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github.com/BioJulia/PopGen.jl_archive

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

Update .gitignore

5cec6b2d243ffd7329768fe9a000ee0289c83b9e authored almost 5 years ago by Pavel V. Dimens <[email protected]>
begin migration from mkdocs to vuepress

a5c0c4fd56a08aac26876c4bbaf4d3bab71d73cb authored almost 5 years ago by Pavel Dimens <[email protected]>
update heterozygosity to correct for pop and popsize

82f37c3405be8e57f57c802e60d6955501558850 authored almost 5 years ago by Pavel Dimens <[email protected]>
Genotype and GenotypeArray

Create aliases for NTuple{N, <:Signed} (Genotype) and the vector of them (GenotypeArray), permi...

97415d524d98ca2dc616552f2e55737c4129ecd7 authored almost 5 years ago by Pavel Dimens <[email protected]>
rename chisq as Χ²

Honestly, because we can.

e8779d1315557f5ae23294146dc4e6e5cdd3f873 authored almost 5 years ago by Pavel Dimens <[email protected]>
So many changes

Edit df calculation in heterozygosity to n_exp_geno - n_obs_alleles. Split out Heterozygosity.jl...

ec555f4b6d3bc18190a5d91cbee26d6c7414d544 authored almost 5 years ago by Pavel Dimens <[email protected]>
small updates

7841eea2e3cdd2598969a11d1204407ad12dfaea authored almost 5 years ago by Pavel Dimens <[email protected]>
chi sq fixes

Continuing the update for Chi Squared tests of hwe, added genotype obs/exp count functions, uniq...

6810ddef9337b23c395b16cd394d03eeff1a8fcb authored almost 5 years ago by Pavel <[email protected]>
Update HardyWeinberg.jl

f33ab563acc355bde2960e2dc8b3b4ddea7cabd9 authored almost 5 years ago by Pavel <[email protected]>
fix allele_freq and add geno_freq_expected

fixed @async issue in allele_freq, along with moving expected genotype frequency calculations ou...

6d53d55009e98ee7aee9300f7f9ea999e21d9df0 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

0f42bd9bd196c40d400074777c1310ffe3572e9a authored almost 5 years ago by Pavel <[email protected]>
Update Project.toml

36008acb51906d890c639ea24a6145ff0e4e3079 authored almost 5 years ago by Pavel <[email protected]>
Update HardyWeinberg.jl

17c4268b404941f87143732db92010e2348d8a29 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
continued updates for Heterozygosity

More patches/updates for the various heterozygosity function in HardyWeinberg.jl to work with th...

de90ddb0a3b2b38c72b72bc7a4715aa92f13ef7c authored almost 5 years ago by Pavel <[email protected]>
fix ioUtils, begin updates for heterozygosity

Added `hetero` function to control output when all genotypes of a locus in a population are miss...

4a3764d3113a6916cfb0461473825bbbcb3063cd authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

c44707f3423cd36aaabbb56acb3a64085e4b9843 authored almost 5 years ago by Pavel <[email protected]>
Update Project.toml

550c0b4d3e08b298216a292609f1d07c642afe15 authored almost 5 years ago by Pavel <[email protected]>
Update juliaprimer.md

Minor spotfixes and clarifications

0ae2890200a64610d00c34157627070efe1d4918 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add determine_marker() and update delimited

added new function determine_marker() to ioUtils.jl, which is used to determine the marker type,...

8710a65e22856dd3ae0b86a8054905e56c247beb authored almost 5 years ago by Pavel V. Dimens <[email protected]>
update docs

51fd0f571a3e84c156f78e22eb07f646e379af32 authored almost 5 years ago by Pavel <[email protected]>
Update popobj_type.md

d95345c48dfb6fedb7c5d9c0bb465a3b702f9f39 authored almost 5 years ago by Pavel <[email protected]>
update all the docs

d999702e7c563954d4565409b5b6f7204dc879b9 authored almost 5 years ago by Pavel <[email protected]>
update allele_freq and geno_freq

16767f72f0be8aa4cdf929647d0b378860353bd0 authored almost 5 years ago by Pavel <[email protected]>
Complete allele_freq

and add allele-freq-by-pop

cbfce6d9dbd46f91ef9ada4131f836a429237a70 authored almost 5 years ago by Pavel <[email protected]>
Update SummaryInfo.jl

82b581723c9dbe574a51a595d4ae3c81a3f5911e authored almost 5 years ago by Pavel <[email protected]>
update allele freq

add alleles(), allele_table(), update allele_avg

dab105854f655dc7e811c50f20621e8f1c5c73fa authored almost 5 years ago by Pavel <[email protected]>
minor fixes

