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"spectrum": 2, "spell": 3, "squar": 3, "stabl": 2, "standard": 2, "standardis": 1, "start": [2, 3], "start_siz": [0, 3], "start_tim": 0, "step": [2, 3], "still": 2, "stop": 2, "str": 2, "straightforward": 2, "strictli": 2, "string": [2, 3], "strip": 2, "strongli": 2, "structur": 2, "style": 3, "subsequ": 2, "success": 2, "suffer": 3, "sum": 2, "support": 2, "suppos": 3, "syntax": [2, 3], "system": 3, "t": 2, "tab": 3, "tabl": [0, 1], "take": 2, "taken": 2, "task": 2, "technic": 2, "tediou": 1, "tempor": 2, "ten": [0, 2], "term": [2, 3], "termin": 3, "text": 2, "than": [2, 3], "thei": [2, 3], "them": 2, "therefor": 2, "thi": [0, 1, 3], "thing": 2, "think": [2, 3], "those": [1, 2], "thousand": 3, "three": 3, "through": [2, 3], "thu": [0, 2], "ti": 1, "time": [0, 1], "time_boundari": 2, "time_interv": 2, "time_unit": [0, 3], "titl": 2, "toler": 2, "tool": 1, "top": 3, "topolog": 2, "toward": [2, 3], "tracker": 2, "transcrib": 1, "transfer": 2, "transform": 2, "travel": 3, "treat": 3, "tri": 2, "trick": 2, "true": 2, "try": 3, "tskit": 1, "tutori": [1, 2], "two": [0, 2, 3], "type": [2, 3], "typeerror": 2, "ultim": 2, "understand": 2, "unfortun": 1, "union": 2, "uniqu": 2, "unit": 2, "unknown": 2, "unless": 2, "unresolv": 2, "until": 3, "up": [2, 3], "updat": 2, "url": 3, "us": [1, 2, 3], "user": [1, 2], "usual": 2, "utah": [0, 3], "v": 2, "validate_item": 2, "validator_nam": 2, "valu": 2, "valueerror": 2, "vari": 2, "variabl": 2, "variou": [0, 2, 3], "ve": 3, "veri": 3, "via": [2, 3], "visit": 2, "wa": [2, 3], "wai": [2, 3], "want": 3, "warn": 2, "we": [1, 2, 3], "well": [0, 3], "western": [0, 3], "what": 2, "when": [1, 2, 3], "where": 2, "wherea": 3, "whether": [2, 3], "which": [1, 2, 3], "while": 2, "who": 3, "why": 2, "wide": 2, "wiggl": 2, "wish": [2, 3], "within": [2, 3], "without": [2, 3], "word": [2, 3], "work": [1, 2], "worri": 3, "would": [2, 3], "writabl": 2, "write": [1, 2], "writer": 2, "written": [2, 3], "x": [2, 3], "y": [2, 3], "yaml": 2, "year": [0, 2, 3], "yml": 3, "yoruba": [0, 3], "you": [1, 2, 3], "youngest": 2, "your": [1, 2], "yri": [0, 3], "zero": [2, 3], "zigzag": 3, "zip": 2}, "titles": ["Gallery", "Introduction", "Specification", "Tutorial"], "titleterms": {"2009": 0, "2019": 0, "A": 3, "accept": 1, "admixtur": [0, 3], "africa": 0, "al": 0, "an": 3, "ancestor": [2, 3], "answer": 3, "appendix": 2, "applic": 2, "asymmetr": 3, "backward": 2, "branch": 3, "chang": 3, "clone": 3, "cloning_r": 2, "common": 2, "concept": 2, "consider": 2, "continu": 3, "convent": 2, "convert": 2, "data": 2, "default": [2, 3], "deme": [1, 2, 3], "denisovan": 0, "descript": 2, "dest": 2, "directli": 1, "document": 2, "doi": 2, "don": 3, "end_siz": 2, "end_tim": 2, "epoch": [2, 3], "et": 0, "event": 3, "exampl": 2, "excercis": 3, "expans": 0, "exponenti": 3, "format": 1, "forward": 2, "galleri": 0, "gener": 3, "generation_tim": 2, "gutenkunst": 0, "have": 3, "human": 2, "i": [1, 2, 3], "implement": 2, "import": 2, "infin": 2, "input": 1, "introduct": [1, 2], "jacob": 0, "level": 2, "machin": 2, "mdm": 2, "metadata": 2, "migrat": [2, 3], "model": [0, 2], "multipl": 3, "name": 2, "necessari": 1, "note": 2, "out": 0, "output": 1, "parser": 2, "popul": 2, "proport": 2, "puls": [2, 3], "question": 3, "rate": 2, "reader": 2, "refer": 2, "relat": 1, "resolut": 2, "schema": 2, "self": 3, "selfing_r": 2, "sequenti": 2, "set": 3, "size": [2, 3], "size_funct": 2, "softwar": 1, "sort": 2, "sourc": 2, "specif": [1, 2], "split": 3, "start_siz": 2, "start_tim": [2, 3], "support": 1, "symmetr": [2, 3], "t": 3, "terminologi": [2, 3], "thi": 2, "time": [2, 3], "time_unit": 2, "todo": [2, 3], "too": 3, "top": 2, "tutori": 3, "unit": 3, "valid": 2, "valu": 3, "what": [1, 3], "who": 2, "why": [1, 3], "yaml": 3, "zigzag": 0}}) \ No newline at end of file diff --git a/main/specification.html b/main/specification.html index fbe8717..bf4f347 100644 --- a/main/specification.html +++ b/main/specification.html @@ -2102,7 +2102,7 @@

