From 9d40b61f8336ec69235d1adf5869baaaf2b9bd1e Mon Sep 17 00:00:00 2001 From: PopSim-bot Date: Wed, 1 Nov 2023 02:26:40 +0000 Subject: [PATCH] Automated doc build for refs/heads/main --- main/.buildinfo | 2 +- ...8e22ebf67ac88f63d3d7ab1d32fd8b10b4f289.svg | 22055 +++++++++++++++ ...2341ee2ff277fc991ebf89a4356f123f18ddf0.svg | 14385 ---------- ...2b0734154d3433d4232b8ad36f112069cedbde.svg | 14385 ++++++++++ ...f67cf258ae2367aa951931171f1e529d399fe.svg} | 28 +- ...55d3c89a6097c45128df21b24aa4058650f64d.svg | 22175 ---------------- main/api.html | 382 +- main/introduction.html | 2 +- main/quickstart.html | 4 +- 9 files changed, 36649 insertions(+), 36769 deletions(-) create mode 100644 main/_images/6caa213d29b7e47d8e9868ca058e22ebf67ac88f63d3d7ab1d32fd8b10b4f289.svg delete mode 100644 main/_images/9dbe811fdf798e166aafd4bbe02341ee2ff277fc991ebf89a4356f123f18ddf0.svg create mode 100644 main/_images/a9a28f0b7928223c5a005ea0962b0734154d3433d4232b8ad36f112069cedbde.svg rename main/_images/{612c4c300a2808c20b427d4e262175e1070dc2dbe9dd7082b1f7baacdfd590de.svg => d5b6aa8d1c32679000a4471fd60f67cf258ae2367aa951931171f1e529d399fe.svg} (95%) delete mode 100644 main/_images/e9bba2c165aa0c95f1082b473c55d3c89a6097c45128df21b24aa4058650f64d.svg diff --git a/main/.buildinfo b/main/.buildinfo index 82cd17b..dc656f4 100644 --- a/main/.buildinfo +++ b/main/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: fcd32ce65ef48eead3aef817ecda61ba +config: 521e35a383e1b59ae4b55a29fc4e677e tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/main/_images/6caa213d29b7e47d8e9868ca058e22ebf67ac88f63d3d7ab1d32fd8b10b4f289.svg b/main/_images/6caa213d29b7e47d8e9868ca058e22ebf67ac88f63d3d7ab1d32fd8b10b4f289.svg new file mode 100644 index 0000000..d4566cd --- /dev/null +++ b/main/_images/6caa213d29b7e47d8e9868ca058e22ebf67ac88f63d3d7ab1d32fd8b10b4f289.svg @@ -0,0 +1,22055 @@ + + + + + + + + 2023-11-01T02:26:29.736717 + image/svg+xml + + + Matplotlib v3.8.1, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/main/_images/9dbe811fdf798e166aafd4bbe02341ee2ff277fc991ebf89a4356f123f18ddf0.svg b/main/_images/9dbe811fdf798e166aafd4bbe02341ee2ff277fc991ebf89a4356f123f18ddf0.svg deleted file mode 100644 index ef0ef5d..0000000 --- a/main/_images/9dbe811fdf798e166aafd4bbe02341ee2ff277fc991ebf89a4356f123f18ddf0.svg +++ /dev/null @@ -1,14385 +0,0 @@ - - - - - - - - 2023-09-01T03:05:02.412007 - image/svg+xml - - - Matplotlib v3.7.2, https://matplotlib.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - 2023-09-01T03:04:59.724499 - image/svg+xml - - - Matplotlib v3.7.2, https://matplotlib.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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Loading and saving Demes graphs
Parameters:
    -

  • filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object +

  • filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object with a read() method.

    • -

  • format (str) – The format of the input file. Either “yaml” or “json”.

    • +

  • format (str) – The format of the input file. Either “yaml” or “json”.

Returns:
@@ -212,9 +212,9 @@

Loading and saving Demes graphs
Parameters:
    -

  • filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object +

  • filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object with a read() method.

    • -

  • format (str) – The format of the input file. Either “yaml” or “json”.

    • +

  • format (str) – The format of the input file. Either “yaml” or “json”.

Returns:
@@ -222,7 +222,7 @@

Loading and saving Demes graphsReturn type: -

dict

+

dict

@@ -236,8 +236,8 @@

Loading and saving Demes graphs
Parameters:
    -

  • string (str) – The string to be loaded.

