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1.5.18 #320

Merged
merged 253 commits into from
Jun 8, 2024
Merged

1.5.18 #320

merged 253 commits into from
Jun 8, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Nov 24, 2021

  1. Merge pull request #233 from marouenbg/update-desc 

    update website
    @marouenbg
    marouenbg authored Nov 24, 2021
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Commits on Dec 21, 2021

  1. add crane and docs

    @marouenbg
    marouenbg committed Dec 21, 2021
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  2. update crane

    @marouenbg
    marouenbg committed Dec 21, 2021
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  3. update worflow

    @marouenbg
    marouenbg committed Dec 21, 2021
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Commits on Dec 22, 2021

  1. Merge pull request #235 from marouenbg/add-crane 

    add crane and docs
    @marouenbg
    marouenbg authored Dec 22, 2021
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Commits on Jan 29, 2022

  1. update crane

    @marouenbg
    marouenbg committed Jan 29, 2022
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  2. update workflows

    @marouenbg
    marouenbg committed Jan 29, 2022
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  3. update workflows

    @marouenbg
    marouenbg committed Jan 29, 2022
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  4. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  5. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  6. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  7. update workfolw

    @marouenbg
    marouenbg committed Jan 29, 2022
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  8. Update main.yml

    @marouenbg
    marouenbg authored Jan 29, 2022
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  9. Update main.yml

    @marouenbg
    marouenbg authored Jan 29, 2022
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  10. Update main.yml

    @marouenbg
    marouenbg authored Jan 29, 2022
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Commits on Jan 30, 2022

  1. Merge pull request #236 from marouenbg/fix-crane-alpaca 

    update crane
    @marouenbg
    marouenbg authored Jan 30, 2022
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Commits on Feb 15, 2022

  1. fix lioness py

    @marouenbg
    marouenbg committed Feb 15, 2022
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  2. udpate lioness in R

    @marouenbg
    marouenbg committed Feb 15, 2022
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Commits on Feb 16, 2022

  1. include calculations python

    @marouenbg
    marouenbg committed Feb 16, 2022
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Commits on Feb 17, 2022

  1. update panda rm missing

    @marouenbg
    marouenbg committed Feb 17, 2022
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  2. update panda

    @marouenbg
    marouenbg committed Feb 17, 2022
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  3. update lioness joblib

    @marouenbg
    marouenbg committed Feb 17, 2022
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  4. revert commits

    @marouenbg
    marouenbg committed Feb 17, 2022
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  5. fix conflcit

    @marouenbg
    marouenbg committed Feb 17, 2022
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  6. ALPACA fix to NAs in community assignement

    @marouenbg
    marouenbg committed Feb 17, 2022
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Commits on Feb 18, 2022

  1. version bump

    @marouenbg
    marouenbg committed Feb 18, 2022
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  2. Merge pull request #238 from marouenbg/upgrade-alpaca 

    ALPACA fix to NAs in community assignment
    @marouenbg
    marouenbg authored Feb 18, 2022
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  3. revert lioness

    @marouenbg
    marouenbg committed Feb 18, 2022
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  4. update crane with alpaca changes

    @marouenbg
    marouenbg committed Feb 18, 2022
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  5. update lioness

    @marouenbg
    marouenbg committed Feb 18, 2022
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  6. Merge pull request #239 from marouenbg/update-crane 

    update crane with alpaca changes
    @marouenbg
    marouenbg authored Feb 18, 2022
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  7. update lioness python

    @marouenbg
    marouenbg committed Feb 18, 2022
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  8. fix test

    @marouenbg
    marouenbg committed Feb 18, 2022
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  9. update workflows

    @marouenbg
    marouenbg committed Feb 18, 2022
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Commits on Feb 19, 2022

  1. put back github actions

    @marouenbg
    marouenbg committed Feb 19, 2022
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  2. Merge pull request #237 from marouenbg/fix-panda-py 

    fix lioness py
    @marouenbg
    marouenbg authored Feb 19, 2022
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Commits on Feb 22, 2022

  1. Fixed typo

    Kate Hoff Shutta committed Feb 22, 2022
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Commits on Feb 25, 2022

  1. Added LIONESS-pearson option + unit test

    Kate Hoff Shutta committed Feb 25, 2022
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  2. Merge branch 'kate-dev' of https://github.com/katehoffshutta/netZooR … 

    …into kate-dev
    Kate Hoff Shutta committed Feb 25, 2022
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  3. changed param labels in LIONESS example

    Kate Hoff Shutta committed Feb 25, 2022
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Commits on Feb 28, 2022

  1. updated docs for lioness() function

    Kate Hoff Shutta committed Feb 28, 2022
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Commits on Mar 1, 2022

  1. Update main.yml

    @marouenbg
    marouenbg authored Mar 1, 2022
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  2. Merge branch 'devel' into kate-dev

    @marouenbg
    marouenbg authored Mar 1, 2022
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  3. Update main.yml

    @marouenbg
    marouenbg authored Mar 1, 2022
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  4. Merge pull request #241 from katehoffshutta/kate-dev 

    Kate dev
    @marouenbg
    marouenbg authored Mar 1, 2022
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Commits on Apr 26, 2022

