{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":190646802,"defaultBranch":"master","name":"netZooR","ownerLogin":"netZoo","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2019-06-06T20:40:00.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/51125278?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1709932345.0","currentOid":""},"activityList":{"items":[{"before":"2aa10738ff01e9bc76c5995eef5644df79b529ab","after":"75ca57726c2e06408207f352151bea1783e20e19","ref":"refs/heads/master","pushedAt":"2024-03-08T21:09:00.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"1.5.17 (#315)\n\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Added COBRA method (#293)\r\n\r\n* 1.4.0 (#289)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Added COBRA method\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Update README.md\r\n\r\n* Update TIGER (#297)\r\n\r\n* Smaller changes in COBRA (#296)\r\n\r\n* 1.4.0 (#289)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Added COBRA method\r\n\r\n* Exported COBRA and improved description\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Cobra docs (#298)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* add cobra docs\r\n\r\n* build new website\r\n\r\n* update package\r\n\r\n* update package\r\n\r\n* add package\r\n\r\n* export pandaR classes\r\n\r\n* add site html\r\n\r\n* import classes from PANDA\r\n\r\n* import classes from PANDA\r\n\r\n* import classes from PANDA\r\n\r\n* import classes from PANDA\r\n\r\n* import classes from PANDA\r\n\r\n* import classes from PANDA\r\n\r\n* import classes from PANDA\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Fixed dependency on uchardet (#301)\r\n\r\n* Fixed dependency on uchardet\r\n\r\n* Removed RCy3 from Imports\r\n\r\n* Added RCy3 back to Imports\r\n\r\n* Feature: included pcor decomposition natively in cobra (#299)\r\n\r\n* Feature: included pcor decomposition natively in cobra\r\n\r\n* Feature: included pcor decomposition natively in cobra\r\n\r\n* Feature: included pcor decomposition natively in cobra\r\n\r\n* Update COBRA.R\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update README.md\r\n\r\n* Fix dragon (#306)\r\n\r\n* add DRAGON outline\r\n\r\n* implemented vars and esqs, added tests\r\n\r\n* added optim\r\n\r\n* Added fn to get shrunken cov and unit tests\r\n\r\n* Update DESCRIPTION\r\n\r\n* Update DESCRIPTION\r\n\r\n* mechanics for prec mat and parcor\r\n\r\n* added testdata directory\r\n\r\n* fixed test paths\r\n\r\n* Update test-dragon.R\r\n\r\n* added export function and tests\r\n\r\n* updated docs\r\n\r\n* added ex datasets\r\n\r\n* fixed bug w/self-edges in GGM\r\n\r\n* fixed GGM diagonal issue\r\n\r\n* fixed merge conflicts in docs\r\n\r\n* fixed more merge conflicts\r\n\r\n* Fix 309 (#310)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix 309\r\n\r\n* Update README.md\r\n\r\n* Aadd yarn (#314)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* add yarn\r\n\r\n* add yarn\r\n\r\n* add yarn\r\n\r\n* change yarn vignette\r\n\r\n* change yarn vignette\r\n\r\n* change yarn vignette\r\n\r\n* add download data set\r\n\r\n* add download data set\r\n\r\n* update yarn\r\n\r\n* update yarn\r\n\r\n* update yarn\r\n\r\n* update yarn\r\n\r\n* add download file\r\n\r\n* add download file\r\n\r\n* add download file\r\n\r\n* update workflow\r\n\r\n* update workflow\r\n\r\n* update to R 4.3\r\n\r\n* update to R 4.3\r\n\r\n* Add monster desc (#312)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* add monster description\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\nCo-authored-by: Soel Micheletti <soel.micheletti@hotmail.it>\r\nCo-authored-by: Tara Eicher <taraeicher@yahoo.com>","shortMessageHtmlLink":"1.5.17 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2167632241\" data-permission-text=\"Title is private\" 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properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Added COBRA method (#293)\r\n\r\n* 1.4.0 (#289)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Added COBRA method\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Update README.md\r\n\r\n* Update TIGER (#297)\r\n\r\n* Smaller changes in COBRA (#296)\r\n\r\n* 1.4.0 (#289)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Added COBRA method\r\n\r\n* Exported COBRA and improved 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information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Added COBRA method\r\n\r\n* Exported COBRA and improved description\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>","shortMessageHtmlLink":"Smaller changes in COBRA (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1899685175\" data-permission-text=\"Title is private\" data-url=\"https://github.com/netZoo/netZooR/issues/296\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/netZoo/netZooR/pull/296/hovercard\" href=\"https://github.com/netZoo/netZooR/pull/296\">#296</a>)"}},{"before":"c1123dcaabb1324d337a99ca8a65ea9445d1f315","after":"40734cdeea9c00edcb78c5a9726d4053fb81eef8","ref":"refs/heads/devel","pushedAt":"2023-09-18T14:13:03.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Update TIGER (#297)","shortMessageHtmlLink":"Update TIGER (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1899949583\" data-permission-text=\"Title is private\" data-url=\"https://github.com/netZoo/netZooR/issues/297\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/netZoo/netZooR/pull/297/hovercard\" href=\"https://github.com/netZoo/netZooR/pull/297\">#297</a>)"}},{"before":"e1001f5b9e61d18822ac7317fdaa499b1b90b377","after":"c1123dcaabb1324d337a99ca8a65ea9445d1f315","ref":"refs/heads/devel","pushedAt":"2023-09-07T18:58:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"e92699b39a593aadc3f7efcb2bccc8ff67d1a10b","after":"e1001f5b9e61d18822ac7317fdaa499b1b90b377","ref":"refs/heads/devel","pushedAt":"2023-09-02T14:07:40.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Added COBRA method (#293)\n\n* 1.4.0 (#289)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>\r\n\r\n* Added COBRA method\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>","shortMessageHtmlLink":"Added COBRA method (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1878210301\" data-permission-text=\"Title is private\" data-url=\"https://github.com/netZoo/netZooR/issues/293\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/netZoo/netZooR/pull/293/hovercard\" href=\"https://github.com/netZoo/netZooR/pull/293\">#293</a>)"}},{"before":"81cb072fd4f3e1b47b99ef2ce67d1cad6a83bde1","after":"ac2288424300dad5455ff079ab29f92fc6c4a3c3","ref":"refs/heads/master","pushedAt":"2023-06-02T20:25:38.035Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"1.4.0 (#289)\n\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_15 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_15 branch\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* Fix news file formatting\r\n\r\n  o was not rendering list properly\r\n\r\n* bump x.y.z version to even y prior to creation of RELEASE_3_16 branch\r\n\r\n* bump x.y.z version to odd y following creation of RELEASE_3_16 branch\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\n* DRAGON and unit tests work in progress (#267)\r\n\r\n- add DRAGON in R and unit tests\r\n\r\n* update lioness (#276)\r\n\r\n* update lioness code (#277)\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* Update LIONESS.R\r\n\r\n* add note about the function (#279)\r\n\r\n* add note about the function\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update sourcePPI.R\r\n\r\n* Update sourcePPI.R\r\n\r\n* add details about sourcePPI (#280)\r\n\r\n* add parallelization option to lioness (#281)\r\n\r\n* 1.2.1 (#271)\r\n\r\n* add bioc information\r\n\r\n* update website\r\n\r\n* add crane and docs\r\n\r\n* update crane\r\n\r\n* update worflow\r\n\r\n* update crane\r\n\r\n* update workflows\r\n\r\n* update