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Source code for stdpopsim.slim_engine

         extended_events = copy.deepcopy(extended_events)
 
     # Reassign event times according to integral SLiM ticks.
-    # This collapses the time deltas used in HomSap/AmericanAdmixture_4B11,
+    # This collapses the time deltas used in HomSap/AmericanAdmixture_4B18,
     # and calculates times for GenerationAfter objects.
     def fix_time(event):
         for attr in ("time", "start_time", "end_time"):
diff --git a/main/_modules/stdpopsim/species.html b/main/_modules/stdpopsim/species.html
index a63df87..48cdbc4 100644
--- a/main/_modules/stdpopsim/species.html
+++ b/main/_modules/stdpopsim/species.html
@@ -82,6 +82,7 @@ 
Source code for stdpopsim.species
 """
 
 import logging
+import warnings
 
 import attr
 
@@ -335,6 +336,17 @@ 
Source code for stdpopsim.species
             right=right,
         )

 
+    def _warn_browning(self, model_id):
+        if model_id == "AmericanAdmixture_4B11":
+            warnings.warn(
+                "In stdpopsim <= 0.2.1, the AmericanAdmixture_4B18 model "
+                "was named AmericanAdmixture_4B11; but since it comes "
+                "from a 2018 paper, this is corrected. The model name "
+                "AmericanAdmixture_4B11 will work for now but is deprecated."
+            )
+            model_id = "AmericanAdmixture_4B18"
+        return model_id
+
 
[docs]    def get_demographic_model(self, id):
         """
         Returns a demographic model with the specified ``id``.
@@ -346,6 +358,8 @@ 
Source code for stdpopsim.species
         :rtype: :class:`DemographicModel`
         :return: A :class:`DemographicModel` that defines the requested model.
         """
+        # TODO: remove this after a release or two. See #841.
+        id = self._warn_browning(id)
         for model in self.demographic_models:
             if model.id == id:
                 return model
diff --git a/main/_sources/tutorial.rst.txt b/main/_sources/tutorial.rst.txt
index 5b05c82..5c21185 100644
--- a/main/_sources/tutorial.rst.txt
+++ b/main/_sources/tutorial.rst.txt
@@ -475,7 +475,7 @@ demographic models are available for humans:
    # OutOfAfrica_3G09
    # OutOfAfrica_2T12
    # Africa_1T12
-   # AmericanAdmixture_4B11
+   # AmericanAdmixture_4B18
    # OutOfAfricaArchaicAdmixture_5R19
    # Zigzag_1S14
    # AncientEurasia_9K19
@@ -1557,8 +1557,8 @@ This prints detailed information about all of the available models to
 the terminal.
 In this tutorial, we will use the model of African-American admixture from
 `Browning et al. (2018) `_.
-From the help output (or the :ref:`Catalog `),
-we can see that this model has id ``AmericanAdmixture_4B11``,
+From the help output (or the :ref:`Catalog `),
+we can see that this model has id ``AmericanAdmixture_4B18``,
 and allows samples to be drawn from 4 contemporary populations representing African,
 European, Asian and African-American groups.
 
@@ -1577,7 +1577,7 @@ To check that we have set up the simulation correctly, we may first wish to perf
 dry run using the ``-D`` option.
 This will print information about the simulation to the terminal:
 
-.. command-output:: stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh38 -d AmericanAdmixture_4B11 AFR:2 EUR:2 ASIA:2 ADMIX:2 -D
+.. command-output:: stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh38 -d AmericanAdmixture_4B18 AFR:2 EUR:2 ASIA:2 ADMIX:2 -D
     :ellipsis: 18
 
 Once we're sure, we can remove the ``-D`` flag to run the simulation
@@ -1586,7 +1586,7 @@ Once we're sure, we can remove the ``-D`` flag to run the simulation
 .. code-block:: console
 
     $ stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh38 \
-    $    -d AmericanAdmixture_4B11 AFR:2 EUR:2 ASIA:2 ADMIX:2
+    $    -d AmericanAdmixture_4B18 AFR:2 EUR:2 ASIA:2 ADMIX:2
 
 2. Calculating divergences
 --------------------------
diff --git a/main/catalog.html b/main/catalog.html
index efa9c51..4dd3268 100644
--- a/main/catalog.html
+++ b/main/catalog.html
@@ -214,7 +214,7 @@
 
  • Three population out-of-Africa
    • 
 
  • Two population out-of-Africa
    • 
 
  • African population
    • 
-
  • American admixture
    • 
+
  • American admixture
    • 
 
  • Three population out-of-Africa with archaic admixture
    • 
 
  • Periodic growth and decline.
    • 
 
  • Multi-population model of ancient Eurasia
    • 
@@ -5776,7 +5776,7 @@ 
    Genome
    Africa_1T12
    