  1. bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

    @nturaga
    nturaga committed Apr 26, 2022
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  2. bump x.y.z version to odd y following creation of RELEASE_3_15 branch

    @nturaga
    nturaga committed Apr 26, 2022
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Commits on Jun 10, 2022

  1. Update DESCRIPTION

    @marouenbg
    marouenbg authored Jun 10, 2022
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Commits on Jun 16, 2022

  1. fix crane issue #240

    @marouenbg
    marouenbg committed Jun 16, 2022
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  2. Merge pull request #244 from marouenbg/fix-crane 

    fix crane issue #240
    @marouenbg
    marouenbg authored Jun 16, 2022
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Commits on Jun 23, 2022

  1. expanded PANDA and LIONESS description

    @katehoffshutta
    katehoffshutta committed Jun 23, 2022
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Commits on Jun 24, 2022

  1. update crane fix

    @marouenbg
    marouenbg committed Jun 24, 2022
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  2. added ALPACA, EGRET, and OTTER descriptions

    @katehoffshutta
    katehoffshutta committed Jun 24, 2022
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  3. Update README.md

    @katehoffshutta
    katehoffshutta authored Jun 24, 2022
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  4. Merge pull request #245 from marouenbg/fix-crane-2 

    update crane fix
    @marouenbg
    marouenbg authored Jun 24, 2022
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Commits on Jun 27, 2022

  1. typo in na.rm

    @marouenbg
    marouenbg committed Jun 27, 2022
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  2. Merge pull request #246 from marouenbg/fix-crane-3 

    typo in na.rm
    @marouenbg
    marouenbg authored Jun 27, 2022
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  3. update workflow

    @marouenbg
    marouenbg committed Jun 27, 2022
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  4. update workflow2

    @marouenbg
    marouenbg committed Jun 27, 2022
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  5. fix-actions-3

    @marouenbg
    marouenbg committed Jun 27, 2022
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  6. add r lib v2

    @marouenbg
    marouenbg committed Jun 27, 2022
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  7. add r lib v2

    @marouenbg
    marouenbg committed Jun 27, 2022
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Commits on Jun 28, 2022

  1. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  2. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  3. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  4. update condor test

    @marouenbg
    marouenbg committed Jun 28, 2022
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  5. show testthat output

    @marouenbg
    marouenbg committed Jun 28, 2022
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  6. add pandoc and use cache

    @marouenbg
    marouenbg committed Jun 28, 2022
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  7. use built in check

    @marouenbg
    marouenbg committed Jun 28, 2022
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  8. use built in check

    @marouenbg
    marouenbg committed Jun 28, 2022
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  9. update actions with built in check

    @marouenbg
    marouenbg committed Jun 28, 2022
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  10. bump version

    @marouenbg
    marouenbg committed Jun 28, 2022
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  11. use built in coverage

    @marouenbg
    marouenbg committed Jun 28, 2022
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  12. use built in coverage

    @marouenbg
    marouenbg committed Jun 28, 2022
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  13. remove sudo

    @marouenbg
    marouenbg committed Jun 28, 2022
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  14. update actions

    @marouenbg
    marouenbg committed Jun 28, 2022
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  15. update actions

    @marouenbg
    marouenbg committed Jun 28, 2022
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  16. removed sudo from actions

    @marouenbg
    marouenbg committed Jun 28, 2022
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  17. ugrade to R42

    @marouenbg
    marouenbg committed Jun 28, 2022
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  18. remove virtualenv

    @marouenbg
    marouenbg committed Jun 28, 2022
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  19. remove virtualenv

    @marouenbg
    marouenbg committed Jun 28, 2022
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  20. remove virtualenv

    @marouenbg
    marouenbg committed Jun 28, 2022
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Commits on Jun 29, 2022

  1. modify condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  2. update condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  3. update condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  4. adding retiucualte to covr

    @marouenbg
    marouenbg committed Jun 29, 2022
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  5. adding retiucualte to covr

    @marouenbg
    marouenbg committed Jun 29, 2022
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  6. add panda test to coverignore

    @marouenbg
    marouenbg committed Jun 29, 2022
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  7. update actions

    @marouenbg
    marouenbg committed Jun 29, 2022
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  8. remove lioness tests from coverage

    @marouenbg
    marouenbg committed Jun 29, 2022
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  9. remove lioness tests from coverage

    @marouenbg
    marouenbg committed Jun 29, 2022
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  10. added MONSTER and SAMBAR

    @katehoffshutta
    katehoffshutta committed Jun 29, 2022
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  11. Merge branch 'master' of https://github.com/katehoffshutta/netZooR

    @katehoffshutta
    katehoffshutta committed Jun 29, 2022
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  12. remove lionessR test

    @marouenbg
    marouenbg committed Jun 29, 2022
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  13. Added CONDOR and YARN

    @katehoffshutta
    katehoffshutta committed Jun 29, 2022
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  14. Update README.md

    @katehoffshutta
    katehoffshutta authored Jun 29, 2022
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  15. Merge branch 'devel' into master

    @marouenbg
    marouenbg authored Jun 29, 2022
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  16. put back otter in rbuild

    @marouenbg
    marouenbg committed Jun 29, 2022
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  17. remove condor test

    @marouenbg
    marouenbg committed Jun 29, 2022
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Commits on Jun 30, 2022