pulses#< description=(str, None), start_time=((str, numbers.Number), is_positive_or_json_infinity), ancestors=(list, is_list_of_identifiers), - proportions=(list, is_list_of_fractions), + proportions=(list, is_list_of_proportions), ), ) @@ -2110,8 +2110,8 @@

pulses#< end_time=(numbers.Number, is_non_negative_and_finite), start_size=(numbers.Number, is_positive_and_finite), end_size=(numbers.Number, is_positive_and_finite), - selfing_rate=(numbers.Number, is_fraction), - cloning_rate=(numbers.Number, is_fraction), + selfing_rate=(numbers.Number, is_rate), + cloning_rate=(numbers.Number, is_rate), size_function=(str, None), ) check_defaults(global_epoch_defaults, allowed_epoch_defaults) @@ -2130,7 +2130,7 @@

pulses#< ), ancestors=pop_list(deme_data, "ancestors", [], str, is_identifier), proportions=pop_list( - deme_data, "proportions", None, numbers.Number, is_fraction + deme_data, "proportions", None, numbers.Number, is_proportion ), ) @@ -2155,8 +2155,8 @@

pulses#< end_size=pop_number( epoch_data, "end_size", None, is_positive_and_finite ), - selfing_rate=pop_number(epoch_data, "selfing_rate", 0, is_fraction), - cloning_rate=pop_number(epoch_data, "cloning_rate", 0, is_fraction), + selfing_rate=pop_number(epoch_data, "selfing_rate", 0, is_rate), + cloning_rate=pop_number(epoch_data, "cloning_rate", 0, is_rate), size_function=pop_string(epoch_data, "size_function", None), ) check_empty(epoch_data) @@ -2171,7 +2171,7 @@

pulses#< check_defaults( migration_defaults, dict( - rate=(numbers.Number, is_fraction), + rate=(numbers.Number, is_rate), start_time=((numbers.Number, str), is_positive_or_json_infinity), end_time=(numbers.Number, is_non_negative_and_finite), source=(str, is_identifier), @@ -2182,7 +2182,7 @@

pulses#< for migration_data in pop_list(data, "migrations", []): insert_defaults(migration_data, migration_defaults) graph.add_migration( - rate=pop_number(migration_data, "rate", validator=is_fraction), + rate=pop_number(migration_data, "rate", validator=is_rate), start_time=pop_number( migration_data, "start_time", @@ -2211,7 +2211,7 @@

