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github.com/BioJulia/PopGen.jl_archive

Population Genetics functions in Julia.
https://github.com/BioJulia/PopGen.jl_archive

fix writing error

c5cafa0525fc628f8dcf7fab76931211fad6e081 authored about 4 years ago by Pavel Dimens <[email protected]>
Merge pull request #38 from pdimens/compathelper/new_version/2020-10-21-00-39-01-821-1863737854

CompatHelper: add new compat entry for "ProgressMeter" at version "1.4"

19bc662c4f2754eefd5c6b1003d85c2ca79032d4 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-39-01-821-1863737854

c3baa8ae6db20252b8ede9c86d7b865e70a88ea3 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #37 from pdimens/compathelper/new_version/2020-10-21-00-38-48-549-3636675641

CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

80aa73407e795749ebfa2bf26a424fbdf45d5c9d authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-38-48-549-3636675641

a8af53e33652a8c8a735f5d41087eb511b913519 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #36 from pdimens/compathelper/new_version/2020-10-21-00-38-35-372-195295088

CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

38ed8fb56cced6c40da9996fa489f34423c08d57 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-38-35-372-195295088

044e644314f183cc2d43193cb84a927ab61e806d authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #35 from pdimens/compathelper/new_version/2020-10-21-00-38-22-290-3951012692

CompatHelper: add new compat entry for "GZip" at version "0.5"

103279a84f9504f52b9c2ee3522686ab68e3d0a0 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #34 from pdimens/compathelper/new_version/2020-10-21-00-38-08-626-3144937314

CompatHelper: add new compat entry for "Requires" at version "1.1"

8d5beae4a2157e84d4fe7c60fb46b9fba2fc1a8a authored about 4 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for "ProgressMeter" at version "1.4"

62f3d4d669b9d911623a416f1c8c4bcc7dd3ee58 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

278f67f14bd3b25262ea3c69eac90641ab71910f authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

096c0e09c842bde1be47b75562e431bc0b38ba58 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "GZip" at version "0.5"

a048017f5b53d972fb8b614e42e8978776a96bbf authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "Requires" at version "1.1"

363af4c970dec21a5bc97786811f2216ea66651c authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Merge pull request #31 from pdimens/compathelper/new_version/2020-09-19-00-31-59-552-1643953571

CompatHelper: bump compat for "JLD2" to "0.2"

621473ce196a85d9e33d48e5dd103b9871357be2 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #32 from pdimens/compathelper/new_version/2020-10-08-00-29-11-667-4016622870

CompatHelper: bump compat for "Distributions" to "0.24"

bfe3d11c8b4dcf8472416a532314fabe4cc48f5f authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #33 from pdimens/kinship

merge Kinship into dev for release staging

d3b8f5bda9f09a9113c011b28333774547c36c36 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Update ci_dev.yaml

7aae937afb391d5656aad55b14cb19824e1fbe14 authored about 4 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: bump compat for "Distributions" to "0.24"

3ec4dfc3fee12e0bb992bc6755afa6abe2dae653 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
parse length(pairs) once

ec116dfa8e3dd06bd52b99d5de86b19d338045ca authored over 4 years ago by Pavel Dimens <[email protected]>
typo

5ee7f4cde7ffaffc35828220f31219184776979c authored over 4 years ago by Pavel Dimens <[email protected]>
typos

9dfa61445011a0714c80109d781460a0c6e5b350 authored over 4 years ago by Pavel Dimens <[email protected]>
CompatHelper: bump compat for "JLD2" to "0.2"

7c762595e2b837b9d5055ca50652c2199f0c3886 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
add Structure file support

3be7b5fd9a1d8a23c646713a18b8bfca027b23e7 authored over 4 years ago by Pavel Dimens <[email protected]>
move Simulations.jl to PopGenSims.jl

3212cc60a459a60650cc939e1b78bbc90274a168 authored over 4 years ago by Pavel Dimens <[email protected]>
docstring

ede0c23970c926f24c3855b9bcba15684a4e199f authored over 4 years ago by Pavel Dimens <[email protected]>
add conditions for sim relatedness

a014ca2b778632cb8ea42e6d281c8360b6b4c021 authored over 4 years ago by Pavel Dimens <[email protected]>
add StaticArrays and sort method

cfff2eec335d37b76beb35b030e3a74082d76ef7 authored over 4 years ago by Pavel Dimens <[email protected]>
boot output from df to NamedTuple + merge function

2e3717fb20e702cf5f5c4902b3c0f6d2db3206f2 authored over 4 years ago by Pavel Dimens <[email protected]>
parallelize permutations

b946a37f7ce598e92db2ae0f82af249f59f62622 authored over 4 years ago by Pavel Dimens <[email protected]>
rm depr line

