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Support for v2.23 emod release (#6)
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* support for new emod release emod-malaria v0.0.72

* support for per-species migration

* support for MosquitoRelease parameter changes: Fraction to Ratio

* support for new Blood_Meal_Mortality parameter

* small improvements and updates


Co-authored-by: Bridenbecker <[email protected]>
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@stitova-idm @Bridenbecker
stitova-idm and Bridenbecker authored Oct 31, 2024
1 parent a985081 commit f6c5905
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6 changes: 3 additions & 3 deletions docs/csv/campaign-mosquitorelease.csv
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Expand Up @@ -27,11 +27,11 @@
""New_Property_Value"": ""HasHealthCare:YES""
}
"
"Released_Fraction","float","0","1","0","The fraction of the current population of mosquitoes to relEase (the population from the previous time step) The population depends on the gender of the mosquitoes being released. This depends on Released_Type being set to FRACTION.",".. code-block:: json
"Released_Ratio","float","0","3.40E+038","0","The number of released mosquitoes is proportional to the mosquito population from the previous timestep, specifically considering mosquitoes of the same gender as those being released. This approach is used when on Released_Type is set to RATIO.",".. code-block:: json

{
""Released_type"": ""FRACTION"",
""Released_Fraction"": 0.4
""Released_type"": ""RATIO"",
""Released_Ratio"": 0.4
}
"
"Released_Genome","array of strings","NA","NA","[]","This defines the alleles of the genome of the vectors to be released. It must define all of the alleles including the gender gene. '*' is not allowed. See **Vector_Species_Params** for more information.",".. code-block:: json
Expand Down
95 changes: 46 additions & 49 deletions docs/csv/config-migration-malaria.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -72,33 +72,6 @@
""Sea_Migration_Filename"": ""../inputs/sea_migration.bin""
}
"
"Enable_Vector_Migration","boolean","0","1","0","Controls whether or not vectors can migrate. **Vector_Sampling_Type** must be set to TRACK_ALL_VECTORS or SAMPLE_IND_VECTORS. Specific migration types must be enabled or disabled. ",".. code-block:: json

{
""Vector_Sampling_Type"": ""TRACK_ALL_VECTORS"",
""Enable_Vector_Migration"": 1,
""Enable_Vector_Migration_Local"": 1,
""Vector_Migration_Filename_Local"": ""../inputs/vector_local.bin""
}
"
"Enable_Vector_Migration_Local","boolean","0","1","0","Controls whether or not vectors may migrate to adjacent nodes. **Enable_Vector_Migration** must be set to true (1). ",".. code-block:: json

{
""Vector_Sampling_Type"": ""TRACK_ALL_VECTORS"",
""Enable_Vector_Migration"": 1,
""Enable_Vector_Migration_Local"": 1,
""Vector_Migration_Filename_Local"": ""../inputs/vector_local.bin""
}
"
"Enable_Vector_Migration_Regional","boolean","0","1","0","Controls whether or not vectors can migration to non-adjacent nodes. **Enable_Vector_Migration** must be set to true (1).",".. code-block:: json

{
""Vector_Sampling_Type"": ""TRACK_ALL_VECTORS"",
""Enable_Vector_Migration"": 1,
""Enable_Vector_Migration_Regional"": 1,
""Vector_Migration_Filename_Regional"": ""../inputs/vector_regional.bin""
}
"
"Family_Migration_Filename","string","NA","NA","""""","The name of the binary file to use to configure family migration. **Enable_Family_Migration** must be set to true (1). See :doc:`software-migration` for information on migration files.",".. code-block:: json

{
Expand Down Expand Up @@ -213,43 +186,66 @@ WAYPOINTS_HOME
""Sea_Migration_Roundtrip_Probability"": 0
}
"
"Vector_Migration_Filename_Local","string","NA","NA","UNSPECIFIED_FILE","The path to the vector migration file which defines patterns of vector migration to adjacent nodes. **Enable_Vector_Migration** must be set to 1. The file must be in .bin format.",".. code-block:: json
"Vector_Migration_Filename","string","NA","NA","","The path to the vector migration file which defines patterns of vector migration to other nodes. The file must be in .bin format.",".. code-block:: json

{
""Vector_Migration_Filename_Local"": ""5x5_Households_Local_Vector_Migration.bin""
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Filename"": ""5x5_Households_Local_Vector_Migration.bin""
}
]
}
"
"Vector_Migration_Filename_Regional","string","NA","NA","UNSPECIFIED_FILE","The path to the vector migration file which defines patterns of vector migration to non-adjacent nodes. **Enable_Vector_Migration** must be set to 1. The file must be in .bin format.",".. code-block:: json