  1. remove condor test

    @marouenbg
    marouenbg committed Jun 30, 2022
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  2. remove lioness docs

    @marouenbg
    marouenbg committed Jun 30, 2022
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  3. add lioness to buildingore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  4. donttest lionesss

    @marouenbg
    marouenbg committed Jun 30, 2022
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  5. remove coverage from ubuntu test

    @marouenbg
    marouenbg committed Jun 30, 2022
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  6. remove rbuilignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  7. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  8. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  9. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  10. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  11. update rbuildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  12. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  13. add back buildignore

    @marouenbg
    marouenbg committed Jun 30, 2022
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  14. add back buildignore

    @marouenbg
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  22. put back tests

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  23. add padanedge diff test

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  24. add back egeret test

    @marouenbg
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  25. add monster test

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Commits on Jul 1, 2022

  1. fix monster test

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  2. tolerance in expect equal

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  3. tolerance in expect equal

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  4. tolerance in expect equal

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  5. tolerance in expect equal

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  6. add sourceppi

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  7. fixed PANDA tests

    @marouenbg
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Commits on Jul 5, 2022

  1. modify panda test

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  2. update lioness test

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  3. fix expect message

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  4. update tests

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  5. update tests

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  6. update tests

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  7. update tests

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  8. update tests

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  9. update tests

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Commits on Jul 6, 2022

  1. reduced lioness test data

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  2. reduced lioness test data

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  3. reduced lioness test data

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  4. reduced lioness test data

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  5. reduce test size

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  6. Merge pull request #247 from marouenbg/fix-actions 

    update GitHub actions workflow
    @marouenbg
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  7. Merge pull request #248 from katehoffshutta/master 

    Extended zoo animal descriptions on readme
    @marouenbg
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Commits on Jul 7, 2022

  1. fix desc

    @marouenbg
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  2. updating bioc (#250) 

    * updating bioc

* remove empty lines

* remove empty lines
    @marouenbg
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  3. Merge branch 'master' into devel

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  4. Merge branch 'master' of https://github.com/netZoo/netZooR

    @marouenbg
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  5. update citation

    @marouenbg
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  6. update citation

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  7. Merge branch 'master' into devel

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  8. Merge branch 'master' of https://github.com/netZoo/netZooR

    @marouenbg
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  9. update citation

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Commits on Jul 15, 2022

  1. Update README.md

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  2. Update README.md

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  3. Update main.yml

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  4. Update main.yml

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  5. Update .Rbuildignore

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Commits on Jul 19, 2022

  1. Update .Rbuildignore

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  2. update lioness test

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  3. removed two last lioness tests

    @marouenbg
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  4. removed two last lioness tests

    @marouenbg
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  5. removed two last lioness tests

    @marouenbg
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  6. no saving of lioness networks

    @marouenbg
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  7. no saving of lioness networks

    @marouenbg
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  8. no saving of lioness networks

    @marouenbg
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Commits on Jul 20, 2022

  1. no saving of lioness networks

    @marouenbg
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  2. update lioness test

    @marouenbg
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  3. lower sizeof test

    @marouenbg
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  4. update test data

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  5. update test data

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  6. update test data

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  7. Merge remote-tracking branch 'upstream/devel'

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  9. reduce panda tests

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  10. remove old test data

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  11. remove old test data

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  12. Merge branch 'master' into devel

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  13. Merge remote-tracking branch 'upstream/master'

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  14. Merge remote-tracking branch 'upstream/master'

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Commits on Jul 21, 2022

  1. Update main.yml

    @marouenbg
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Commits on Aug 16, 2022

  1. 1.1.16 

    update pandapy with header argument (#260)
    @marouenbg
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Commits on Aug 23, 2022

  1. trying collapse readme (#261) 

    * trying collapse readme

* collapse animal description
    @marouenbg
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  2. Update README.md

    @marouenbg
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Commits on Oct 31, 2022

  1. Fix news file formatting 

      o was not rendering list properly
    @lshep
    lshep committed Oct 31, 2022
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Commits on Nov 1, 2022

  1. bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

    @jwokaty
    jwokaty committed Nov 1, 2022
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  2. bump x.y.z version to odd y following creation of RELEASE_3_16 branch

    @jwokaty
    jwokaty committed Nov 1, 2022
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Commits on Nov 25, 2022

  1. update biconda (#265)

    @marouenbg
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Commits on Dec 15, 2022

  1. add spider (#269) 

    * add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug
    @marouenbg
    marouenbg authored Dec 15, 2022
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Commits on Dec 19, 2022

  1. Merge branch 'master' into devel

    @marouenbg
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  2. Merge remote-tracking branch 'upstream/master'

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  3. adding spider

    @marouenbg
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Commits on Dec 21, 2022

  1. DRAGON and unit tests work in progress (#267) 

    - add DRAGON in R and unit tests
    @katehoffshutta
    katehoffshutta authored Dec 21, 2022
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Commits on Jan 10, 2023

  1. update lioness (#276)

    @marouenbg
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Commits on Jan 17, 2023

  1. update lioness code (#277)

    @marouenbg
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  2. Update LIONESS.R

    @marouenbg
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  3. Update LIONESS.R

    @marouenbg
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Commits on Jan 18, 2023