 
    African population
    
 
-
    AmericanAdmixture_4B11
    
+
    AmericanAdmixture_4B18
    
 
    American admixture
    
 
 
    OutOfAfricaArchaicAdmixture_5R19
    
@@ -6265,8 +6265,8 @@ 
    Genome
 
    
-
    
-
    American admixture
    
+
    
+
    American admixture
    
 
    
         Demographic model for American admixture, taken from Browning et al. 2018.
         This model extends the Gravel et al. (2011) model of African/European/Asian
@@ -6281,7 +6281,7 @@ 
    GenomeDetails
    
 
    
 
    ID:
    
-
    AmericanAdmixture_4B11
    
+
    AmericanAdmixture_4B18
    
 
    
 
    Description:
    
 
    American admixture
    
@@ -6427,7 +6427,7 @@ 
    Genome
+_images/sec_catalog_homsap_models_americanadmixture_4b18.png
 
    
 
    
 
    Three population out-of-Africa with archaic admixture
    
diff --git a/main/changelogs.html b/main/changelogs.html
index e70dcb9..888d330 100644
--- a/main/changelogs.html
+++ b/main/changelogs.html
@@ -98,6 +98,9 @@ 
    [0.2.1a] - 2024-07-06
+
  • The 2018 Browning et al HomSap demographic model previously named
+“AmericanAdmixture_4B11” is now named “AmericanAdmixture_4B18”; the old name
+works but throws a deprecation warning. (@petrelharp, #1603)
    • 
 
  • 
 
    The time_units attribute of tree sequence metadata is now set to “generations”
    for SLiM output, avoiding the “time units mismatch warning”.
 (@nspope, #1567)
    
diff --git a/main/cli_arguments.html b/main/cli_arguments.html
index a82dd5a..283486d 100644
--- a/main/cli_arguments.html
+++ b/main/cli_arguments.html
@@ -1866,8 +1866,8 @@ 
    Named ArgumentsDefault: False
    
 
    
 
    -d, --demographic-model
    
-
    Possible choices: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B11, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21
    
-
    Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B11, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21. Please see –help-models for details of these models.
    
+
    Possible choices: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B18, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21
    
+
    Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B18, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21. Please see –help-models for details of these models.
    
 
    
 
    --dfe
    
 
    Possible choices: Gamma_K17, Gamma_H17, LogNormal_H17, Mixed_K23
    
diff --git a/main/objects.inv b/main/objects.inv
index 80fbc88..57d613e 100644
Binary files a/main/objects.inv and b/main/objects.inv differ
diff --git a/main/searchindex.js b/main/searchindex.js
index c0cc89d..c4ff5e9 100644
--- a/main/searchindex.js
+++ b/main/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/main/tutorial.html b/main/tutorial.html
index 4682e3d..3047895 100644
--- a/main/tutorial.html
+++ b/main/tutorial.html
@@ -324,7 +324,7 @@ 
    Choose a model and a sampling scheme# OutOfAfrica_3G09
 # OutOfAfrica_2T12
 # Africa_1T12
-# AmericanAdmixture_4B11
+# AmericanAdmixture_4B18
 # OutOfAfricaArchaicAdmixture_5R19
 # Zigzag_1S14
 # AncientEurasia_9K19
@@ -1602,8 +1602,8 @@ 
    1. Simulating the datasetBrowning et al. (2018).
-From the help output (or the Catalog),
-we can see that this model has id AmericanAdmixture_4B11,
+From the help output (or the Catalog),
+we can see that this model has id AmericanAdmixture_4B18,
 and allows samples to be drawn from 4 contemporary populations representing African,
 European, Asian and African-American groups.
    
 
    Using the --help-genetic-maps option, we can also see what genetic maps
@@ -1640,10 +1640,10 @@ 
    1. Simulating the dataset-D option.
 This will print information about the simulation to the terminal:
    
-
    $ stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh38 -d AmericanAdmixture_4B11 AFR:2 EUR:2 ASIA:2 ADMIX:2 -D
+
    $ stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh38 -d AmericanAdmixture_4B18 AFR:2 EUR:2 ASIA:2 ADMIX:2 -D
 Simulation information:
     Engine: msprime (1.3.3)
-    Model id: AmericanAdmixture_4B11
+    Model id: AmericanAdmixture_4B18
     Model description: American admixture
     Seed: 13
     Population: number_samples (sampling_time_generations):
@@ -1665,7 +1665,7 @@ 
    1. Simulating the dataset-D flag to run the simulation
 (this took around 8 minutes to run on a laptop).
    
 
    $ stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh38 \
-$    -d AmericanAdmixture_4B11 AFR:2 EUR:2 ASIA:2 ADMIX:2
+$    -d AmericanAdmixture_4B18 AFR:2 EUR:2 ASIA:2 ADMIX:2
 
    
 
    
 
    •