{
""Vector_Migration_Filename_Regional"": ""5x5_Households_Regional_Vector_Migration.bin""
}
"
"Vector_Migration_Food_Modifier","float","0","3.40E+38","0","The preference of a vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Used only when **Vector_Sampling_Type** is set to TRACK_ALL_VECTORS. **Enable_Vector_Migration** must be set to 1. ",".. code-block:: json
"Vector_Migration_Food_Modifier","float","0","3.40E+38","0","The preference of a female vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Only affects female vector migration. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""Vector_Migration_Food_Modifier"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Food_Modifier"": 1.0
}
]
}
"
"Vector_Migration_Habitat_Modifier","float","0","3.40E+38","0","The preference of a vector to migrate toward a node with more habitat. Only used when **Vector_Sampling_Type** is set to TRACK_ALL_VECTORS. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json
"Vector_Migration_Habitat_Modifier","float","0","3.40E+38","0","The preference of a female vector to migrate toward a node with more habitat. Only affects female vector migration. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""Vector_Migration_Habitat_Modifier"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Habitat_Modifier"": 1.0
}
]
}
"
"Vector_Migration_Modifier_Equation","enum","NA","NA","LINEAR","The functional form of vector migration modifiers. **Enable_Vector_Migration** must be set to 1.
"Vector_Migration_Modifier_Equation","enum","NA","NA","LINEAR","The functional form of female vector migration modifiers. **Vector_Migration_Filename** must be defined.
Possible values are:
LINEAR
EXPONENTIAL",".. code-block:: json

{
""Vector_Migration_Modifier_Equation"": ""EXPONENTIAL""
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Modifier_Equation"": ""EXPONENTIAL"",
""Vector_Migration_Habitat_Modifier"": 1.0,
""Vector_Migration_Food_Modifier"": 1.0,
""Vector_Migration_Stay_Put_Modifier"": 1.0
}
]
}
"
"Vector_Migration_Stay_Put_Modifier","float","0","3.40E+38","0","The preference of a vector to remain in its current node rather than migrate to another node. Used only when **Vector_Sampling_Type** is set to TRACK_ALL_VECTORS. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json
"Vector_Migration_Stay_Put_Modifier","float","0","3.40E+38","0","The preference of a female vector to remain in its current node rather than migrate to another node. Only affects female vector migration. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""Vector_Migration_Stay_Put_Modifier"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Stay_Put_Modifier"": 1.0
}
]
}
"
"x_Air_Migration","float","0","3.40E+38","1","Scale factor for the rate of migration by air, as provided by the migration file. **Enable_Air_Migration** must be set to 1.",".. code-block:: json
Expand Down Expand Up @@ -282,15 +278,16 @@ EXPONENTIAL",".. code-block:: json
""x_Sea_Migration"": 1
}
"
"x_Vector_Migration_Local","float","0","3.40E+38","1","Scale factor for the rate of vector migration to adjacent nodes, as provided by the vector migration file. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json
"x_Vector_Migration","float","0","3.40E+38","1","Scale factor for the rate of vector migration to other nodes, as provided by the vector migration file. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""x_Vector_Migration_Local"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Filename"": ""5x5_Households_Local_Vector_Migration.bin"",
""x_Vector_Migration"": 1.0
}
]
}
"
"x_Vector_Migration_Regional","float","0","3.40E+38","1","Scale factor for the rate of vector migration to non-adjacent nodes, as provided by the vector migration file. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json