  1. Update LIONESS.R

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Commits on Feb 10, 2023

  1. add note about the function (#279) 

    * add note about the function

* Update sourcePPI.R
    @marouenbg
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Commits on Feb 13, 2023

  1. Update README.md

    @marouenbg
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  2. Update README.md

    @marouenbg
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Commits on Feb 15, 2023

  1. Update sourcePPI.R

    @marouenbg
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  2. Update sourcePPI.R

    @marouenbg
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  3. add details about sourcePPI (#280)

    @marouenbg
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Commits on Feb 22, 2023

  1. add parallelization option to lioness (#281) 

    * 1.2.1 (#271)

* add bioc information

* update website

* add crane and docs

* update crane

* update worflow

* update crane

* update workflows

* update workflows

* update workfolw

* update workfolw

* update workfolw

* update workfolw

* Update main.yml

* Update main.yml

* Update main.yml

* fix lioness py

* udpate lioness in R

* include calculations python

* update panda rm missing

* update panda

* update lioness joblib

* revert commits

* ALPACA fix to NAs in community assignement

* version bump

* revert lioness

* update crane with alpaca changes

* update lioness

* update lioness python

* fix test

* update workflows

* put back github actions

* Fixed typo

* Added LIONESS-pearson option + unit test

* changed param labels in LIONESS example

* updated docs for lioness() function

* Update main.yml

* Update main.yml

* Update DESCRIPTION

* fix crane issue #240

* expanded PANDA and LIONESS description

* update crane fix

* added ALPACA, EGRET, and OTTER descriptions

* Update README.md

* typo in na.rm

* update workflow

* update workflow2

* fix-actions-3

* add r lib v2

* add r lib v2

* update condor test

* update condor test

* update condor test

* update condor test

* show testthat output

* add pandoc and use cache

* use built in check

* use built in check

* update actions with built in check

* bump version

* use built in coverage

* use built in coverage

* remove sudo

* update actions

* update actions

* removed sudo from actions

* ugrade to R42

* remove virtualenv

* remove virtualenv

* remove virtualenv

* modify condor test

* update condor test

* update condor test

* adding retiucualte to covr

* adding retiucualte to covr

* add panda test to coverignore

* update actions

* remove lioness tests from coverage

* remove lioness tests from coverage

* added MONSTER and SAMBAR

* remove lionessR test

* Added CONDOR and YARN

* Update README.md

* put back otter in rbuild

* remove condor test

* remove condor test

* remove lioness docs

* add lioness to buildingore

* donttest lionesss

* remove coverage from ubuntu test

* remove rbuilignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* put back tests

* add padanedge diff test

* add back egeret test

* add monster test

* fix monster test

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* add sourceppi

* fixed PANDA tests

* modify panda test

* update lioness test

* fix expect message

* update tests

* update tests

* update tests

* update tests

* update tests

* update tests

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduce test size

* updating bioc (#250)

* updating bioc

* remove empty lines

* remove empty lines

* update citation

* update citation

* Update README.md

* Update README.md

* Update main.yml

* Update main.yml

* Update .Rbuildignore

* Update .Rbuildignore

* update lioness test

* removed two last lioness tests

* removed two last lioness tests

* removed two last lioness tests

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* update lioness test

* lower sizeof test

* update test data

* update test data

* update test data

* reduce panda tests

* remove old test data

* remove old test data

* Update main.yml

* 1.1.16

update pandapy with header argument (#260)

* trying collapse readme (#261)

* trying collapse readme

* collapse animal description

* Update README.md

* update biconda (#265)

* add spider (#269)

* add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug

Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>

* 1.2.2 (#273)

- add DRAGON

* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
    @laurenhsu1 @marouenbg @katehoffshutta
    4 people authored Feb 22, 2023
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Commits on Mar 14, 2023

  1. fix monster error

    @marouenbg
    marouenbg committed Mar 14, 2023
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  2. fix monster

    @marouenbg
    marouenbg committed Mar 14, 2023
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  3. Merge branch 'devel' of git.bioconductor.org:packages/netZooR into devel

    @marouenbg
    marouenbg committed Mar 14, 2023
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  4. 1.3.2

    @marouenbg
    marouenbg committed Mar 14, 2023
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  5. update tests

    @marouenbg
    marouenbg committed Mar 14, 2023
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  6. update bioc verssion

    @marouenbg
    marouenbg committed Mar 14, 2023
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Commits on Mar 16, 2023

  1. update monster test

    @marouenbg
    marouenbg committed Mar 16, 2023
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  2. update argument description

    @marouenbg
    marouenbg committed Mar 16, 2023
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  3. update argument description

    @marouenbg
    marouenbg committed Mar 16, 2023
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  4. changed date

    @marouenbg
    marouenbg committed Mar 16, 2023
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Commits on Mar 19, 2023

  1. updaate docs

    @marouenbg
    marouenbg committed Mar 19, 2023
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Commits on Mar 20, 2023

  1. update dragon verbose

    @marouenbg
    marouenbg committed Mar 20, 2023
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Commits on Mar 21, 2023

  1. update spider

    @marouenbg
    marouenbg committed Mar 21, 2023
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Commits on Mar 22, 2023

  1. prepare for puma

    @marouenbg
    marouenbg committed Mar 22, 2023
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Commits on Apr 12, 2023