    • -

  • format (str) – The format of the input string. Either “yaml” or “json”.

    • +

  • string (str) – The string to be loaded.

    • +

  • format (str) – The format of the input string. Either “yaml” or “json”.

Returns:
@@ -260,8 +260,8 @@

Loading and saving Demes graphs
Parameters:
    -

  • string (str) – The string to be loaded.

    • -

  • format (str) – The format of the input string. Either “yaml” or “json”.

    • +

  • string (str) – The string to be loaded.

    • +

  • format (str) – The format of the input string. Either “yaml” or “json”.

Returns:
@@ -269,7 +269,7 @@

Loading and saving Demes graphsReturn type: -

dict

+

dict

@@ -283,7 +283,7 @@

Loading and saving Demes graphsSpecification.

Parameters:
-

filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object +

filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object with a read() method.

Returns:
@@ -305,10 +305,10 @@

Loading and saving Demes graphsParameters:

  • graph (demes.Graph) – The graph to dump.

    • -

  • filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a +

  • filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a write() method.

    • -

  • format (str) – The format of the output file. Either “yaml” or “json”.

    • -

  • simplified (bool) – If True, the output file follows the Human Data Model, +

  • format (str) – The format of the output file. Either “yaml” or “json”.

    • +

  • simplified (bool) – If True, the output file follows the Human Data Model, which has many fields omitted and is thus more compact. If False, the output file is fully-resolved and follows the Machine Data Model.

    • @@ -327,8 +327,8 @@

    Loading and saving Demes graphsParameters:

    • graph (demes.Graph) – The graph to dump.

      • -

    • format (str) – The format of the output file. Either “yaml” or “json”.

      • -

    • simplified (bool) – If True, returns a string following the Human Data Model, +

    • format (str) – The format of the output file. Either “yaml” or “json”.

      • +

    • simplified (bool) – If True, returns a string following the Human Data Model, which has many fields omitted and is thus more compact. If False, returns a string that is fully-resolved following the Machine Data Model.

      • @@ -338,7 +338,7 @@

      Loading and saving Demes graphs

      The YAML or JSON string.

    Return type:
    -

    str

    +

    str

@@ -351,9 +351,9 @@

Loading and saving Demes graphsParameters:

  • graphs – An iterable of graphs to dump.

    • -

  • filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a +

  • filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a write() method.

    • -

  • simplified (bool) – If True, the output file follows the Human Data Model, +

  • simplified (bool) – If True, the output file follows the Human Data Model, which has many fields omitted and is thus more compact. If False, the output file is fully-resolved and follows the Machine Data Model.

    • @@ -377,7 +377,7 @@

    Building Demes graphsGraph object using the resolve() method.

    Variables:
    -

    data (dict) –

    The data dictionary of the demographic model’s current state. +

    data (dict) –

    The data dictionary of the demographic model’s current state. The objects nested within this dictionary should follow Demes’ data model, as described in the Human Data Model schema.

    @@ -395,16 +395,16 @@

    Building Demes graphs
    Parameters:
      -

    • description (str) – A human readable description of the demography.

      • -

    • time_units (str) – The units of time used for the demography. This is +

    • description (str) – A human readable description of the demography.

      • +

    • time_units (str) – The units of time used for the demography. This is commonly years or generations, but can be any string.

      • -

    • generation_time (float) – The generation time of demes, in units given +

    • generation_time (float) – The generation time of demes, in units given by the time_units parameter.

      • -

    • doi (list[str]) – If the graph describes a published demography, the DOI(s) +

    • doi (list[str]) – If the graph describes a published demography, the DOI(s) should be be given here as a list.

      • -

    • defaults (dict) – A dictionary of default values, following the +

    • defaults (dict) – A dictionary of default values, following the Human Data Model schema for defaults.

      • -

    • metadata (dict) – A dictionary of arbitrary additional data.

      • +

    • metadata (dict) – A dictionary of arbitrary additional data.

    @@ -419,15 +419,15 @@

    Building Demes graphs
    Parameters:
      -

    • name (str) – A string identifier for the deme.

      • -

    • description (str) – A description of the deme.

      • -

    • ancestors (list[str]) – List of deme names for the deme’s ancestors.

      • -

    • proportions (list[float]) – The proportions of ancestry from each ancestor. +

    • name (str) – A string identifier for the deme.

