github.com/BioJulia/PopGen.jl commits | Ecosyste.ms: OpenCollective

Queller & Goodnight

9afa0248da6e972839e4b3a312636ec31c37b85f authored about 5 years ago by Jason Selwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

58622e7e216ea084a1c0256174a96af9bb290f5b authored about 5 years ago by Pavel <[email protected]>

big docs cleanup for latest

29beb9cef5d48f646c4dcf2d92c1de356a3ce66c authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

bbf84f60aa9d8552543cb966168b19b59c2851d4 authored about 5 years ago by jdselwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

953dbf52a557912bb3a687b1cc5d23d525778e99 authored about 5 years ago by jdselwyn <[email protected]>

update docs

3b54c7fc15eaf4bd1644528611901c80dbd8c1f6 authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

642cdf8cb3004ceb6e7f738ede11dcb205d6b968 authored about 5 years ago by jdselwyn <[email protected]>

replace logo in docs

757184578a214d67117bbfcad50119daf3d8b054 authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

c91f0f9bd6b68a13856d1826183d7b680086ceea authored about 5 years ago by Pavel <[email protected]>

fix hwe and update docs

57361068d6b8563710c3f0aedb57103ea807a213 authored about 5 years ago by Pavel <[email protected]>

Update README.md

fdc13bd585bd31d67b8c1d6de7651ad85a6d75cd authored about 5 years ago by Pavel V. Dimens <[email protected]>

update docs a bit, rewrite summary()

315835881f77eeca23304e2b8f440e5ce7dbcd1d authored about 5 years ago by Pavel <[email protected]>

vfc() to PopObj improvements

4dc9c7b0c5a3cabfe08f325c22bd1ca831f0c76b authored about 5 years ago by Pavel <[email protected]>

add generic method to allele_ and geno_ functions

Additional method(s) will accomodate generic typing for PopObj's that have unequal ploidy across...

44344cc2c6a62566774ab314eca262caea43bfdc authored about 5 years ago by Pavel <[email protected]>

rewrite missing(), add read()

eb5250c3f6650d45fc8f59d5a05b372ef6d74c23 authored about 5 years ago by Pavel <[email protected]>

fixed all broken f() in AlleleFreq

moved allele_avg to SummaryInfo.jl

a6d993158e0b2530618022abc6cf0baffe06523b authored about 5 years ago by Pavel <[email protected]>

add info comment to richness

80ef0b1a0bca9b5fda155486e303992218cc0ea3 authored about 5 years ago by Pavel <[email protected]>

optimize for speed and allocations

c1ff6c782819813b8a4b241105fc15887cc86b45 authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

4d00852a1e5b83be9ee84ffdc2a62f7a8dbd5636 authored about 5 years ago by Pavel <[email protected]>

Update AlleleFreq.jl

9f5fdd74a0914f76ef8f079e2b76b46fe5adec33 authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

79731099af6b6992f1936b7a1d2d5697fd56e050 authored about 5 years ago by jdselwyn <[email protected]>

Update SummaryInfo.jl

4abc30ef65739b3f3a090f7bdec98e287bfb51da authored about 5 years ago by jdselwyn <[email protected]>

fixed nancycats

4acdb674093d1d8f6b8431e7371caacb1539c83b authored about 5 years ago by Pavel <[email protected]>

Create SummaryInfo.jl

Basic allelic richness. To be built upon

6e6f0867620d89363d9ddb61268ded968993b252 authored about 5 years ago by jdselwyn <[email protected]>

replace x with data and remove popopt

9712e9a8081a04eb790e2e890123301243f866aa authored about 5 years ago by Pavel <[email protected]>

fix everything I broke with genepop()

bb52c3dc16aba79859eb26768c758082a4af7e5a authored about 5 years ago by Pavel <[email protected]>

Update README.md

40ee17db48155cd77e98072bb671d81cbab72e7c authored about 5 years ago by Pavel V. Dimens <[email protected]>

Merge branch 'JuliaDB' into dev

905935672b2983ff3d35cfeaddaeab534d782bd5 authored about 5 years ago by Pavel <[email protected]>

clean up Read.jl and optimize a bit

added phase() function to make file importers more modular and allow map() usage within the read...