  1. add puma (#270) 

    * add puma

* update PUMA

* updating mirna interactions

* add PUMA in readme

* Update PUMA.R
    @marouenbg
    marouenbg authored Apr 12, 2023
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  2. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Apr 12, 2023
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Commits on Apr 29, 2023

  1. Create TIGER.R (#272) 

    add TIGER.R
    @cchen22
    cchen22 authored Apr 29, 2023
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Commits on May 30, 2023

  1. Add lioness update (#284) 

    * update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* update lioness append code
    @marouenbg
    marouenbg authored May 30, 2023
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Commits on May 31, 2023

  1. Update puma (#286) 

    * update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* fix puma examples

* fix puma examples

* update docs
    @marouenbg
    marouenbg authored May 31, 2023
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  2. Add TIGER (#283) 

    * Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
    @cchen22 @marouenbg
    cchen22 and marouenbg authored May 31, 2023
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Commits on Jun 2, 2023

  1. Update DESCRIPTION

    @marouenbg
    marouenbg authored Jun 2, 2023
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  2. Add TIGER description to README file (#288) 

    * Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

* Update README.md

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
    @cchen22 @marouenbg
    cchen22 and marouenbg authored Jun 2, 2023
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  3. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Jun 2, 2023
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Commits on Sep 2, 2023

  1. Added COBRA method (#293) 

    * 1.4.0 (#289)

* add bioc information

* update website

* add crane and docs

* update crane

* update worflow

* update crane

* update workflows

* update workflows

* update workfolw

* update workfolw

* update workfolw

* update workfolw

* Update main.yml

* Update main.yml

* Update main.yml

* fix lioness py

* udpate lioness in R

* include calculations python

* update panda rm missing

* update panda

* update lioness joblib

* revert commits

* ALPACA fix to NAs in community assignement

* version bump

* revert lioness

* update crane with alpaca changes

* update lioness

* update lioness python

* fix test

* update workflows

* put back github actions

* Fixed typo

* Added LIONESS-pearson option + unit test

* changed param labels in LIONESS example

* updated docs for lioness() function

* Update main.yml

* Update main.yml

* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

* bump x.y.z version to odd y following creation of RELEASE_3_15 branch

* Update DESCRIPTION

* fix crane issue #240

* expanded PANDA and LIONESS description

* update crane fix

* added ALPACA, EGRET, and OTTER descriptions

* Update README.md

* typo in na.rm

* update workflow

* update workflow2

* fix-actions-3

* add r lib v2

* add r lib v2

* update condor test

* update condor test

* update condor test

* update condor test

* show testthat output

* add pandoc and use cache

* use built in check

* use built in check

* update actions with built in check

* bump version

* use built in coverage

* use built in coverage

* remove sudo

* update actions

* update actions

* removed sudo from actions

* ugrade to R42

* remove virtualenv

* remove virtualenv

* remove virtualenv

* modify condor test

* update condor test

* update condor test

* adding retiucualte to covr

* adding retiucualte to covr

* add panda test to coverignore

* update actions

* remove lioness tests from coverage

* remove lioness tests from coverage

* added MONSTER and SAMBAR

* remove lionessR test

* Added CONDOR and YARN

* Update README.md

* put back otter in rbuild

* remove condor test

* remove condor test

* remove lioness docs

* add lioness to buildingore

* donttest lionesss

* remove coverage from ubuntu test

* remove rbuilignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* put back tests

* add padanedge diff test

* add back egeret test

* add monster test

* fix monster test

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* add sourceppi

* fixed PANDA tests

* modify panda test

* update lioness test

* fix expect message

* update tests

* update tests

* update tests

* update tests

* update tests

* update tests

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduce test size

* updating bioc (#250)

* updating bioc

* remove empty lines

* remove empty lines

* update citation

* update citation

* update citation

* Update README.md

* Update README.md

* Update main.yml

* Update main.yml

* Update .Rbuildignore

* Update .Rbuildignore

* update lioness test

* removed two last lioness tests

* removed two last lioness tests

* removed two last lioness tests

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* update lioness test

* lower sizeof test

* update test data

* update test data

* update test data

* reduce panda tests

* remove old test data

* remove old test data

* Update main.yml

* 1.1.16

update pandapy with header argument (#260)

* trying collapse readme (#261)

* trying collapse readme

* collapse animal description

* Update README.md

* Fix news file formatting

  o was not rendering list properly

* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

* bump x.y.z version to odd y following creation of RELEASE_3_16 branch

* update biconda (#265)

* add spider (#269)

* add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug

* DRAGON and unit tests work in progress (#267)

- add DRAGON in R and unit tests

* update lioness (#276)

* update lioness code (#277)

* Update LIONESS.R

* Update LIONESS.R

* Update LIONESS.R

* add note about the function (#279)

* add note about the function

* Update sourcePPI.R

* Update README.md

* Update README.md

* Update sourcePPI.R

* Update sourcePPI.R

* add details about sourcePPI (#280)

* add parallelization option to lioness (#281)

* 1.2.1 (#271)