3de926eb750373b3eccbd1baaac36a619138ea78 authored almost 5 years ago by Pavel <[email protected]>
remove @show_only

4c0a471e7772caafdbe7c46daf265752d11ab029 authored almost 5 years ago by Pavel <[email protected]>
finish updating Manipulate to IndexedTables

8b5ceb888d52943cb748727795e4329b77bcb14a authored almost 5 years ago by Pavel <[email protected]>
add inbounds

ffb74d289f6ee2569855f743ed2a4577eb18ce7b authored almost 5 years ago by Pavel <[email protected]>
Update Manipulate.jl

4e7cb5e55470996c78dc1f9e082937abfe6dadd2 authored almost 5 years ago by Pavel <[email protected]>
fix all populations!() functions

845664cc34874489953e9181cfde7d7ec59b56cb authored almost 5 years ago by Pavel <[email protected]>
make gulfsharks() work for new structure

e0faa664bc4f2aae15d89af9a92347169490f16b authored almost 5 years ago by Pavel <[email protected]>
update deps

0416e8d1a09db8fefe50d52523f4c65f5fd61467 authored almost 5 years ago by Pavel <[email protected]>
reorganize files

33b7ea954177ca0b0951cd9157c23d8f32cb934b authored almost 5 years ago by Pavel <[email protected]>
update: locations, loci, meta, missing

d33197edaaa1b8fc017a9af8546d255edfcc01ba authored almost 5 years ago by Pavel V. Dimens <[email protected]>
update summary, locations! PopObj

Make PopObj an abstract type, and rename PopObj struct to PopData

667589278368650a40b04136a7313fcc0b7c239d authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update Manipulate.jl

be4a63fc44cf029557739120065a9117eccda470 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
start pecking away at Manipulate.jl

11024d1346c78aa2c61b015ed2b043fabf47d582 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
wrap up new popgen import

4274873373eebcb7c309fc2ad55f5cbd7dcd1ff5 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

b7f37e23931dbec5309e6aac2eee7c491d4c6d1e authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

26e04c5d3d37aa9280f1bfb9af310d0acc21c3f2 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update readgen_new.jl

d4b985cbe478cd7e2bce32f3e59880466a02dd6d authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

6df239c6353f092abad4335d66a4ab636e5d71c7 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
get workable genepop reader

Needs to be optimized for speed/memory at row merge section

e33cb4e242e2db22d652f96a24776563a9f0862b authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

45e712264e381884ef448003be2fdfd96d827882 authored almost 5 years ago by Pavel <[email protected]>
Update orcid.png

b16b20ba896ddbf14a4bb58f54a7af052af81b94 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

21a43e31f939a77380f4d19b3210dc06f85e8e58 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
fix nancycats ID's

21280634a4128b9bfd9b1b42fa11859289ccbd2e authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

6c5edf20d6d0e12de385a8d411d985e80aa06d9a authored almost 5 years ago by Pavel <[email protected]>
Update install_carbon.png

273b93b1829e6e3d3ae8dc5b237884ee6c84a23f authored almost 5 years ago by Pavel <[email protected]>
Update HardyWeinberg.jl

f285d1592267ad9ddd4f89326e2c601cdbf6f406 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
create ishet() functions for super fast heterozygosity

3be1ef5abbb24294b3ce137ac25fba742e07c4d8 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

86ec47cb68256131c65204a084b956fd02bc5a92 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

23a2222f48bfb410fd192fe8e73a2a929382224c authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update newtypes_JDB.jl

bbf881ab97ded05880957ebbaa5aed75c6ffd0bd authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopObj.jl

5379d654556fa3c0b13123664957d6fa22172e90 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

f4f894cdc75d652da34e281720e9bdc093f7682f authored almost 5 years ago by Pavel V. Dimens <[email protected]>
update show

a553793e65039cb2325f902305909bb8a6699673 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

c541bf2566175d23ce1ce421433693108b122173 authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

61abdf4f7d4dead505eee6ee96b30a8c4856d00b authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

multi-threaded

1a5fb4e0c2c08bc077510b062dd3bc5a19a42822 authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

4591a8a05b580570748119e47e56a09ddccb73c0 authored almost 5 years ago by Jason Selwyn <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

5536daeff0abf0403600f5aedea0e3e98212e834 authored almost 5 years ago by Jason Selwyn <[email protected]>
Update PairwiseRelatedness.jl

1a0e153dd78c9f3bd445803a94bf006b40bd99b7 authored almost 5 years ago by Jason Selwyn <[email protected]>
add convenience types and Base.show() overload for it