59e837ce9dd1c4a3e787c760edd0ba0669baf7c6 authored about 5 years ago by Pavel <[email protected]>

Update README.md

4658e45dc633dab69cd9b7e8ccb3002c07781fa7 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

8cf3dafa097f0d3bf05f38bbe3e979124192326c authored about 5 years ago by Pavel V. Dimens <[email protected]>

Add files via upload

6c023c8afe1b38e1c697fefd9b73e1532904c156 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

9316bcd5cf819494b6253f9792f81bbcfa876720 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

386bcd05e2d89a5aba598bd8abd658d71f1086c9 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Add files via upload

25e89964c332c57c103e27ffc23440183831de88 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

7b3177da01e24693e536dcf98ec38c8af0beba37 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

a7babe01cd21c6b2ab396aa9bf2d73c387fe2dd9 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

f8db2552ba3d63a0ea11f7b3bcc2f51927cb25eb authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

277201a5ac3a60c5a05e26f6faf59fe486a67f39 authored about 5 years ago by Pavel V. Dimens <[email protected]>

all sorts of stuff

more JuliaDB effort (incomplete), changing carbon img to gif

41789430f528e0384e32cb5d483b0edcb91c0030 authored about 5 years ago by Pavel <[email protected]>

Merge branch 'JuliaDB' of https://github.com/pdimens/PopGen.jl into JuliaDB

d21272df1655775fd8035275773cf4613a5ff218 authored about 5 years ago by Pavel <[email protected]>

Add files via upload

5658976adf9ecf49aa726dcb641a60d9d347fe34 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

d773890e1f4f65dc186fcfde68397937a4e9541b authored about 5 years ago by Pavel V. Dimens <[email protected]>

New logo!

de633adf2d2c51f15afc9ed0033cf3c8d8a14659 authored about 5 years ago by Pavel V. Dimens <[email protected]>

more tables testing

786932503145d87a55c4cc3ced0b318e55640b92 authored about 5 years ago by Pavel <[email protected]>

Update AlleleFreq.jl

759732ad1f73c7ea6b9026a48b6d691d88cfafc7 authored about 5 years ago by Pavel <[email protected]>

start table output setup

8803dc0391c8f2d0669c5832c93790b2dd4b5a61 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update AlleleFreq.jl

minor optimizations

0e5131502e42b432e3bb4c7e4cf36fff00ac32cd authored about 5 years ago by Pavel <[email protected]>

some early changes

rename instances of x::PopObj with data::PopObj for clarity. In general, be more verbose/obvious...

a622c727c250af53641ae6f6719bf81d0b813654 authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

e732335f34e9ff9607e64ddda9fc4e699a4b6e9c authored about 5 years ago by Jason Selwyn <[email protected]>

minor touchups

6eda29b9609a7a442384b57e457f151d5975221a authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

8a90ea1cf151faf5ed752d8a4c87f59d0e277136 authored about 5 years ago by Jason Selwyn <[email protected]>

Update PairwiseRelatedness.jl

803730039e73fee1bfdf9c6e6e3c1ba364cdd77b authored about 5 years ago by Jason Selwyn <[email protected]>

update allele_avg docstring

0455b99254f0959c4a0446235a9bd07bcc120655 authored about 5 years ago by Pavel <[email protected]>

add rounding to allele_avg

da526595e18f38014205cbd1d51b5b9be3a08e0b authored about 5 years ago by Pavel <[email protected]>

add allele_avg

953ca14b2575666096f0b526e01085fc3fb7f9b0 authored about 5 years ago by Pavel <[email protected]>

finish basic FST

d2df618a6c30a2743ea66087854a8ace02e81354 authored about 5 years ago by Pavel <[email protected]>

setting up some stuff for Fstats and adding @info tags

23e414042edb94d2561cba466cbed70949873d32 authored about 5 years ago by Pavel V. Dimens <[email protected]>

start basic fstats

d078e42f5a018f8355fce7224d2c9544b5e3d714 authored about 5 years ago by Pavel V. Dimens <[email protected]>

progress bar

131b3316fede4489bbdbf7b5aa0ae525536ff146 authored about 5 years ago by jdselwyn <[email protected]>

add linear algebra

f9113c0e99dcc2e8365cf4afa55f7ced8aa2a370 authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

8961fae8f90e7619c61807adfea4313d44f16c9e authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

e1b0e7dcd0eddb68ad7537cb230a48f86b1849cf authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

2169c224bb1dcf8ca5e4b56e1fc6ccbbd718c66c authored about 5 years ago by jdselwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

d79604caa4c659f6c53a448502955651096de4c4 authored about 5 years ago by jdselwyn <[email protected]>

solver tests

f08bf2f3a0ae63b8d7b3ef5e41536ea1da44c2b3 authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

82421bed5ecdc5f088dfb617ae588da27fc1936d authored about 5 years ago by jdselwyn <[email protected]>

add allele_freq(tuple)