* add bioc information

* update website

* add crane and docs

* update crane

* update worflow

* update crane

* update workflows

* update workflows

* update workfolw

* update workfolw

* update workfolw

* update workfolw

* Update main.yml

* Update main.yml

* Update main.yml

* fix lioness py

* udpate lioness in R

* include calculations python

* update panda rm missing

* update panda

* update lioness joblib

* revert commits

* ALPACA fix to NAs in community assignement

* version bump

* revert lioness

* update crane with alpaca changes

* update lioness

* update lioness python

* fix test

* update workflows

* put back github actions

* Fixed typo

* Added LIONESS-pearson option + unit test

* changed param labels in LIONESS example

* updated docs for lioness() function

* Update main.yml

* Update main.yml

* Update DESCRIPTION

* fix crane issue #240

* expanded PANDA and LIONESS description

* update crane fix

* added ALPACA, EGRET, and OTTER descriptions

* Update README.md

* typo in na.rm

* update workflow

* update workflow2

* fix-actions-3

* add r lib v2

* add r lib v2

* update condor test

* update condor test

* update condor test

* update condor test

* show testthat output

* add pandoc and use cache

* use built in check

* use built in check

* update actions with built in check

* bump version

* use built in coverage

* use built in coverage

* remove sudo

* update actions

* update actions

* removed sudo from actions

* ugrade to R42

* remove virtualenv

* remove virtualenv

* remove virtualenv

* modify condor test

* update condor test

* update condor test

* adding retiucualte to covr

* adding retiucualte to covr

* add panda test to coverignore

* update actions

* remove lioness tests from coverage

* remove lioness tests from coverage

* added MONSTER and SAMBAR

* remove lionessR test

* Added CONDOR and YARN

* Update README.md

* put back otter in rbuild

* remove condor test

* remove condor test

* remove lioness docs

* add lioness to buildingore

* donttest lionesss

* remove coverage from ubuntu test

* remove rbuilignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* put back tests

* add padanedge diff test

* add back egeret test

* add monster test

* fix monster test

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* add sourceppi

* fixed PANDA tests

* modify panda test

* update lioness test

* fix expect message

* update tests

* update tests

* update tests

* update tests

* update tests

* update tests

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduce test size

* updating bioc (#250)

* updating bioc

* remove empty lines

* remove empty lines

* update citation

* update citation

* Update README.md

* Update README.md

* Update main.yml

* Update main.yml

* Update .Rbuildignore

* Update .Rbuildignore

* update lioness test

* removed two last lioness tests

* removed two last lioness tests

* removed two last lioness tests

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* update lioness test

* lower sizeof test

* update test data

* update test data

* update test data

* reduce panda tests

* remove old test data

* remove old test data

* Update main.yml

* 1.1.16

update pandapy with header argument (#260)

* trying collapse readme (#261)

* trying collapse readme

* collapse animal description

* Update README.md

* update biconda (#265)

* add spider (#269)

* add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug

Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>

* 1.2.2 (#273)

- add DRAGON

* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>

* fix monster error

* fix monster

* 1.3.2

* update tests

* update bioc verssion

* update monster test

* update argument description

* update argument description

* changed date

* updaate docs

* update dragon verbose

* update spider

* add puma (#270)

* add puma

* update PUMA

* updating mirna interactions

* add PUMA in readme

* Update PUMA.R

* Create TIGER.R (#272)

add TIGER.R

* Add lioness update (#284)

* update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* update lioness append code

* Update puma (#286)

* update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* fix puma examples

* fix puma examples

* update docs

* Add TIGER (#283)

* Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>

* Update DESCRIPTION

* Add TIGER description to README file (#288)

* Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

* Update README.md

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>

---------

Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Co-authored-by: lshep <lori.shepherd@roswellpark.org>
Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>
Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>

* Added COBRA method

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Co-authored-by: lshep <lori.shepherd@roswellpark.org>
Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>
Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>
    @soelmicheletti @marouenbg
    @nturaga @katehoffshutta @lshep @jwokaty @laurenhsu1 @cchen22
    9 people authored Sep 2, 2023
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Commits on Sep 7, 2023

  1. Update README.md

    @marouenbg
    marouenbg authored Sep 7, 2023
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Commits on Sep 18, 2023

  1. Update TIGER (#297)

    @cchen22
    cchen22 authored Sep 18, 2023
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  2. Smaller changes in COBRA (#296) 

    * 1.4.0 (#289)