{
""x_Vector_Migration_Regional"": 1.0
}
"
166 changes: 44 additions & 122 deletions docs/csv/config-scalars-malaria.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -112,30 +112,8 @@ ANNUAL_BOXCAR_FUNCTION
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Acquire_Modifier"": 0.2,
""Adult_Life_Expectancy"": 20,
""Anthropophily"": 0.65,
""Aquatic_Arrhenius_1"": 84200000000,
""Aquatic_Arrhenius_2"": 8328,
""Aquatic_Mortality_Rate"": 0.1,
""Days_Between_Feeds"": 3,
""Egg_Batch_Size"": 100,
""Habitats"": [
{
""Habitat_Type"": ""TEMPORARY_RAINFALL"",
""Max_Larval_Capacity"": 11250000000
}
],
""Immature_Duration"": 2,
""Indoor_Feeding_Fraction"": 1,
""Infected_Arrhenius_1"": 117000000000,
""Infected_Arrhenius_2"": 8336,
""Infected_Egg_Batch_Factor"": 0.8,
""Infectious_Human_Feed_Mortality_Factor"": 1.5,
""Male_Life_Expectancy"": 10,
""Temperature_Dependent_Feeding_Cycle"": ""NO_TEMPERATURE_DEPENDENCE"",
""Transmission_Rate"": 0.5,
""Vector_Sugar_Feeding_Frequency"": ""VECTOR_SUGAR_FEEDING_NONE""
""Infected_Arrhenius_2"": 8336
}
]
}
Expand All @@ -146,30 +124,8 @@ ANNUAL_BOXCAR_FUNCTION
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Acquire_Modifier"": 0.2,
""Adult_Life_Expectancy"": 20,
""Anthropophily"": 0.65,
""Aquatic_Arrhenius_1"": 84200000000,
""Aquatic_Arrhenius_2"": 8328,
""Aquatic_Mortality_Rate"": 0.1,
""Days_Between_Feeds"": 3,
""Egg_Batch_Size"": 100,
""Habitats"": [
{
""Habitat_Type"": ""TEMPORARY_RAINFALL"",
""Max_Larval_Capacity"": 11250000000
}
],
""Immature_Duration"": 2,
""Indoor_Feeding_Fraction"": 1,
""Infected_Arrhenius_1"": 117000000000,
""Infected_Arrhenius_2"": 8336,
""Infected_Egg_Batch_Factor"": 0.8,
""Infectious_Human_Feed_Mortality_Factor"": 1.5,
""Male_Life_Expectancy"": 10,
""Temperature_Dependent_Feeding_Cycle"": ""NO_TEMPERATURE_DEPENDENCE"",
""Transmission_Rate"": 0.5,
""Vector_Sugar_Feeding_Frequency"": ""VECTOR_SUGAR_FEEDING_NONE""
""Infected_Arrhenius_2"": 8336
}
]
}
Expand All @@ -180,64 +136,7 @@ ANNUAL_BOXCAR_FUNCTION
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Acquire_Modifier"": 0.2,
""Adult_Life_Expectancy"": 20,
""Anthropophily"": 0.65,
""Aquatic_Arrhenius_1"": 84200000000,
""Aquatic_Arrhenius_2"": 8328,
""Aquatic_Mortality_Rate"": 0.1,
""Days_Between_Feeds"": 3,
""Egg_Batch_Size"": 100,
""Habitats"": [
{
""Habitat_Type"": ""TEMPORARY_RAINFALL"",
""Max_Larval_Capacity"": 11250000000
}
],
""Immature_Duration"": 2,
""Indoor_Feeding_Fraction"": 1,
""Infected_Arrhenius_1"": 117000000000,
""Infected_Arrhenius_2"": 8336,
""Infected_Egg_Batch_Factor"": 0.8,
""Infectious_Human_Feed_Mortality_Factor"": 1.5,
""Male_Life_Expectancy"": 10,
""Temperature_Dependent_Feeding_Cycle"": ""NO_TEMPERATURE_DEPENDENCE"",
""Transmission_Rate"": 0.5,
""Vector_Sugar_Feeding_Frequency"": ""VECTOR_SUGAR_FEEDING_NONE""
}
]
}
"
"Infectious_Human_Feed_Mortality_Factor","float","0","1000","1.5","The (dimensionless) factor used to modify the death rate of mosquitoes when feeding on humans, to account for the higher mortality rate infected mosquitoes experience during human feeds versus uninfected mosquitoes. ",".. code-block:: json