      • +

    • description (str) – A description of the deme.

      • +

    • ancestors (list[str]) – List of deme names for the deme’s ancestors.

      • +

    • proportions (list[float]) – The proportions of ancestry from each ancestor. This list has the same length as ancestors, and must sum to 1.

      • -

    • start_time (float) – The deme’s start time.

      • -

    • epochs (list[dict]) – List of epoch dictionaries. Each dictionary +

    • start_time (float) – The deme’s start time.

      • +

    • epochs (list[dict]) – List of epoch dictionaries. Each dictionary follows the Human Data Model schema for an epoch object.

      • -

    • defaults (dict) – A dictionary of default deme values, following the +

    • defaults (dict) – A dictionary of default deme values, following the Human Data Model schema for deme defaults.

    @@ -452,15 +452,15 @@

    Building Demes graphs
    Parameters:
      -

    • demes (list[str]) – List of deme names. If specified, migration is symmetric +

    • demes (list[str]) – List of deme names. If specified, migration is symmetric between all pairs of demes in this list.

      • -

    • source (str) – The name of the source deme. If specified, migration is asymmetric +

    • source (str) – The name of the source deme. If specified, migration is asymmetric from this deme.

      • -

    • dest (str) – The name of the destination deme. If specified, migration is +

    • dest (str) – The name of the destination deme. If specified, migration is asymmetric into this deme.

      • -

    • rate (float) – The rate of migration per generation.

      • -

    • start_time (float) – The time at which the migration rate is enabled.

      • -

    • end_time (float) – The time at which the migration rate is disabled.

      • +

    • rate (float) – The rate of migration per generation.

      • +

    • start_time (float) – The time at which the migration rate is enabled.

      • +

    • end_time (float) – The time at which the migration rate is disabled.

    @@ -478,12 +478,12 @@

    Building Demes graphs
    Parameters:
      -

    • sources (list(str)) – A list of names of the source deme(s).

      • -

    • dest (str) – The name of the destination deme.

      • -

    • proportion (list(float)) – At the instant after migration, this is the expected proportion(s) +

    • sources (list(str)) – A list of names of the source deme(s).

      • +

    • dest (str) – The name of the destination deme.

      • +

    • proportion (list(float)) – At the instant after migration, this is the expected proportion(s) of individuals in the destination deme made up of individuals from the source deme(s).

      • -

    • time (float) – The time at which migrations occur.

      • +

    • time (float) – The time at which migrations occur.

    @@ -547,21 +547,21 @@

    Working with Demes graphs
    Variables:
      -

    • description (str) – A human readable description of the demography.

      • -

    • time_units (str) – The units of time used for the demography. This is +

    • description (str) – A human readable description of the demography.

      • +

    • time_units (str) – The units of time used for the demography. This is commonly years or generations, but can be any string. This field is intended to be useful for documenting a demography, but the actual value provided here should not be relied upon.

      • -

    • generation_time (float) – The generation time of demes, in units given +

    • generation_time (float) – The generation time of demes, in units given by the time_units parameter. Concretely, dividing all times by generation_time will convert the graph to have time units in generations. See also: in_generations().

      • -

    • doi (list[str]) – A list of publications that describe the demographic model.

      • -

    • metadata (dict) – A dictionary of arbitrary additional data.

      • -

    • demes (list[Deme]) – The demes in the demographic model.

      • -

    • migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.

      • -

    • pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.

      • +

    • doi (list[str]) – A list of publications that describe the demographic model.

      • +

    • metadata (dict) – A dictionary of arbitrary additional data.

      • +

    • demes (list[Deme]) – The demes in the demographic model.

      • +

    • migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.

      • +

    • pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.

    @@ -576,10 +576,10 @@

    Working with Demes graphs
    Parameters:
    -

    deme_name (str) – The name of the deme.

    +

    deme_name (str) – The name of the deme.

    Return type:
    -

    bool

    +

    bool

    Returns:

    True if the deme is in the graph, False otherwise.

    @@ -598,7 +598,7 @@

    Working with Demes graphs
    Parameters:
    -

    deme_name (str) – The name of the deme.

    +

    deme_name (str) – The name of the deme.

    Return type:

    Deme

    @@ -618,7 +618,7 @@

    Working with Demes graphs

    A data dictionary following the Machine Data Model.