436172df4f9ab2203d4e8f8f81c66b4adde2b791 authored over 4 years ago by Pavel Dimens <[email protected]>
fix typo introduced in last commit (oops!)

ccbb96a73558070375b0ea74cac21ee527d598d5 authored over 4 years ago by Pavel Dimens <[email protected]>
swap long<->lat cols in genepop importer

50cf2565bd73fd57f4ec997ee30b1133c324631a authored over 4 years ago by Pavel Dimens <[email protected]>
add write-to-structure

c92dc189d500f05acbcd63ee6b244ccbc5bd1405 authored over 4 years ago by Pavel Dimens <[email protected]>
add fastStructure formatting support

202c14fd99e4d52efed77e942506918fecee9a5b authored over 4 years ago by Pavel Dimens <[email protected]>
add Structure file importer

70a8d124f30386987a00adafc68cefffc8c4d44d authored over 4 years ago by Pavel Dimens <[email protected]>
fix genepop writing error

bcef39e7363889312f02713e873e6905f3e4928f authored over 4 years ago by Pavel Dimens <[email protected]>
touchups

d52a293c75a05496ccb5bb57f64222678bea92e4 authored over 4 years ago by Pavel Dimens <[email protected]>
minor fixes

b35ac1625065e69086358700fd7f56cf3f41d9df authored over 4 years ago by Pavel Dimens <[email protected]>
update to correct @spawn and cooler progressbar

7022dffec85e10dd1c195b2688368badc8c6f528 authored over 4 years ago by Pavel Dimens <[email protected]>
typo

20a7e9ac13a295f8c5f7890706f9524c18271ee2 authored over 4 years ago by Pavel Dimens <[email protected]>
remove dev code and fix docstring

dbbfec1c7cc611ae583664d6cbd6b02515407403 authored over 4 years ago by Pavel Dimens <[email protected]>
add simulation

1db5dabd78ba76e9970f7e189f15abcc16ced272 authored over 4 years ago by Pavel Dimens <[email protected]>
remove dev text

16944fd61087c2f10f6fc82448e64b607a1528ad authored over 4 years ago by Pavel Dimens <[email protected]>
fix datasets (oops!)

8b0a8ef0b73a038d3e08813a0eaa70abcb1af8c8 authored over 4 years ago by Pavel Dimens <[email protected]>
minor docstring format error

8d882e87b8626b370b53f1712f73cacb24c02496 authored over 4 years ago by Pavel Dimens <[email protected]>
update install text

7fdb50593dbf402566c6cd59142c3254fa45992f authored over 4 years ago by Pavel Dimens <[email protected]>
update cats/sharks to use PooledArrays

a26f92dae2a50bf5e444749d6c1806271cac2a03 authored over 4 years ago by Pavel Dimens <[email protected]>
slight color change

ae3e76228b9308abb228e6d8b90af0ae591e3aed authored over 4 years ago by Pavel Dimens <[email protected]>
fix shadows

a22912c38dce392dcda70617a99922928e8aa344 authored over 4 years ago by Pavel Dimens <[email protected]>
update install graphic

c06457c5f23a82cad33071569ab0dda08f9be21c authored over 4 years ago by Pavel Dimens <[email protected]>
swap CategoricalArrays for PooledArrays

03c87c7ab70619deefae2a0675f462e1e9778aa5 authored over 4 years ago by Pavel Dimens <[email protected]>
fixes for mixed ploidy

0e8a9bd21b8c716e400ed78ba79971bb7a4e91e9 authored over 4 years ago by Pavel Dimens <[email protected]>
fix vcf reader and begin requires tests

4801b62f6dd013a1aa6f0f438abb4962a2b2d507 authored over 4 years ago by Pavel Dimens <[email protected]>
fix docstrings

d300e609066620cb696c7da757e692900bcdc1fe authored over 4 years ago by Pavel Dimens <[email protected]>
rewrite of VCF/BCF

69aae3e83ea91167edc586f82fc5e35c3d9282bc authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

b2c196d16254142948b4471d23b8139cadae68e2 authored over 4 years ago by jdselwyn <[email protected]>
add moments-based estimators to module

4b37b74ae6641fa349d9190670d888f839e0bccb authored over 4 years ago by Pavel Dimens <[email protected]>
remove redundant broadcast ops

d5bdfdf2ccd4e2b7b0e4e158b74dc1f434f3aba4 authored over 4 years ago by Pavel Dimens <[email protected]>
fix multithreading on fstat perm

798791bd1f8f148a131861695d90c9ce9de9c6ad authored over 4 years ago by Pavel Dimens <[email protected]>
minor cleanup

1d22be9825ce76f642e98ec37c6a79d2f233d121 authored over 4 years ago by Pavel Dimens <[email protected]>
minor update to docstring

