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Added BosTau demographies from Boitard et al. (2016) #1593

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merged 2 commits into from
Dec 13, 2024
Merged

Added BosTau demographies from Boitard et al. (2016) #1593

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585b9f8
Polish BosTauBoitard2016
gregorgorjanc Dec 12, 2024
9f28b6e
BosTau models - setting generation interval time to a number instead …
gregorgorjanc Dec 12, 2024
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44 changes: 44 additions & 0 deletions docs/parameter_tables/BosTau/Angus_1B16.csv
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Original file line number Diff line number Diff line change
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Population size,"33,810",Ancestral population size
Population size,"56,981",Pop. size during 1st time interval
Population size,"85,228",Pop. size during 2nd time interval
Population size,"87,426",Pop. size during 3rd time interval
Population size,"83,576",Pop. size during 4th time interval
Population size,"80,651",Pop. size during 5th time interval
Population size,"69,328",Pop. size during 6th time interval
Population size,"56,775",Pop. size during 7th time interval
Population size,"47,892",Pop. size during 8th time interval
Population size,"35,998",Pop. size during 9th time interval
Population size,"24,300",Pop. size during 10th time interval
Population size,"16,441",Pop. size during 11th time interval
Population size,"12,042",Pop. size during 12th time interval
Population size,"10,827",Pop. size during 13th time interval
Population size,"6,837",Pop. size during 14th time interval
Population size,"4,836",Pop. size during 15th time interval
Population size,"2,558",Pop. size during 16th time interval
Population size,"1,224",Pop. size during 17th time interval
Population size,"709",Pop. size during 18th time interval
Population size,"412",Pop. size during 19th time interval
Population size,"291",Pop. size during 20th time interval
Time (gen.),"129,999",Begining of 1st time interval
Time (gen.),"83,043",Begining of 2nd time interval
Time (gen.),"53,045",Begining of 3rd time interval
Time (gen.),"33,881",Begining of 4th time interval
Time (gen.),"21,638",Begining of 5th time interval
Time (gen.),"13,817",Begining of 6th time interval
Time (gen.),"8,821",Begining of 7th time interval
Time (gen.),"5,629",Begining of 8th time interval
Time (gen.),"3,590",Begining of 9th time interval
Time (gen.),"2,287",Begining of 10th time interval
Time (gen.),"1,455",Begining of 11th time interval
Time (gen.),"923",Begining of 12th time interval
Time (gen.),"584",Begining of 13th time interval
Time (gen.),"367",Begining of 14th time interval
Time (gen.),"228",Begining of 15th time interval
Time (gen.),"139",Begining of 16th time interval
Time (gen.),"83",Begining of 17th time interval
Time (gen.),"47",Begining of 18th time interval
Time (gen.),"24",Begining of 19th time interval
Time (gen.),"9",Begining of 20th time interval
Generation time (yrs.),5,Generation time
Mutation rate,1e-8,Per-base per-generation mutation rate
Recombination rate,5.00e-9,Per-base per-generation recombination rate
44 changes: 44 additions & 0 deletions docs/parameter_tables/BosTau/Fleckvieh_1B16.csv
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Original file line number Diff line number Diff line change
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Population size,"31,131",Ancestral population size
Population size,"70,789",Pop. size during 1st time interval
Population size,"91,228",Pop. size during 2nd time interval
Population size,"85,607",Pop. size during 3rd time interval
Population size,"82,448",Pop. size during 4th time interval
Population size,"82,844",Pop. size during 5th time interval
Population size,"72,920",Pop. size during 6th time interval
Population size,"61,479",Pop. size during 7th time interval
Population size,"54,358",Pop. size during 8th time interval
Population size,"38,069",Pop. size during 9th time interval
Population size,"28,547",Pop. size during 10th time interval
Population size,"20,963",Pop. size during 11th time interval
Population size,"18,176",Pop. size during 12th time interval
Population size,"13,604",Pop. size during 13th time interval
Population size,"10,546",Pop. size during 14th time interval
Population size,"7,414",Pop. size during 15th time interval
Population size,"5,689",Pop. size during 16th time interval
Population size,"4,184",Pop. size during 17th time interval
Population size,"3,395",Pop. size during 18th time interval
Population size,"2,812",Pop. size during 19th time interval
Population size,"2,227",Pop. size during 20th time interval
Time (gen.),"129,999",Begining of 1st time interval
Time (gen.),"83,043",Begining of 2nd time interval
Time (gen.),"53,045",Begining of 3rd time interval
Time (gen.),"33,881",Begining of 4th time interval
Time (gen.),"21,638",Begining of 5th time interval
Time (gen.),"13,817",Begining of 6th time interval
Time (gen.),"8,821",Begining of 7th time interval
Time (gen.),"5,629",Begining of 8th time interval
Time (gen.),"3,590",Begining of 9th time interval
Time (gen.),"2,287",Begining of 10th time interval
Time (gen.),"1,455",Begining of 11th time interval
Time (gen.),"923",Begining of 12th time interval
Time (gen.),"584",Begining of 13th time interval
Time (gen.),"367",Begining of 14th time interval
Time (gen.),"228",Begining of 15th time interval
Time (gen.),"139",Begining of 16th time interval
Time (gen.),"83",Begining of 17th time interval
Time (gen.),"47",Begining of 18th time interval