4502aca411ca88f3495da54dea9a964ae61cc431 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'master' into pdimens

d1c568816abfcc157f43e4ebaac1adc492fd4e08 authored almost 5 years ago by Pavel <[email protected]>
add condition to genepop() to purge trailing whitespace columns

replace populations!() with 4 different methods and update docstring accordingly

b78dc27d20aa615e1f5839eb6ce8352cd5d8cca4 authored almost 5 years ago by Pavel <[email protected]>
Update PairwiseRelatedness.jl

2021032a75145244b76313fc6cad1a739e2c50a7 authored almost 5 years ago by jdselwyn <[email protected]>
Merge branch 'pdimens' of https://github.com/pdimens/PopGen.jl into pdimens

c09158e604b8899cf4db19a8d2c00c668a7529d1 authored almost 5 years ago by Pavel <[email protected]>
docs reorganization

a8d9ed26a717b58ba62540ae30bca0ba8415b318 authored almost 5 years ago by Pavel <[email protected]>
Update PopGen.jl

d11378f90b0039d7d620894cd456bb808ecb9ff2 authored almost 5 years ago by jdselwyn <[email protected]>
update Read.jl docstrings

e4fad0895c36b40a2006a7f7897b8c1fb402e0c9 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
fix nancycats formatting

63ef20fcb384b4f5f033f7bf965af8efeac3155d authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update Read.jl

add Missing method for phase_dip

57fa346a553b52d5218e02ba007ae476daaf2676 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add CSV to deps

57676daa18d57cb90b7c1d8d89a78bcaf923f2e8 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

a26d2302eb1e849f19241396de29f2ded3a947aa authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add CSV dep

6f852e2abd6a7a8550f6c72f0a89a6a850d67363 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update PopGen.jl

b5296a4192bb22eb3ae509490922ae3f00ac897b authored almost 5 years ago by jdselwyn <[email protected]>
entire rewrite of delimited() and genepop() and read()

delimtied is faster and lighter
genepop is same speed but uses up to 70% less RAM
read is parsim...

1b54863a8444c65ebe359c92608263c9fca0df03 authored almost 5 years ago by Pavel <[email protected]>
Delete Project.toml

744548631ccc089816dccb8f2c6b16d67244d251 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Delete Manifest.toml

65d16e2b15630800eeaf59197fbc12d6c71e4a17 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
add playtest folder and add to gitignore

4a540654acda70ee085e80e6be759486316f3412 authored almost 5 years ago by Pavel <[email protected]>
minor playtest organization

91e5778692163f9eab3b1629cdb86040a34fc73f authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

da8897a302c4cfee032a000f1c3a5338d9e51455 authored almost 5 years ago by Pavel <[email protected]>
leverage CSV.jl for delim file import

ed186d5a4b26362af192be938375fa8bd23a75e4 authored almost 5 years ago by Pavel <[email protected]>
rewrite of missing()

And updating docs to reflect changes.
Absolutely breaks plot_missing(), but that needs to be rew...

ef9bb111427bfbfc0860e7394abd75c8c19e4b0b authored almost 5 years ago by Pavel V. Dimens <[email protected]>
fix nancycats data + early het fix

cfa37313110fa375c7a3c4a55fba886af8a183bf authored almost 5 years ago by Pavel <[email protected]>
deps and module fixes

77da1ba2ae0ec1052e8061869319b3e64f85ade7 authored almost 5 years ago by Pavel <[email protected]>
update dependencies

0c853457a18efdadda7b154618951c3a8e4a9a0c authored almost 5 years ago by Pavel <[email protected]>
fix bcf() error, minor populations() update

b7b77d6150fdcf69240354e5cdafad7797ef4919 authored almost 5 years ago by Pavel <[email protected]>
fix broken het function

bad29d8122df1028d995bbaf2e67b2c2e86539ea authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'master' into dev

cc36574692e8f1319d9ca3e4fadbad08cb024991 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update mkdocs.yml

a3304a6d7ae0cfbdaec24379847b86bce21672b9 authored almost 5 years ago by Pavel <[email protected]>
refine populations()

99ce4c2b22b57561a2adcbd34d8acd1dc0e68275 authored almost 5 years ago by Pavel <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

ea439ecc0edbf298a4c52347c883ba910985a8c5 authored almost 5 years ago by Pavel <[email protected]>
Update community.md

46cca32ed333f752a5a6a81beb6e507933e1c1ab authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update community.md

17ca261913f61914ec172d6d3f22ef4aa02bd8af authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Update mkdocs.yml

e4f4d4059bad79d8b5aae5891c6236b64d493626 authored almost 5 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

0044d6292b52edc3b078feedca41595af8d3722e authored almost 5 years ago by Pavel V. Dimens <[email protected]>