pulses#< sources=(list, is_nonempty_list_of_identifiers), dest=(str, is_identifier), time=(numbers.Number, is_positive_and_finite), - proportions=(list, is_nonempty_list_of_fractions_with_sum_less_than_1), + proportions=(list, is_nonempty_list_of_proportions_with_sum_less_than_1), ), ) for pulse_data in pop_list(data, "pulses", []): @@ -2231,7 +2231,7 @@

pulses#< "proportions", default=[], required_type=numbers.Number, - validator=is_fraction, + validator=is_proportion, ), ) check_empty(pulse_data) @@ -2275,10 +2275,14 @@

pulses#< return value >= 0 and not math.isinf(value) -def is_fraction(value): +def is_rate(value): return 0 <= value <= 1 +def is_proportion(value): + return 0 < value <= 1 + + def is_nonempty(value): return len(value) > 0 @@ -2295,12 +2299,12 @@

pulses#< return is_list_of_identifiers(value) and len(value) > 0 -def is_list_of_fractions(value): - return all(isinstance(v, numbers.Number) and is_fraction(v) for v in value) +def is_list_of_proportions(value): + return all(isinstance(v, numbers.Number) and is_proportion(v) for v in value) -def is_nonempty_list_of_fractions_with_sum_less_than_1(value): - return is_list_of_fractions(value) and len(value) > 0 and sum(value) <= 1 +def is_nonempty_list_of_proportions_with_sum_less_than_1(value): + return is_list_of_proportions(value) and len(value) > 0 and sum(value) <= 1 def validate_item(name, value, required_type, validator=None): diff --git a/main/tutorial.html b/main/tutorial.html index 1b4bca0..4b61d56 100644 --- a/main/tutorial.html +++ b/main/tutorial.html @@ -463,7 +463,7 @@

YAML#
-_images/0d0e2e19b3fc4be5b48c133f40f883acd203f5d5fbf99a5b2346e189a6b9026a.svg +_images/98298340836881856933de6aaf98fb4108b43a3f8db5305615d3b4d437b9f6b8.svg
@@ -509,7 +509,7 @@

What is a deme?
-_images/2c3b5ff00e84efc4de6157db7126436e0ac7096f282ee7730de00f15d873fc22.svg +_images/c53daf74fa34bb8d89b7d9c5b86f8f79607ab3726703a5c7afd6af43b4a83407.svg
@@ -553,7 +553,7 @@

Default values
-_images/8319b81aaf94f417384134ba4d5cd3e92917575f01f7cedef2ba0511e79459b6.svg +_images/d5183d6d5c660eb452a9091e577465b5e33561bca976807521233dd37c614893.svg
@@ -590,7 +590,7 @@

What is an epoch?
-_images/1d13fd5b060a03a718716f8fbeb01c391251ebe395c7eaad348eaf015eee538c.svg +_images/bca47307066a90795636cf261663583775d8a5936561599d9b97903d5e3b27f4.svg
@@ -625,7 +625,7 @@

What is an epoch?
-_images/a9014aee1cd8a5a6074470c4f39ef918845d8a416f10b31cac20feddeb51f547.svg +_images/3728b1ec5eb006aa203c25f12412b0fd8ac1168ee76579aac5102c7d92ff2f3f.svg
@@ -688,7 +688,7 @@

Exponential size changes
-_images/05111bc176a490f75a92812b51d6ba6672eba0be6f57368e8573aebce8161bb1.svg +_images/59bd7b981c682399c72521e58610de4a958df0f533027c4862598877e8fa4cc3.svg
@@ -764,7 +764,7 @@

A split event
-_images/109a221aa42c4279f4d3b33fc4b96df0bb18bbacd58267b85b6da729d2833125.svg +_images/e16e158834e932548ff3543e3e9f353f68e8ffd48e340e8175823426d808b64b.svg
@@ -814,7 +814,7 @@

A split event
-_images/fa2d539bb8f1eea0c7783712cf189b2cedb6859971211d2e3538c1eea0f5350b.svg +_images/ec55914b094a933f6f2b601923a583d60fffe1c7efe551b6faaae6fcf3aec7ab.svg
@@ -855,7 +855,7 @@