* add bioc information

* update website

* add crane and docs

* update crane

* update worflow

* update crane

* update workflows

* update workflows

* update workfolw

* update workfolw

* update workfolw

* update workfolw

* Update main.yml

* Update main.yml

* Update main.yml

* fix lioness py

* udpate lioness in R

* include calculations python

* update panda rm missing

* update panda

* update lioness joblib

* revert commits

* ALPACA fix to NAs in community assignement

* version bump

* revert lioness

* update crane with alpaca changes

* update lioness

* update lioness python

* fix test

* update workflows

* put back github actions

* Fixed typo

* Added LIONESS-pearson option + unit test

* changed param labels in LIONESS example

* updated docs for lioness() function

* Update main.yml

* Update main.yml

* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

* bump x.y.z version to odd y following creation of RELEASE_3_15 branch

* Update DESCRIPTION

* fix crane issue #240

* expanded PANDA and LIONESS description

* update crane fix

* added ALPACA, EGRET, and OTTER descriptions

* Update README.md

* typo in na.rm

* update workflow

* update workflow2

* fix-actions-3

* add r lib v2

* add r lib v2

* update condor test

* update condor test

* update condor test

* update condor test

* show testthat output

* add pandoc and use cache

* use built in check

* use built in check

* update actions with built in check

* bump version

* use built in coverage

* use built in coverage

* remove sudo

* update actions

* update actions

* removed sudo from actions

* ugrade to R42

* remove virtualenv

* remove virtualenv

* remove virtualenv

* modify condor test

* update condor test

* update condor test

* adding retiucualte to covr

* adding retiucualte to covr

* add panda test to coverignore

* update actions

* remove lioness tests from coverage

* remove lioness tests from coverage

* added MONSTER and SAMBAR

* remove lionessR test

* Added CONDOR and YARN

* Update README.md

* put back otter in rbuild

* remove condor test

* remove condor test

* remove lioness docs

* add lioness to buildingore

* donttest lionesss

* remove coverage from ubuntu test

* remove rbuilignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* put back tests

* add padanedge diff test

* add back egeret test

* add monster test

* fix monster test

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* add sourceppi

* fixed PANDA tests

* modify panda test

* update lioness test

* fix expect message

* update tests

* update tests

* update tests

* update tests

* update tests

* update tests

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduce test size

* updating bioc (#250)

* updating bioc

* remove empty lines

* remove empty lines

* update citation

* update citation

* update citation

* Update README.md

* Update README.md

* Update main.yml

* Update main.yml

* Update .Rbuildignore

* Update .Rbuildignore

* update lioness test

* removed two last lioness tests

* removed two last lioness tests

* removed two last lioness tests

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* update lioness test

* lower sizeof test

* update test data

* update test data

* update test data

* reduce panda tests

* remove old test data

* remove old test data

* Update main.yml

* 1.1.16

update pandapy with header argument (#260)

* trying collapse readme (#261)

* trying collapse readme

* collapse animal description

* Update README.md

* Fix news file formatting

  o was not rendering list properly

* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

* bump x.y.z version to odd y following creation of RELEASE_3_16 branch

* update biconda (#265)

* add spider (#269)

* add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug

* DRAGON and unit tests work in progress (#267)

- add DRAGON in R and unit tests

* update lioness (#276)

* update lioness code (#277)

* Update LIONESS.R

* Update LIONESS.R

* Update LIONESS.R

* add note about the function (#279)

* add note about the function

* Update sourcePPI.R

* Update README.md

* Update README.md

* Update sourcePPI.R

* Update sourcePPI.R

* add details about sourcePPI (#280)

* add parallelization option to lioness (#281)

* 1.2.1 (#271)

* add bioc information

* update website

* add crane and docs

* update crane

* update worflow

* update crane

* update workflows

* update workflows

* update workfolw

* update workfolw

* update workfolw

* update workfolw

* Update main.yml

* Update main.yml

* Update main.yml

* fix lioness py

* udpate lioness in R

* include calculations python

* update panda rm missing

* update panda

* update lioness joblib

* revert commits

* ALPACA fix to NAs in community assignement

* version bump

* revert lioness

* update crane with alpaca changes

* update lioness

* update lioness python

* fix test

* update workflows

* put back github actions

* Fixed typo

* Added LIONESS-pearson option + unit test

* changed param labels in LIONESS example

* updated docs for lioness() function

* Update main.yml

* Update main.yml

* Update DESCRIPTION

* fix crane issue #240

* expanded PANDA and LIONESS description

* update crane fix

* added ALPACA, EGRET, and OTTER descriptions

* Update README.md

* typo in na.rm

* update workflow

* update workflow2

* fix-actions-3

* add r lib v2

* add r lib v2

* update condor test

* update condor test

* update condor test

* update condor test

* show testthat output

* add pandoc and use cache

* use built in check

* use built in check

* update actions with built in check

* bump version

* use built in coverage

* use built in coverage

* remove sudo

* update actions

* update actions

* removed sudo from actions

* ugrade to R42

* remove virtualenv

* remove virtualenv

* remove virtualenv

* modify condor test

* update condor test

* update condor test

* adding retiucualte to covr

* adding retiucualte to covr

* add panda test to coverignore

* update actions

* remove lioness tests from coverage

* remove lioness tests from coverage

* added MONSTER and SAMBAR

* remove lionessR test

* Added CONDOR and YARN

* Update README.md

* put back otter in rbuild

* remove condor test

* remove condor test

* remove lioness docs

* add lioness to buildingore

* donttest lionesss

* remove coverage from ubuntu test

* remove rbuilignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* put back tests

* add padanedge diff test

* add back egeret test

* add monster test

* fix monster test

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* add sourceppi

* fixed PANDA tests

* modify panda test

* update lioness test

* fix expect message

* update tests

* update tests

* update tests

* update tests

* update tests

* update tests

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduce test size

* updating bioc (#250)

* updating bioc

* remove empty lines

* remove empty lines

* update citation

* update citation

* Update README.md

* Update README.md

* Update main.yml

* Update main.yml

* Update .Rbuildignore

* Update .Rbuildignore

* update lioness test

* removed two last lioness tests

* removed two last lioness tests

* removed two last lioness tests

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* update lioness test

* lower sizeof test

* update test data

* update test data

* update test data

* reduce panda tests

* remove old test data

* remove old test data

* Update main.yml

* 1.1.16

update pandapy with header argument (#260)