Added method to allele_freq to work on a single genotype (tuple)

3ae3b3cfee483666b9443faaf918963165db1e5c authored about 5 years ago by Pavel <[email protected]>

housekeeping: organize functions alphabetically

ef4ca3681dd674278a0b0ca4488af02b9acbb82a authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

75b393bb5614e8cd11d8c732b788769833c13a3c authored about 5 years ago by Pavel <[email protected]>

Typed variable inputs

f76d703759c88b0cfd9f7f97e0b985f5bf51ce42 authored about 5 years ago by jdselwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

47ab6193fc2a55a0856a6e62b327e52bb6db3b1a authored about 5 years ago by Pavel <[email protected]>

add prelim relatedness docs

9339dac88b556eb43e305c1b062def240bdf73c0 authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

389e299ae2ec0c562fe64da57148ed1f77ff7a53 authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

268032d73cc351c24662e5ad8fa0f42c16ffb951 authored about 5 years ago by jdselwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

5ffb4a4ba26bee969890caef7edf17e2adf5d3f5 authored about 5 years ago by Pavel <[email protected]>

Create relatedness.md

e9d1dd51ccf0a296e72087ddaa891397c77e6d18 authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

9cca98616887a0b29184089942d711ca0ccae4c8 authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

9d99fc390a483068a2ed18136eb6fa30ed2dc41d authored about 5 years ago by jdselwyn <[email protected]>

minor touchups

e8f7a631ad36f90bc92de0df0906871a248de854 authored about 5 years ago by Pavel <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

aa3057aaab47a1dcc844d5645003e6d80db2e229 authored about 5 years ago by Pavel <[email protected]>

add new deps

8d6e14f84d6fb91bcb9821351bf7ce2c955473ba authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

edd507b348a11f2bcf2ac6f531e3707b59c181a1 authored about 5 years ago by jdselwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

9ab137cd7402200500f8436d41442efac0a49262 authored about 5 years ago by jdselwyn <[email protected]>

Update PairwiseRelatedness.jl

012741ba6599c072a2c823f364c0c223d8550de5 authored about 5 years ago by jdselwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

ede9f8ac2b5f7cafdb77548ae028b15087e19f87 authored about 5 years ago by Pavel <[email protected]>

Update popobj_type.md

737c995ba75fe33805c1e7ef75a43283c79d84ae authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

e9f489773bc6ae6e9963bd3a63ce2086783e4379 authored about 5 years ago by Jason Selwyn <[email protected]>

Update PairwiseRelatedness.jl

3d1f7f81a4513b607c5038121860ca68ccd901ef authored about 5 years ago by Jason Selwyn <[email protected]>

Update PairwiseRelatedness.jl

1c3ae3161d7b1c4832bc259de81ed63ec692dba7 authored about 5 years ago by Jason Selwyn <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

b58b25b4fdc921cc5c35ae97b3ba71b4354efd98 authored about 5 years ago by Jason Selwyn <[email protected]>

Update PairwiseRelatedness.jl

a16b76d7502d98f5e8582532fda0a99be7f76663 authored about 5 years ago by Jason Selwyn <[email protected]>

Update README.md

c1f4c45210abc043f5bcd600a7b3773e26733f39 authored about 5 years ago by Pavel V. Dimens <[email protected]>

Update README.md

fb9974c43b1f4b6a91bda96294f5dfe93d69abd2 authored about 5 years ago by Pavel <[email protected]>

some housekeeping for docs

2b7f9cbc361fa833bac71c72fdf10730e649ac7c authored about 5 years ago by Pavel <[email protected]>

rename allele_freq_mini to allele_freq

4bf5b9d4812ccc73caf0d64e3e7117a59bb92e0b authored about 5 years ago by Pavel <[email protected]>

fix hwe_test(..by_pop = true...)

Corrections are now accurate across dataframes

d3dc9e6dfb1b2a5485aa7fe36dbf4a8091a95469 authored about 5 years ago by Pavel <[email protected]>

change info lines in readers

and update Pr_L_S output

0baea7679f25231a960e4bb636289a2b3ac610eb authored about 5 years ago by Pavel <[email protected]>

Update PairwiseRelatedness.jl

39ed3db5a271e1beb667e19f1a2e8dc99aac4726 authored about 5 years ago by Jason Selwyn <[email protected]>

Update PairwiseRelatedness.jl

1e8c0aa7a494e44b187110312c75e58656f2d8e4 authored about 5 years ago by Jason Selwyn <[email protected]>