Time (gen.),"24",Begining of 19th time interval
Time (gen.),"9",Begining of 20th time interval
Generation time (yrs.),5,Generation time
Mutation rate,1e-8,Per-base per-generation mutation rate
Recombination rate,3.89e-9,Per-base per-generation recombination rate
44 changes: 44 additions & 0 deletions docs/parameter_tables/BosTau/HolsteinFriesian_1B16.csv
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Original file line number Diff line number Diff line change
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Population size,"31,652",Ancestral population size
Population size,"65,485",Pop. size during 1st time interval
Population size,"86,206",Pop. size during 2nd time interval
Population size,"79,079",Pop. size during 3rd time interval
Population size,"71,209",Pop. size during 4th time interval
Population size,"72,841",Pop. size during 5th time interval
Population size,"63,092",Pop. size during 6th time interval
Population size,"52,882",Pop. size during 7th time interval
Population size,"50,726",Pop. size during 8th time interval
Population size,"36,512",Pop. size during 9th time interval
Population size,"27,155",Pop. size during 10th time interval
Population size,"23,783",Pop. size during 11th time interval
Population size,"20,159",Pop. size during 12th time interval
Population size,"15,602",Pop. size during 13th time interval
Population size,"11,367",Pop. size during 14th time interval
Population size,"6,908",Pop. size during 15th time interval
Population size,"3,892",Pop. size during 16th time interval
Population size,"1,815",Pop. size during 17th time interval
Population size,"1,320",Pop. size during 18th time interval
Population size,"1,076",Pop. size during 19th time interval
Population size,"793",Pop. size during 20th time interval
Time (gen.),"129,999",Begining of 1st time interval
Time (gen.),"83,043",Begining of 2nd time interval
Time (gen.),"53,045",Begining of 3rd time interval
Time (gen.),"33,881",Begining of 4th time interval
Time (gen.),"21,638",Begining of 5th time interval
Time (gen.),"13,817",Begining of 6th time interval
Time (gen.),"8,821",Begining of 7th time interval
Time (gen.),"5,629",Begining of 8th time interval
Time (gen.),"3,590",Begining of 9th time interval
Time (gen.),"2,287",Begining of 10th time interval
Time (gen.),"1,455",Begining of 11th time interval
Time (gen.),"923",Begining of 12th time interval
Time (gen.),"584",Begining of 13th time interval
Time (gen.),"367",Begining of 14th time interval
Time (gen.),"228",Begining of 15th time interval
Time (gen.),"139",Begining of 16th time interval
Time (gen.),"83",Begining of 17th time interval
Time (gen.),"47",Begining of 18th time interval
Time (gen.),"24",Begining of 19th time interval
Time (gen.),"9",Begining of 20th time interval
Generation time (yrs.),5,Generation time
Mutation rate,1e-8,Per-base per-generation mutation rate
Recombination rate,3.66e-9,Per-base per-generation recombination rate
44 changes: 44 additions & 0 deletions docs/parameter_tables/BosTau/Jersey_1B16.csv
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Original file line number Diff line number Diff line change
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Population size,"30,275",Ancestral population size
Population size,"53,856",Pop. size during 1st time interval
Population size,"76,905",Pop. size during 2nd time interval
Population size,"67,505",Pop. size during 3rd time interval
Population size,"75,739",Pop. size during 4th time interval
Population size,"77,971",Pop. size during 5th time interval
Population size,"78,608",Pop. size during 6th time interval
Population size,"63,277",Pop. size during 7th time interval
Population size,"51,777",Pop. size during 8th time interval
Population size,"33,713",Pop. size during 9th time interval
Population size,"22,549",Pop. size during 10th time interval
Population size,"13,960",Pop. size during 11th time interval
Population size,"13,460",Pop. size during 12th time interval
Population size,"10,474",Pop. size during 13th time interval
Population size,"8,106",Pop. size during 14th time interval
Population size,"5,766",Pop. size during 15th time interval
Population size,"3,704",Pop. size during 16th time interval
Population size,"1,640",Pop. size during 17th time interval
Population size,"947",Pop. size during 18th time interval
Population size,"561",Pop. size during 19th time interval
Population size,"388",Pop. size during 20th time interval
Time (gen.),"129,999",Begining of 1st time interval
Time (gen.),"83,043",Begining of 2nd time interval
Time (gen.),"53,045",Begining of 3rd time interval
Time (gen.),"33,881",Begining of 4th time interval
Time (gen.),"21,638",Begining of 5th time interval
Time (gen.),"13,817",Begining of 6th time interval
Time (gen.),"8,821",Begining of 7th time interval
Time (gen.),"5,629",Begining of 8th time interval
Time (gen.),"3,590",Begining of 9th time interval
Time (gen.),"2,287",Begining of 10th time interval
Time (gen.),"1,455",Begining of 11th time interval
Time (gen.),"923",Begining of 12th time interval
Time (gen.),"584",Begining of 13th time interval
Time (gen.),"367",Begining of 14th time interval
Time (gen.),"228",Begining of 15th time interval
Time (gen.),"139",Begining of 16th time interval
Time (gen.),"83",Begining of 17th time interval
Time (gen.),"47",Begining of 18th time interval
Time (gen.),"24",Begining of 19th time interval
Time (gen.),"9",Begining of 20th time interval
Generation time (yrs.),5,Generation time
Mutation rate,1e-8,Per-base per-generation mutation rate
Recombination rate,4.58e-9,Per-base per-generation recombination rate
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