    Return type:
    -

    dict

    +

    dict

    @@ -632,7 +632,7 @@

    Working with Demes graphs

    A data dictionary following the Human Data Model.

Return type:
-

dict

+

dict

@@ -656,10 +656,10 @@

Working with Demes graphsParameters:

  • other (Graph) – The graph to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose().

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -690,7 +690,7 @@

Working with Demes graphsMerge, and Admix objects.

Return type:
-

dict[str, list]

+

dict[str, list]

@@ -701,7 +701,7 @@

Working with Demes graphs
Parameters:
-

data (dict) – A data dictionary following either the +

data (dict) – A data dictionary following either the Human Data Model or the Machine Data Model.

Returns:
@@ -732,7 +732,7 @@

Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]

Returns true if the graph and other implement essentially the same demographic model. Numerical values are compared using the -math.isclose() function, from which this method takes its name. +math.isclose() function, from which this method takes its name. Furthermore, the following implementation details are ignored during the comparison:

@@ -747,17 +747,17 @@

Working with Demes graphsParameters:

  • other (Graph) – The graph to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose().

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two graphs implement the same model, False otherwise.

Return type:
-

bool

+

bool

@@ -807,7 +807,7 @@

Working with Demes graphsend_times are a list of end times for each matrix.

Return type:
-

tuple[list[list[list[float]]], list[float]]

+

tuple[list[list[list[float]]], list[float]]

@@ -831,7 +831,7 @@

Working with Demes graphs

A NetworkX compatible dict-of-lists graph of the demes’ predecessors.

Return type:
-

dict[str, list[str]]

+

dict[str, list[str]]

@@ -842,7 +842,7 @@

Working with Demes graphs
Parameters:
-

names (dict) – A dictionary with deme names and new names.

+

names (dict) – A dictionary with deme names and new names.

Returns:

A demographic model with renamed demes.

@@ -872,7 +872,7 @@

Working with Demes graphs

A NetworkX compatible dict-of-lists graph of the demes’ successors.

Return type:
-

dict[str, list[str]]

+

dict[str, list[str]]

@@ -887,15 +887,15 @@

Working with Demes graphs
Variables:
    -

  • name (str) – A concise string that identifies the deme.

    • -

  • description (str) – A description of the deme.

    • -

  • start_time (float) – The time at which the deme begins to exist.

    • -

  • ancestors (list[str]) – List of deme names for the deme’s ancestors.

    • -

  • proportions (list[float]) – The proportions of ancestry from each ancestor, +

  • name (str) – A concise string that identifies the deme.

    • +

  • description (str) – A description of the deme.

    • +

  • start_time (float) – The time at which the deme begins to exist.

    • +

  • ancestors (list[str]) – List of deme names for the deme’s ancestors.

    • +

  • proportions (list[float]) – The proportions of ancestry from each ancestor, ordered to correspond with the same order as the ancestors list. If there are one or more ancestors, the proportions sum to 1.

    • -

  • epochs (list[Epoch]) – A list of epochs that span the time interval over which the +

  • epochs (list[Epoch]) – A list of epochs that span the time interval over which the deme exists. Epoch time intervals are non-overlapping, completely cover the deme’s existence time interval, and are listed in time-descending order (from the past @@ -914,10 +914,10 @@

    Working with Demes graphsParameters:

    • other (Deme) – The deme to compare against.

      • -

    • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

      • -

    • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

      • +

    • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

      • +

    • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

    @@ -929,7 +929,7 @@

    Working with Demes graphs
    Return type:
    -

    float

    +

    float

@@ -943,17 +943,17 @@

Working with Demes graphsParameters:

  • other (Deme) – The deme to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two demes are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -967,13 +967,13 @@

Working with Demes graphs
Parameters:
-

time (float) – The time at which the size should be calculated.

+

time (float) – The time at which the size should be calculated.

Returns:

The deme size.

Return type:
-

float

+

float

@@ -984,7 +984,7 @@

Working with Demes graphs
Return type:
-

float

+

float

@@ -1004,16 +1004,16 @@

Working with Demes graphs
Variables:
    -

  • start_time (float) – The start time of the epoch. +

  • start_time (float) – The start time of the epoch. This value is greater than zero and may be infinity.

    • -

  • end_time (float) – The end time of the epoch. +

  • end_time (float) – The end time of the epoch. This value is greater than or equal to zero and finite.