A branch event
-_images/80faeae10043fd01f3cd0585e2bba9e2ee1303386af78bde37d73d87f65b5b89.svg +_images/1dae64ccdf0cbf0b0ed93ed417c0962260b44bb908ea079d121d8981e30086eb.svg
@@ -902,7 +902,7 @@

Multiple ancestors
-_images/5de46ba0aeb3101833842078da0b79b8012f65f42f6c13de0364c4c3d5d49613.svg +_images/f84b2d4c1ac3026dbf1922893adc6c653d1128789e28290c16ccdf32df03c535.svg
@@ -957,7 +957,7 @@

Asymmetric migration
-_images/9333695097ea8cd7974aed01f43a765caebfd767f4843d7d281ed430718e8ba9.svg +_images/6434b1c946d1c32ce632a4bcb8458f1caa2da625384f01a34ba4fd31b5feacc1.svg
@@ -1002,7 +1002,7 @@

Asymmetric migration
-_images/70317cb544769a3e7f6310ef3679ef589e307e3c1d1da4ad2d9ebc2d90424481.svg +_images/a1bee1f2646f2de6874d0fda85b5aafb3a9253b5d6131443f96d07542782f5d4.svg
@@ -1043,7 +1043,7 @@

Asymmetric migration
-_images/e8e4ac67dbb64e58297a4e661dea2c5397a56514c4bd63b9c7471c62016fd694.svg +_images/bc226e91c43274555b695e8b64be18c5aee7405dd84e4ad1750d28452f1ebd1c.svg
@@ -1100,7 +1100,7 @@

Symmetric migration
-_images/5139f5ee49c93cf336d079034875465fb38c3e5bd9cb2929932e868078bff92f.svg +_images/e9df002179fb6e582b493e491a7cdc2b82f64ef64ea3fbf84e95d2e5a996619e.svg
@@ -1140,7 +1140,7 @@

Symmetric migration
-_images/ae663ce4ae65b8e7772f1e00cb8f5f806f325c7a05aee7c3b60488ce8dbf4e89.svg +_images/06c74463c88e2efca6214df563e00aca67f727323fd0c4681e01ea90c4b1dfb0.svg
@@ -1188,7 +1188,7 @@

Symmetric migration
-_images/c24ab025d2be1c62463cd970f8ede2dadffceae338c0d772e9725ed208b71f2f.svg +_images/ef59baf2315f4e1cdc4b704d14d76cd76f621ad3b0aa6b3f8b59036035223259.svg
@@ -1247,7 +1247,7 @@

A pulse of admixture
-_images/ba94776fd26aca1f63e8959a5dbaffbd7dd8c5272b62a84e09f913ff7a56b198.svg +_images/99efc9379290432ebfc8d6fe7b570ebcad216df1769c04401c15ac2e02be422e.svg
@@ -1333,7 +1333,7 @@

A pulse of admixture
-_images/32457e9f3de524715f458372c93c6726246e3799386134d4653ff097d8db11ca.svg +_images/6827c21dc326839074b255d8d15153d8b391216916096915ec85893a6a200181.svg
@@ -1371,7 +1371,7 @@

A pulse of admixture
-_images/cc6c7255ce6a74bb8ec5bd9b39e259c72ce851879bfe2684ef403755d580525e.svg +_images/6d39786aa91211e7afd1f2951bc2a7a09cce298b3518a1c64c8a0fa6e23027e6.svg
@@ -1414,7 +1414,7 @@

A pulse of admixture
-_images/15ccf483c46cd19fd9a7af92463da76d09b789afb3a0457eba5ed7178c92d4ff.svg +_images/e252e93e2f01e1c49550b68aace9e6d57b3388c44de8c529346f5ca9b2206560.svg
@@ -1515,7 +1515,7 @@

Time units and generation time
-_images/647cec3d5d3e76f699c79a8624fd5ec1a7fa72595eee089925b6f95850f80fef.svg +_images/0bb82fcea005469a26e10f6677064d297c65dec94ff80ec041bfea65c3a1f7ed.svg