert,222,,,,,,,,,1,,1,1
+Det,7111,,,,,,,,,,0.1 * DetNLNode,,0.1 * DetNLNode
+Plant,500,700,1000,,,,,,,,0.1 * Plant,,0.1 * Plant
+Invert,822,,,,,,,,,,,,0.1 * Invert
+Vert,222,,,,,,,,,,,,0.1 * Vert
diff --git a/inst/example_input_xlsx/demo_admat_input.xlsx b/inst/example_input_xlsx/demo_admat_input.xlsx
diff --git a/inst/example_input_xlsx/demo_net_input.xlsx b/inst/example_input_xlsx/demo_net_input.xlsx
diff --git a/inst/example_limfiles/Autumn_Unweighted_Network_LIMfile.R b/inst/example_limfiles/Autumn_Unweighted_Network_LIMfile.R
@@ -2,15 +2,15 @@
 ! Network LIM Declaration File
 ! Composed with autoLIMR
 ! Author: gemma
-! Date: 2023-02-13
+! Date: 2023-06-17
 
 ! Respiration included: Yes
 ! U included: Yes
 
 ! Living compartments: 3
 ! Non-living compartments: 1
-! External compartments: 9
-! Boundary flows: 12
+! External compartments: 7
+! Boundary flows: 10
 ! Internal flows: 6
 
 ! Abbreviations
@@ -38,9 +38,7 @@ DetNLNode = 8000.0
 
 CO2
 DetNLNodeImport
-InvertImport
 PlantImport
-VertImport
 DetNLNodeExport
 InvertExport
 PlantExport
@@ -52,9 +50,9 @@ VertExport
 
 ! Consumption (Q) / Gross Primary Production (GPP) Variables
 
-Invert_Q = Flowto(Invert) - Invert_IM
+Invert_Q = Flowto(Invert)
 Plant_GPP = Flowto(Plant) - Plant_IM
-Vert_Q = Flowto(Vert) - Vert_IM
+Vert_Q = Flowto(Vert)
 
 ! Production (P/NPP) Variables
 
@@ -68,7 +66,6 @@ Invert_U = Flowto(Invert) - Invert_P - Invert_R - Invert_EX
 Plant_U = Flowto(Plant) - Plant_NPP - Plant_R - Plant_EX
 Vert_U = Flowto(Vert) - Vert_P - Vert_R - Vert_EX
 
-! No Assimilation Efficiency (AE) Variables defined
 
 ### END VARIABLES
 
@@ -87,9 +84,7 @@ Vert_R: Vert -> CO2
 ! Import flows
 
 DetNLNode_IM: DetNLNodeImport -> DetNLNode
-Invert_IM: InvertImport -> Invert
 Plant_IM: PlantImport -> Plant
-Vert_IM: VertImport -> Vert
 
 ! Export flows
 

diff --git a/inst/example_limfiles/Autumn_Weighted_Network_LIMfile.R b/inst/example_limfiles/Autumn_Weighted_Network_LIMfile.R
@@ -1,16 +1,16 @@
 ! Weighted Network
 ! Network LIM Declaration File
 ! Composed with autoLIMR
-! Author: Gemma Gerber
-! Date: 2023-02-13
+! Author: gemma
+! Date: 2023-06-17
 
 ! Respiration included: Yes
 ! U included: Yes
 
 ! Living compartments: 3
 ! Non-living compartments: 1
-! External compartments: 9
-! Boundary flows: 12
+! External compartments: 7
+! Boundary flows: 10
 ! Internal flows: 6
 
 ! Abbreviations
@@ -38,9 +38,7 @@ DetNLNode = 8000.0
 
 CO2
 DetNLNodeImport
-InvertImport
 PlantImport
-VertImport
 DetNLNodeExport
 InvertExport
 PlantExport
@@ -52,9 +50,9 @@ VertExport
 
 ! Consumption (Q) / Gross Primary Production (GPP) Variables
 
-Invert_Q = Flowto(Invert) - Invert_IM
+Invert_Q = Flowto(Invert)
 Plant_GPP = Flowto(Plant) - Plant_IM
-Vert_Q = Flowto(Vert) - Vert_IM
+Vert_Q = Flowto(Vert)
 