    • -

  • start_size (float) – Population size at start_time.

    • -

  • end_size (float) – Population size at end_time. +

  • start_size (float) – Population size at start_time.

    • +

  • end_size (float) – Population size at end_time. If start_size != end_size, the population size changes between the start and end times according to the size_function.

    • -

  • size_function (str) –

    The size change function. This is either +

  • size_function (str) –

    The size change function. This is either constant, exponential or linear, though it is possible that additional values will be added in the future.

    @@ -1041,8 +1041,8 @@

    Working with Demes graphsfloat) – The selfing rate for this epoch.

    • -

  • cloning_rate (float) – The cloning rate for this epoch.

    • +

  • selfing_rate (float) – The selfing rate for this epoch.

    • +

  • cloning_rate (float) – The cloning rate for this epoch.

@@ -1058,10 +1058,10 @@

Working with Demes graphsParameters:

  • other (Epoch) – The epoch to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1076,17 +1076,17 @@

Working with Demes graphsParameters:

  • other (Epoch) – The epoch to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two epochs are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1097,7 +1097,7 @@

Working with Demes graphs
Return type:
-

float

+

float

@@ -1118,11 +1118,11 @@

Continuous demographic events
Variables:
    -

  • source (str) – The source deme for asymmetric migration.

    • -

  • dest (str) – The destination deme for asymmetric migration.

    • -

  • start_time (float) – The time at which the migration rate is activated.

    • -

  • end_time (float) – The time at which the migration rate is deactivated.

    • -

  • rate (float) – The rate of migration per generation.

    • +

  • source (str) – The source deme for asymmetric migration.

    • +

  • dest (str) – The destination deme for asymmetric migration.

    • +

  • start_time (float) – The time at which the migration rate is activated.

    • +

  • end_time (float) – The time at which the migration rate is deactivated.

    • +

  • rate (float) – The rate of migration per generation.

@@ -1137,10 +1137,10 @@

Continuous demographic eventsParameters:

  • other (AsymmetricMigration) – The migration to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1155,17 +1155,17 @@

Continuous demographic eventsParameters:

  • other (AsymmetricMigration) – The migration to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two epochs are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1188,10 +1188,10 @@

Discrete demographic events
Variables:
    -

  • sources (list(str)) – The source deme(s).

    • -

  • dest (str) – The destination deme.

    • -

  • time (float) – The time of migration.

    • -

  • proportions (list(float)) – Immediately following migration, the proportion(s) +

  • sources (list(str)) – The source deme(s).

    • +

  • dest (str) – The destination deme.

    • +

  • time (float) – The time of migration.

    • +

  • proportions (list(float)) – Immediately following migration, the proportion(s) of individuals in the destination deme made up of migrant individuals or having parents from the source deme(s).

@@ -1208,10 +1208,10 @@

Discrete demographic eventsParameters:

  • other (Pulse) – The pulse to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1226,17 +1226,17 @@

Discrete demographic eventsParameters:

  • other (Pulse) – The pulse to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two pulses are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1254,9 +1254,9 @@

Discrete demographic events
Variables:
    -

  • parent (str) – The parental deme.

    • -

  • children (list[str]) – A list of descendant demes.

    • -

  • time (float) – The split time.

    • +

  • parent (str) – The parental deme.

    • +

  • children (list[str]) – A list of descendant demes.

    • +

  • time (float) – The split time.

@@ -1271,10 +1271,10 @@

Discrete demographic eventsParameters:

  • other (Split) – The split to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1290,17 +1290,17 @@

Discrete demographic eventsParameters:

  • other (Split) – The split to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two splits are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1316,9 +1316,9 @@

Discrete demographic events
Variables:
    -

  • parent (str) – The parental deme.

    • -

  • child (str) – The descendant deme.

    • -

  • time (float) – The branch time.

    • +

  • parent (str) – The parental deme.

    • +

  • child (str) – The descendant deme.

    • +

  • time (float) – The branch time.

@@ -1333,10 +1333,10 @@

Discrete demographic eventsParameters:

  • other (Branch) – The branch to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1351,17 +1351,17 @@

Discrete demographic eventsParameters:

  • other (Branch) – The branch to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two branches are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1377,11 +1377,11 @@

Discrete demographic events
Variables:
    -

  • parents (list[str]) – A list of parental demes.

    • -

  • proportions (list[float]) – A list of ancestry proportions, +

  • parents (list[str]) – A list of parental demes.