{
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Acquire_Modifier"": 0.2,
""Adult_Life_Expectancy"": 20,
""Anthropophily"": 0.65,
""Aquatic_Arrhenius_1"": 84200000000,
""Aquatic_Arrhenius_2"": 8328,
""Aquatic_Mortality_Rate"": 0.1,
""Days_Between_Feeds"": 3,
""Egg_Batch_Size"": 100,
""Habitats"": [
{
""Habitat_Type"": ""TEMPORARY_RAINFALL"",
""Max_Larval_Capacity"": 11250000000
}
],
""Immature_Duration"": 2,
""Indoor_Feeding_Fraction"": 1,
""Infected_Arrhenius_1"": 117000000000,
""Infected_Arrhenius_2"": 8336,
""Infected_Egg_Batch_Factor"": 0.8,
""Infectious_Human_Feed_Mortality_Factor"": 1.5,
""Male_Life_Expectancy"": 10,
""Temperature_Dependent_Feeding_Cycle"": ""NO_TEMPERATURE_DEPENDENCE"",
""Transmission_Rate"": 0.5,
""Vector_Sugar_Feeding_Frequency"": ""VECTOR_SUGAR_FEEDING_NONE""
""Infectious_Human_Feed_Mortality_Factor"": 1.5
}
]
}
Expand Down Expand Up @@ -305,31 +204,54 @@ FIXED_SCALING
""Post_Infection_Transmission_Multiplier"": 0.9
}
"
"Vector_Migration_Food_Modifier","float","0","3.40E+38","0","The preference of a vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Used only when **Vector_Sampling_Type** is set to TRACK_ALL_VECTORS. **Enable_Vector_Migration** must be set to 1. ",".. code-block:: json
"Vector_Migration_Food_Modifier","float","0","3.40E+38","0","The preference of a female vector to migrate toward a node currently occupied by humans, independent of the number of humans in the node. Only affects female vector migration. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""Vector_Migration_Food_Modifier"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Food_Modifier"": 1.0
}
]
}
"
"Vector_Migration_Habitat_Modifier","float","0","3.40E+38","0","The preference of a vector to migrate toward a node with more habitat. Only used when **Vector_Sampling_Type** is set to TRACK_ALL_VECTORS. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json
"Vector_Migration_Habitat_Modifier","float","0","3.40E+38","0","The preference of a female vector to migrate toward a node with more habitat. Only affects female vector migration. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""Vector_Migration_Habitat_Modifier"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Habitat_Modifier"": 1.0
}
]
}
"
"Vector_Migration_Modifier_Equation","enum","NA","NA","LINEAR","The functional form of vector migration modifiers. **Enable_Vector_Migration** must be set to 1.
Possible values are:
LINEAR
"Vector_Migration_Modifier_Equation","enum","NA","NA","LINEAR","The functional form of female vector migration modifiers. **Vector_Migration_Filename** must be defined.
Possible values are:
LINEAR
EXPONENTIAL",".. code-block:: json

{
""Vector_Migration_Modifier_Equation"": ""EXPONENTIAL""
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Modifier_Equation"": ""EXPONENTIAL"",
""Vector_Migration_Habitat_Modifier"": 1.0,
""Vector_Migration_Food_Modifier"": 1.0,
""Vector_Migration_Stay_Put_Modifier"": 1.0
}
]
}
"
"Vector_Migration_Stay_Put_Modifier","float","0","3.40E+38","0","The preference of a vector to remain in its current node rather than migrate to another node. Used only when **Vector_Sampling_Type** is set to TRACK_ALL_VECTORS. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json
"Vector_Migration_Stay_Put_Modifier","float","0","3.40E+38","0","The preference of a female vector to remain in its current node rather than migrate to another node. Only affects female vector migration. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""Vector_Migration_Stay_Put_Modifier"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Stay_Put_Modifier"": 1.0
}
]
}
"
"x_Air_Migration","float","0","3.40E+38","1","Scale factor for the rate of migration by air, as provided by the migration file. **Enable_Air_Migration** must be set to 1.",".. code-block:: json
Expand Down Expand Up @@ -386,15 +308,15 @@ EXPONENTIAL",".. code-block:: json
""x_Temporary_Larval_Habitat"": 1
}
"
"x_Vector_Migration_Local","float","0","3.40E+38","1","Scale factor for the rate of vector migration to adjacent nodes, as provided by the vector migration file. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json

{
""x_Vector_Migration_Local"": 1.0
}
"
"x_Vector_Migration_Regional","float","0","3.40E+38","1","Scale factor for the rate of vector migration to non-adjacent nodes, as provided by the vector migration file. **Enable_Vector_Migration** must be set to 1.",".. code-block:: json
"x_Vector_Migration","float","0","3.40E+38","1","Scale factor for the rate of vector migration to other nodes, as provided by the vector migration file. **Vector_Migration_Filename** must be defined. ",".. code-block:: json

{
""x_Vector_Migration_Regional"": 1.0
""Vector_Species_Params"": [
{
""Name"": ""arabiensis"",
""Vector_Migration_Filename"": ""5x5_Households_Local_Vector_Migration.bin"",
""x_Vector_Migration"": 1.0
}
]
}
"
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