 ! Production (P/NPP) Variables
 
@@ -68,7 +66,6 @@ Invert_U = Flowto(Invert) - Invert_P - Invert_R - Invert_EX
 Plant_U = Flowto(Plant) - Plant_NPP - Plant_R - Plant_EX
 Vert_U = Flowto(Vert) - Vert_P - Vert_R - Vert_EX
 
-! No Assimilation Efficiency (AE) Variables defined
 
 ### END VARIABLES
 
@@ -87,9 +84,7 @@ Vert_R: Vert -> CO2
 ! Import flows
 
 DetNLNode_IM: DetNLNodeImport -> DetNLNode
-Invert_IM: InvertImport -> Invert
 Plant_IM: PlantImport -> Plant
-Vert_IM: VertImport -> Vert
 
 ! Export flows
 
@@ -117,7 +112,7 @@ Plant_GPP > 850
 Plant_GPP < 1700
 Plant_NPP > 0.4*Plant_GPP
 Invert_P > 0.2*Invert_Q
-Vert_P > 0.0002
+Vert_P > 2e-04
 Plant_NPP < 0.9*Plant_GPP
 Invert_P < 0.4*Invert_Q
 Plant_R > 0.2*Plant_NPP
@@ -126,6 +121,12 @@ Vert_R > 0.35
 Plant_R < 0.5*Plant_NPP
 Invert_R < 3*Invert_P
 Vert_R < 0.35
+DetNLNode_IM < 0.1*DetNLNode
+Plant_IM < 0.1*Plant
+DetNLNode_EX < 0.1*DetNLNode
+Plant_EX < 0.1*Plant
+Invert_EX < 0.1*Invert
+Vert_EX < 0.1*Vert
 
 ! Adjacency Matrix Inequalities
 

diff --git a/inst/example_limfiles/Spring_Unweighted_Network_LIMfile.R b/inst/example_limfiles/Spring_Unweighted_Network_LIMfile.R
@@ -2,15 +2,15 @@
 ! Network LIM Declaration File
 ! Composed with autoLIMR
 ! Author: gemma
-! Date: 2023-02-13
+! Date: 2023-06-17
 
 ! Respiration included: Yes
 ! U included: Yes
 
 ! Living compartments: 3
 ! Non-living compartments: 1
-! External compartments: 9
-! Boundary flows: 12
+! External compartments: 7
+! Boundary flows: 10
 ! Internal flows: 6
 
 ! Abbreviations
@@ -38,9 +38,7 @@ DetNLNode = 9000.0
 
 CO2
 DetNLNodeImport
-InvertImport
 PlantImport
-VertImport
 DetNLNodeExport
 InvertExport
 PlantExport
@@ -52,9 +50,9 @@ VertExport
 
 ! Consumption (Q) / Gross Primary Production (GPP) Variables
 
-Invert_Q = Flowto(Invert) - Invert_IM
+Invert_Q = Flowto(Invert)
 Plant_GPP = Flowto(Plant) - Plant_IM
-Vert_Q = Flowto(Vert) - Vert_IM
+Vert_Q = Flowto(Vert)
 
 ! Production (P/NPP) Variables
 
@@ -68,7 +66,6 @@ Invert_U = Flowto(Invert) - Invert_P - Invert_R - Invert_EX
 Plant_U = Flowto(Plant) - Plant_NPP - Plant_R - Plant_EX
 Vert_U = Flowto(Vert) - Vert_P - Vert_R - Vert_EX
 
-! No Assimilation Efficiency (AE) Variables defined
 
 ### END VARIABLES
 
@@ -87,9 +84,7 @@ Vert_R: Vert -> CO2
 ! Import flows
 
 DetNLNode_IM: DetNLNodeImport -> DetNLNode
-Invert_IM: InvertImport -> Invert
 Plant_IM: PlantImport -> Plant
-Vert_IM: VertImport -> Vert
 
 ! Export flows
 

diff --git a/inst/example_limfiles/Spring_Weighted_Network_LIMfile.R b/inst/example_limfiles/Spring_Weighted_Network_LIMfile.R
@@ -1,16 +1,16 @@
 ! Weighted Network
 ! Network LIM Declaration File
 ! Composed with autoLIMR
-! Author: Gemma Gerber
-! Date: 2023-02-13
+! Author: gemma
+! Date: 2023-06-17
 
 ! Respiration included: Yes
 ! U included: Yes
 
 ! Living compartments: 3
 ! Non-living compartments: 1
-! External compartments: 9
-! Boundary flows: 12
+! External compartments: 7
+! Boundary flows: 10
 ! Internal flows: 6
 