    • +

  • proportions (list[float]) – A list of ancestry proportions, in order of parents.

    • -

  • child (str) – The descendant deme.

    • -

  • time (float) – The merge time.

    • +

  • child (str) – The descendant deme.

    • +

  • time (float) – The merge time.

@@ -1396,10 +1396,10 @@

Discrete demographic eventsParameters:

  • other (Merge) – The merge to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1414,17 +1414,17 @@

Discrete demographic eventsParameters:

  • other (Merge) – The merge to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two merges are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1440,11 +1440,11 @@

Discrete demographic events
Variables:
    -

  • parents (list[str]) – A list of source demes.

    • -

  • proportions (list[float]) – A list of ancestry proportions, +

  • parents (list[str]) – A list of source demes.

    • +

  • proportions (list[float]) – A list of ancestry proportions, in order of parents.

    • -

  • child (str) – The admixed deme.

    • -

  • time (float) – The admixture time.

    • +

  • child (str) – The admixed deme.

    • +

  • time (float) – The admixture time.

@@ -1459,10 +1459,10 @@

Discrete demographic eventsParameters:

  • other (Admix) – The admixture to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

@@ -1477,17 +1477,17 @@

Discrete demographic eventsParameters:

  • other (Admix) – The admixture to compare against.

    • -

  • rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for math.isclose()

    • -

  • abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for math.isclose().

    • +

  • rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for math.isclose()

    • +

  • abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for math.isclose().

Returns:

True if the two admixtures are equivalent, False otherwise.

Return type:
-

bool

+

bool

@@ -1530,14 +1530,14 @@

Conversion functions
Parameters:
    -

  • command (str) – The ms command line.

    • -

  • N0 (float) – The reference population size (\(N_0\)) used to translate +

  • command (str) – The ms command line.

    • +

  • N0 (float) – The reference population size (\(N_0\)) used to translate from coalescent units. For a command that specifies a \(\theta\) value with the -t theta option, this can be calculated as \(N_0 = \theta / (4 \mu L)\), where \(\mu\) is the per-generation mutation rate and \(L\) is the length of the sequence being simulated.

    • -

  • deme_names (list[str]) – A list of names to use for the demes. +

  • deme_names (list[str]) – A list of names to use for the demes. If not specified, demes will be named deme1, deme2, etc.

@@ -1562,9 +1562,9 @@

Conversion functions
Parameters:
    -

  • N0 (float) – The reference population size used to translate into coalescent units. +

  • N0 (float) – The reference population size used to translate into coalescent units. See from_ms() for details.

    • -

  • samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same +

  • samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same order as the order of demes in the graph. The parameter is ignored for demographic models with only one deme. The given sampling scheme will be used with the -I argument. @@ -1576,7 +1576,7 @@

    Conversion functions

    The ms command line.

Return type:
-

str

+

str

diff --git a/main/introduction.html b/main/introduction.html index 2a61ee8..2124d2c 100644 --- a/main/introduction.html +++ b/main/introduction.html @@ -233,7 +233,7 @@

Example
<Axes: ylabel='time ago (generations)'>
-_images/612c4c300a2808c20b427d4e262175e1070dc2dbe9dd7082b1f7baacdfd590de.svg +_images/d5b6aa8d1c32679000a4471fd60f67cf258ae2367aa951931171f1e529d399fe.svg diff --git a/main/quickstart.html b/main/quickstart.html index 9f5f955..e3cf2c7 100644 --- a/main/quickstart.html +++ b/main/quickstart.html @@ -231,7 +231,7 @@

Loading a Demes graph
-_images/e9bba2c165aa0c95f1082b473c55d3c89a6097c45128df21b24aa4058650f64d.svg
+_images/6caa213d29b7e47d8e9868ca058e22ebf67ac88f63d3d7ab1d32fd8b10b4f289.svg

This YAML file can be loaded into Python with the load() function, to obtain a Graph instance (modify the filename as appropriate).

@@ -402,7 +402,7 @@

Plotting a Demes graph
<Axes: ylabel='time ago (generations)'>
-_images/9dbe811fdf798e166aafd4bbe02341ee2ff277fc991ebf89a4356f123f18ddf0.svg +_images/a9a28f0b7928223c5a005ea0962b0734154d3433d4232b8ad36f112069cedbde.svg