* trying collapse readme (#261)

* trying collapse readme

* collapse animal description

* Update README.md

* update biconda (#265)

* add spider (#269)

* add spider

* udpate spider

* udpate spider

* update spuder with degreeadjust

* fix spider bug

Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>

* 1.2.2 (#273)

- add DRAGON

* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>

* fix monster error

* fix monster

* 1.3.2

* update tests

* update bioc verssion

* update monster test

* update argument description

* update argument description

* changed date

* updaate docs

* update dragon verbose

* update spider

* add puma (#270)

* add puma

* update PUMA

* updating mirna interactions

* add PUMA in readme

* Update PUMA.R

* Create TIGER.R (#272)

add TIGER.R

* Add lioness update (#284)

* update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* update lioness append code

* Update puma (#286)

* update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* fix puma examples

* fix puma examples

* update docs

* Add TIGER (#283)

* Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>

* Update DESCRIPTION

* Add TIGER description to README file (#288)

* Create TIGER.R

add TIGER.R

* Add TIGER

* compile TIGER

1. change the TIGER example to fit LazyData=F mode
2. document all the functions and required packages

* DESCRIPTION depends

Add cmdstanr to DESCRIPTION depends

* onLoad install cmdstan

* Update puma.Rd

* Add data document

* Update README.md

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>

---------

Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Co-authored-by: lshep <lori.shepherd@roswellpark.org>
Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>
Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>

* Added COBRA method

* Exported COBRA and improved description

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Co-authored-by: lshep <lori.shepherd@roswellpark.org>
Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Co-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>
Co-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>
    @soelmicheletti @marouenbg
    @nturaga @katehoffshutta @lshep @jwokaty @laurenhsu1 @cchen22
    9 people authored Sep 18, 2023
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Commits on Sep 25, 2023

  1. Cobra docs (#298) 

    * update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* add cobra docs

* build new website

* update package

* update package

* add package

* export pandaR classes

* add site html

* import classes from PANDA

* import classes from PANDA

* import classes from PANDA

* import classes from PANDA

* import classes from PANDA

* import classes from PANDA

* import classes from PANDA
    @marouenbg
    marouenbg authored Sep 25, 2023
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Commits on Nov 3, 2023

  1. Update README.md

    @marouenbg
    marouenbg authored Nov 3, 2023
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  2. Update main.yml

    @marouenbg
    marouenbg authored Nov 3, 2023
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  3. Update main.yml

    @marouenbg
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  4. Update main.yml

    @marouenbg
    marouenbg authored Nov 3, 2023
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Commits on Nov 9, 2023

  1. Fixed dependency on uchardet (#301) 

    * Fixed dependency on uchardet

* Removed RCy3 from Imports

* Added RCy3 back to Imports
    @taraeicher
    taraeicher authored Nov 9, 2023
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  2. Feature: included pcor decomposition natively in cobra (#299) 

    * Feature: included pcor decomposition natively in cobra

* Feature: included pcor decomposition natively in cobra

* Feature: included pcor decomposition natively in cobra

* Update COBRA.R

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
    @soelmicheletti @marouenbg
    soelmicheletti and marouenbg authored Nov 9, 2023
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Commits on Nov 18, 2023

  1. Merge branch 'master' into devel

    @marouenbg
    marouenbg authored Nov 18, 2023
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  2. Update README.md

    @marouenbg
    marouenbg authored Nov 18, 2023
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Commits on Dec 1, 2023

  1. Fix dragon (#306) 

    * add DRAGON outline

* implemented vars and esqs, added tests

* added optim

* Added fn to get shrunken cov and unit tests

* Update DESCRIPTION

* Update DESCRIPTION

* mechanics for prec mat and parcor

* added testdata directory

* fixed test paths

* Update test-dragon.R

* added export function and tests

* updated docs

* added ex datasets

* fixed bug w/self-edges in GGM

* fixed GGM diagonal issue

* fixed merge conflicts in docs

* fixed more merge conflicts
    @katehoffshutta
    katehoffshutta authored Dec 1, 2023
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Commits on Feb 3, 2024

  1. Fix 309 (#310) 

    * update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* fix 309
    @marouenbg
    marouenbg authored Feb 3, 2024
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Commits on Feb 17, 2024

  1. Update README.md

    @marouenbg
    marouenbg authored Feb 17, 2024
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Commits on Mar 3, 2024

  1. Aadd yarn (#314) 

    * update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* add yarn

* add yarn

* add yarn

* change yarn vignette

* change yarn vignette

* change yarn vignette

* add download data set

* add download data set

* update yarn

* update yarn

* update yarn

* update yarn

* add download file

* add download file

* add download file

* update workflow

* update workflow

* update to R 4.3

* update to R 4.3
    @marouenbg
    marouenbg authored Mar 3, 2024
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Commits on Mar 4, 2024

  1. Add monster desc (#312) 

    * update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* add monster description
    @marouenbg
    marouenbg authored Mar 4, 2024
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Commits on Mar 8, 2024

  1. merged 1.5.17

    @marouenbg
    marouenbg committed Mar 8, 2024
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