 ! Abbreviations
@@ -38,9 +38,7 @@ DetNLNode = 9000.0
 
 CO2
 DetNLNodeImport
-InvertImport
 PlantImport
-VertImport
 DetNLNodeExport
 InvertExport
 PlantExport
@@ -52,9 +50,9 @@ VertExport
 
 ! Consumption (Q) / Gross Primary Production (GPP) Variables
 
-Invert_Q = Flowto(Invert) - Invert_IM
+Invert_Q = Flowto(Invert)
 Plant_GPP = Flowto(Plant) - Plant_IM
-Vert_Q = Flowto(Vert) - Vert_IM
+Vert_Q = Flowto(Vert)
 
 ! Production (P/NPP) Variables
 
@@ -68,7 +66,6 @@ Invert_U = Flowto(Invert) - Invert_P - Invert_R - Invert_EX
 Plant_U = Flowto(Plant) - Plant_NPP - Plant_R - Plant_EX
 Vert_U = Flowto(Vert) - Vert_P - Vert_R - Vert_EX
 
-! No Assimilation Efficiency (AE) Variables defined
 
 ### END VARIABLES
 
@@ -87,9 +84,7 @@ Vert_R: Vert -> CO2
 ! Import flows
 
 DetNLNode_IM: DetNLNodeImport -> DetNLNode
-Invert_IM: InvertImport -> Invert
 Plant_IM: PlantImport -> Plant
-Vert_IM: VertImport -> Vert
 
 ! Export flows
 
@@ -117,7 +112,7 @@ Plant_GPP > 950
 Plant_GPP < 1850
 Plant_NPP > 0.5*Plant_GPP
 Invert_P > 0.3*Invert_Q
-Vert_P > 0.0003
+Vert_P > 3e-04
 Plant_NPP < 1*Plant_GPP
 Invert_P < 0.5*Invert_Q
 Plant_R > 0.3*Plant_NPP

diff --git a/inst/example_limfiles/Summer_Unweighted_Network_LIMfile.R b/inst/example_limfiles/Summer_Unweighted_Network_LIMfile.R
@@ -2,15 +2,15 @@
 ! Network LIM Declaration File
 ! Composed with autoLIMR
 ! Author: gemma
-! Date: 2023-02-13
+! Date: 2023-06-17
 
 ! Respiration included: Yes
 ! U included: Yes
 
 ! Living compartments: 3
 ! Non-living compartments: 1
-! External compartments: 6
-! Boundary flows: 9
+! External compartments: 7
+! Boundary flows: 10
 ! Internal flows: 6
 
 ! Abbreviations
@@ -40,6 +40,7 @@ CO2
 DetNLNodeImport
 PlantImport
 DetNLNodeExport
+InvertExport
 PlantExport
 VertExport
 
@@ -55,17 +56,17 @@ Vert_Q = Flowto(Vert)
 
 ! Production (P/NPP) Variables
 
-Invert_P = Flowfrom(Invert) - Invert_R - Invert_U
+Invert_P = Flowfrom(Invert) - Invert_R - Invert_U - Invert_EX
 Plant_NPP = Flowfrom(Plant) - Plant_R - Plant_U - Plant_EX
 Vert_P = Flowfrom(Vert) - Vert_R - Vert_U - Vert_EX
 
 ! Unused Energy/Material (U) Variables
 
-Invert_U = Flowto(Invert) - Invert_P - Invert_R
+Invert_U = Flowto(Invert) - Invert_P - Invert_R - Invert_EX
 Plant_U = Flowto(Plant) - Plant_NPP - Plant_R - Plant_EX
 Vert_U = Flowto(Vert) - Vert_P - Vert_R - Vert_EX
 
-! Assimilation Efficiency (AE) Variables
+! Assimilation Efficiency (AE) variables
 
 Invert_AE = Invert_P + Invert_R
 Vert_AE = Vert_P + Vert_R
@@ -93,6 +94,7 @@ Plant_IM: PlantImport -> Plant
 
 DetNLNode_EX: DetNLNode -> DetNLNodeExport
 Plant_EX: Plant -> PlantExport
+Invert_EX: Invert -> InvertExport
 Vert_EX: Vert -> VertExport
 
 ! Adjacency Matrix flows