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Added examples derived from test cases.
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examples/defaults_asymmetric_migration_changing_rate.resolved.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| { | ||
| "description": "Set migration source and dest using defaults.", | ||
| "time_units": "generations", | ||
| "doi": [], | ||
| "generation_time": 1, | ||
| "demes": [ | ||
| { | ||
| "description": null, | ||
| "start_time": Infinity, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 1, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0, | ||
| "cloning_rate": 0 | ||
| } | ||
| ], | ||
| "proportions": [], | ||
| "ancestors": [] | ||
| }, | ||
| { | ||
| "description": null, | ||
| "start_time": Infinity, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 1, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0, | ||
| "cloning_rate": 0 | ||
| } | ||
| ], | ||
| "proportions": [], | ||
| "ancestors": [] | ||
| } | ||
| ], | ||
| "migrations": [ | ||
| { | ||
| "rate": 1, | ||
| "start_time": 2, | ||
| "end_time": 1, | ||
| "source": "deme0", | ||
| "dest": "deme1" | ||
| }, | ||
| { | ||
| "rate": 0.5, | ||
| "start_time": 1, | ||
| "end_time": 0, | ||
| "source": "deme0", | ||
| "dest": "deme1" | ||
| } | ||
| ], | ||
| "pulses": [] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| description: Set migration source and dest using defaults. | ||
| time_units: generations | ||
| defaults: | ||
| epoch: {start_size: 1} | ||
| migration: {dest: deme1, source: deme0} | ||
|
|
||
| demes: [{id: deme0}, {id: deme1}] | ||
|
|
||
| migrations: | ||
| - {end_time: 1, rate: 1, start_time: 2} | ||
| - {end_time: 0, rate: 0.5, start_time: 1} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| { | ||
| "description": "Setting deme ancestor and proportion values using defaults.", | ||
| "time_units": "generations", | ||
| "doi": [], | ||
| "generation_time": 1, | ||
| "demes": [ | ||
| { | ||
| "description": null, | ||
| "start_time": 2, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 1, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0, | ||
| "cloning_rate": 0 | ||
| } | ||
| ], | ||
| "proportions": [], | ||
| "ancestors": [] | ||
| }, | ||
| { | ||
| "description": null, | ||
| "start_time": 2, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 1, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0, | ||
| "cloning_rate": 0 | ||
| } | ||
| ], | ||
| "proportions": [], | ||
| "ancestors": [] | ||
| }, | ||
| { | ||
| "description": null, | ||
| "start_time": 1, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 1, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0, | ||
| "cloning_rate": 0 | ||
| } | ||
| ], | ||
| "proportions": [ | ||
| 0.5, | ||
| 0.5 | ||
| ], | ||
| "ancestors": [ | ||
| "deme0", | ||
| "deme1" | ||
| ] | ||
| }, | ||
| { | ||
| "description": null, | ||
| "start_time": 1, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 1, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0, | ||
| "cloning_rate": 0 | ||
| } | ||
| ], | ||
| "proportions": [ | ||
| 0.5, | ||
| 0.5 | ||
| ], | ||
| "ancestors": [ | ||
| "deme0", | ||
| "deme1" | ||
| ] | ||
| } | ||
| ], | ||
| "migrations": [], | ||
| "pulses": [] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| description: Setting deme ancestor and proportion values using defaults. | ||
| time_units: generations | ||
|
|
||
| defaults: | ||
| deme: | ||
| ancestors: [deme0, deme1] | ||
| proportions: [0.5, 0.5] | ||
| start_time: 1 | ||
| epoch: {start_size: 1} | ||
|
|
||
| demes: | ||
| # Two ancestor demes. We must set the ancestor and proportion values | ||
| # explicitly to the empty list because the defaults fields override | ||
| # the static defaults from the schema. | ||
| - id: deme0 | ||
| ancestors: [] | ||
| proportions: [] | ||
| start_time: 2 | ||
| - ancestors: [] | ||
| id: deme1 | ||
| proportions: [] | ||
| start_time: 2 | ||
| # Two child demes, both of which inherit from deme0 and deme1, as set | ||
| # by the defaults. | ||
| - id: deme2 | ||
| - id: deme3 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| { | ||
| "description": "Set epoch values using global defaults.", | ||
| "time_units": "generations", | ||
| "doi": [], | ||
| "generation_time": 1, | ||
| "demes": [ | ||
| { | ||
| "description": null, | ||
| "start_time": Infinity, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 3, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| }, | ||
| { | ||
| "end_time": 2, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| }, | ||
| { | ||
| "end_time": 1, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| }, | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| } | ||
| ], | ||
| "proportions": [], | ||
| "ancestors": [] | ||
| } | ||
| ], | ||
| "migrations": [], | ||
| "pulses": [] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| description: Set epoch values using global defaults. | ||
| time_units: generations | ||
|
|
||
| defaults: | ||
| epoch: {cloning_rate: 0.5, end_size: 2, selfing_rate: 0.1, start_size: 1} | ||
|
|
||
| demes: | ||
| - id: deme0 | ||
| epochs: | ||
| - {end_time: 3} | ||
| - {end_time: 2} | ||
| - {end_time: 1} | ||
| - {end_time: 0} | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| { | ||
| "description": "Set epoch defaults using deme-local values.", | ||
| "time_units": "generations", | ||
| "doi": [], | ||
| "generation_time": 1, | ||
| "demes": [ | ||
| { | ||
| "description": null, | ||
| "start_time": Infinity, | ||
| "epochs": [ | ||
| { | ||
| "end_time": 3, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| }, | ||
| { | ||
| "end_time": 2, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| }, | ||
| { | ||
| "end_time": 1, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| }, | ||
| { | ||
| "end_time": 0, | ||
| "start_size": 1, | ||
| "end_size": 2, | ||
| "size_function": "exponential", | ||
| "selfing_rate": 0.1, | ||
| "cloning_rate": 0.5 | ||
| } | ||
| ], | ||
| "proportions": [], | ||
| "ancestors": [] | ||
| } | ||
| ], | ||
| "migrations": [], | ||
| "pulses": [] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| description: Set epoch defaults using deme-local values. | ||
| time_units: generations | ||
|
|
||
| demes: | ||
| - id: deme0 | ||
| defaults: | ||
| epoch: {cloning_rate: 0.5, end_size: 2, selfing_rate: 0.1, start_size: 1} | ||
| epochs: | ||
| - {end_time: 3} | ||
| - {end_time: 2} | ||
| - {end_time: 1} | ||
| - {end_time: 0} | ||
|
|
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