3a6d96408ab02e024a30ab48aaf44bbf0b8e9bf9 authored over 4 years ago by Pavel Dimens <[email protected]>
slack trigger test

91d3985d2695acd7aee06700634a045add48bc8b authored over 4 years ago by Pavel Dimens <[email protected]>
proper multithreading

ac10bf2495a16188fd49b117ed81405dca6817c7 authored over 4 years ago by Pavel Dimens <[email protected]>
refactor relatedness for threadsafety

28465916fcaa49296435490feea65a77bd730d65 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

a20a3b9e5ad90d95fab5a9d965bd18f740972ca4 authored over 4 years ago by Pavel Dimens <[email protected]>
minor info change

bad332e6eceb69e57d5806df75669f8a5cfe0f20 authored over 4 years ago by Pavel Dimens <[email protected]>
add initial thread safety to relatedness

afd56a90ed258e7a0399160f93e1fb2977bedd68 authored over 4 years ago by Pavel V. Dimens <[email protected]>
add inbreeding toggle for relatedness

aba87f29431c5d339a0c063717cc44d8a0ad34a0 authored over 4 years ago by Pavel Dimens <[email protected]>
add deps

ac8373d7cbdf8f8965db1192b6506dadd85991b7 authored over 4 years ago by Pavel Dimens <[email protected]>
updates

2f0814ba80f434e59290fb2fd2a293fc73138372 authored over 4 years ago by jdselwyn <[email protected]>
Update RelatednessLikelihood.jl

ca5d44b58a8b6a851a86b46a6d0d2b3523e40f85 authored over 4 years ago by jdselwyn <[email protected]>
revise relatedness docstring

d036bf626627af727b3c9962eb9f5cefc3da66bf authored over 4 years ago by Pavel Dimens <[email protected]>
add convex

a9e1094e6d626e53543e99abc957a4911d2dd8dc authored over 4 years ago by Pavel Dimens <[email protected]>
reorganize relatedness files

e0dbc2a725668128d59763af817f5fe41606d8a8 authored over 4 years ago by Pavel Dimens <[email protected]>
drop Missings in favor of nonmissings

53fe98ed805584999942ba46780f12e770bbea90 authored over 4 years ago by Pavel Dimens <[email protected]>
parsimonification

c2e4f543859aad123452c9c6b16a833882c2a1ff authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

800753607dec2800479600389ed3973a8eb06d29 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

b0805bac38e5701bcca0914b5c06d2b27e13a78a authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

3b02fb065d8704ecdf0ea2834ad235c96010a225 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

2ae7de9f353e7eaecd0d2839cb7823ad4f753c04 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

34db10f0970ddc0b7b175dc3d98bf0ab046731aa authored over 4 years ago by Pavel Dimens <[email protected]>
add faster consolidated bootstrap methods

f55a16b4b15aad1335e940303e7d49e03044525c authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

eb90b07a56a7db3c0f7c880a93b1d25199ba15dc authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

db24b298e6203ea15337c04c8aae50274755d7f6 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

478e77bf21b5dcf25025d736c274ea2edbe31112 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

3273e04045fe55bc3576c8b53afbcebc3eda3c81 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

e9ff12c8d17fce3aadfcb1d85b74970f6c06c419 authored over 4 years ago by Pavel Dimens <[email protected]>
sweeping change speeding up bootstrap (incomplete)

f2f0a5d43ebd5f06c2c436095d4b88b55047023f authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

dd6018186251737181990bc271476c0bc890a041 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

52163db7442e31c63163455db270638c815a4538 authored over 4 years ago by jdselwyn <[email protected]>
Merge branch 'kinship' of https://github.com/pdimens/PopGen.jl into kinship

5120ad89edb77359dc102833c0084ea6b401b076 authored over 4 years ago by Pavel Dimens <[email protected]>
add bootstrap before/after skipmissing methods

3a1adc46dc2db500b413a980570c3122819759cc authored over 4 years ago by Pavel Dimens <[email protected]>
Update ProbabilityStates.jl

00c56fac745f995aec8a131a95c283885e7a6f0d authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

3ee35e3f111313f2b082f7c2b8d68e3947c176a6 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

2492eb52ce6ab123d06255c357acf7a3e39ac03b authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

844bd577790e6c051d596531bb661be2f329b7bb authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

1f0f07b728748c36be3aa2167db28ca798e45cd8 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

fd1ea0d0c512ab261e243c46ab7bd784238f2282 authored over 4 years ago by jdselwyn <[email protected]>
Update ProbabilityStates.jl

ee7054aa0eb1c2e6bfcbec3455c0e21d13949919 authored over 4 years ago by jdselwyn <[email protected]>