workflows\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* update workfolw\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* fix lioness py\r\n\r\n* udpate lioness in R\r\n\r\n* include calculations python\r\n\r\n* update panda rm missing\r\n\r\n* update panda\r\n\r\n* update lioness joblib\r\n\r\n* revert commits\r\n\r\n* ALPACA fix to NAs in community assignement\r\n\r\n* version bump\r\n\r\n* revert lioness\r\n\r\n* update crane with alpaca changes\r\n\r\n* update lioness\r\n\r\n* update lioness python\r\n\r\n* fix test\r\n\r\n* update workflows\r\n\r\n* put back github actions\r\n\r\n* Fixed typo\r\n\r\n* Added LIONESS-pearson option + unit test\r\n\r\n* changed param labels in LIONESS example\r\n\r\n* updated docs for lioness() function\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update DESCRIPTION\r\n\r\n* fix crane issue #240\r\n\r\n* expanded PANDA and LIONESS description\r\n\r\n* update crane fix\r\n\r\n* added ALPACA, EGRET, and OTTER descriptions\r\n\r\n* Update README.md\r\n\r\n* typo in na.rm\r\n\r\n* update workflow\r\n\r\n* update workflow2\r\n\r\n* fix-actions-3\r\n\r\n* add r lib v2\r\n\r\n* add r lib v2\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* show testthat output\r\n\r\n* add pandoc and use cache\r\n\r\n* use built in check\r\n\r\n* use built in check\r\n\r\n* update actions with built in check\r\n\r\n* bump version\r\n\r\n* use built in coverage\r\n\r\n* use built in coverage\r\n\r\n* remove sudo\r\n\r\n* update actions\r\n\r\n* update actions\r\n\r\n* removed sudo from actions\r\n\r\n* ugrade to R42\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* remove virtualenv\r\n\r\n* modify condor test\r\n\r\n* update condor test\r\n\r\n* update condor test\r\n\r\n* adding retiucualte to covr\r\n\r\n* adding retiucualte to covr\r\n\r\n* add panda test to coverignore\r\n\r\n* update actions\r\n\r\n* remove lioness tests from coverage\r\n\r\n* remove lioness tests from coverage\r\n\r\n* added MONSTER and SAMBAR\r\n\r\n* remove lionessR test\r\n\r\n* Added CONDOR and YARN\r\n\r\n* Update README.md\r\n\r\n* put back otter in rbuild\r\n\r\n* remove condor test\r\n\r\n* remove condor test\r\n\r\n* remove lioness docs\r\n\r\n* add lioness to buildingore\r\n\r\n* donttest lionesss\r\n\r\n* remove coverage from ubuntu test\r\n\r\n* remove rbuilignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* update rbuildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* add back buildignore\r\n\r\n* put back tests\r\n\r\n* add padanedge diff test\r\n\r\n* add back egeret test\r\n\r\n* add monster test\r\n\r\n* fix monster test\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* tolerance in expect equal\r\n\r\n* add sourceppi\r\n\r\n* fixed PANDA tests\r\n\r\n* modify panda test\r\n\r\n* update lioness test\r\n\r\n* fix expect message\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* update tests\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduced lioness test data\r\n\r\n* reduce test size\r\n\r\n* updating bioc (#250)\r\n\r\n* updating bioc\r\n\r\n* remove empty lines\r\n\r\n* remove empty lines\r\n\r\n* update citation\r\n\r\n* update citation\r\n\r\n* Update README.md\r\n\r\n* Update README.md\r\n\r\n* Update main.yml\r\n\r\n* Update main.yml\r\n\r\n* Update .Rbuildignore\r\n\r\n* Update .Rbuildignore\r\n\r\n* update lioness test\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* removed two last lioness tests\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* no saving of lioness networks\r\n\r\n* update lioness test\r\n\r\n* lower sizeof test\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* update test data\r\n\r\n* reduce panda tests\r\n\r\n* remove old test data\r\n\r\n* remove old test data\r\n\r\n* Update main.yml\r\n\r\n* 1.1.16\r\n\r\nupdate pandapy with header argument (#260)\r\n\r\n* trying collapse readme (#261)\r\n\r\n* trying collapse readme\r\n\r\n* collapse animal description\r\n\r\n* Update README.md\r\n\r\n* update biconda (#265)\r\n\r\n* add spider (#269)\r\n\r\n* add spider\r\n\r\n* udpate spider\r\n\r\n* udpate spider\r\n\r\n* update spuder with degreeadjust\r\n\r\n* fix spider bug\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* 1.2.2 (#273)\r\n\r\n- add DRAGON\r\n\r\n* add option to run lioness on multiple cores by using parallel::mclapply in place of lapply\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\n\r\n* fix monster error\r\n\r\n* fix monster\r\n\r\n* 1.3.2\r\n\r\n* update tests\r\n\r\n* update bioc verssion\r\n\r\n* update monster test\r\n\r\n* update argument description\r\n\r\n* update argument description\r\n\r\n* changed date\r\n\r\n* updaate docs\r\n\r\n* update dragon verbose\r\n\r\n* update spider\r\n\r\n* add puma (#270)\r\n\r\n* add puma\r\n\r\n* update PUMA\r\n\r\n* updating mirna interactions\r\n\r\n* add PUMA in readme\r\n\r\n* Update PUMA.R\r\n\r\n* Create TIGER.R (#272)\r\n\r\nadd TIGER.R\r\n\r\n* Add lioness update (#284)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* update lioness append code\r\n\r\n* Update puma (#286)\r\n\r\n* update documentation\r\n\r\n* remove monster tests\r\n\r\n* reduce monstr test\r\n\r\n* update documentation\r\n\r\n* remove diffedge example\r\n\r\n* reduce monster tests\r\n\r\n* remove spider example\r\n\r\n* update monster examples\r\n\r\n* remove lioness tests\r\n\r\n* remove pada tests\r\n\r\n* add citation\r\n\r\n* fix puma examples\r\n\r\n* fix puma examples\r\n\r\n* update docs\r\n\r\n* Add TIGER (#283)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n* Update DESCRIPTION\r\n\r\n* Add TIGER description to README file (#288)\r\n\r\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>\r\n\r\n---------\r\n\r\nCo-authored-by: Kate Hoff Shutta <kshutta@umass.edu>\r\nCo-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>\r\nCo-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>\r\nCo-authored-by: lshep <lori.shepherd@roswellpark.org>\r\nCo-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>\r\nCo-authored-by: Lauren Hsu <50427381+laurenhsu1@users.noreply.github.com>\r\nCo-authored-by: cchen22 <37237626+cchen22@users.noreply.github.com>","shortMessageHtmlLink":"1.4.0 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1738715465\" data-permission-text=\"Title is private\" data-url=\"https://github.com/netZoo/netZooR/issues/289\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/netZoo/netZooR/pull/289/hovercard\" href=\"https://github.com/netZoo/netZooR/pull/289\">#289</a>)"}},{"before":"67d44440d396df58b95d2bf7a0c4bb5436348d1c","after":"e92699b39a593aadc3f7efcb2bccc8ff67d1a10b","ref":"refs/heads/devel","pushedAt":"2023-06-02T19:44:04.506Z","pushType":"push","commitsCount":2,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Merge branch 'master' into devel","shortMessageHtmlLink":"Merge branch 'master' into devel"}},{"before":"fe1fe45ad2210bc2533879780d3eb969d4e881af","after":"67d44440d396df58b95d2bf7a0c4bb5436348d1c","ref":"refs/heads/devel","pushedAt":"2023-06-02T19:37:53.953Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Add TIGER description to README file (#288)\n\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n* Update README.md\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>","shortMessageHtmlLink":"Add TIGER description to README file (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1738669856\" data-permission-text=\"Title is private\" data-url=\"https://github.com/netZoo/netZooR/issues/288\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/netZoo/netZooR/pull/288/hovercard\" href=\"https://github.com/netZoo/netZooR/pull/288\">#288</a>)"}},{"before":"8312861bbd62de9500848e9cebfe9ba7f4587afb","after":"fe1fe45ad2210bc2533879780d3eb969d4e881af","ref":"refs/heads/devel","pushedAt":"2023-06-02T14:37:06.751Z","pushType":"push","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Update DESCRIPTION","shortMessageHtmlLink":"Update DESCRIPTION"}},{"before":"e6c9280a37599c68870a563b6ed5cda815dded14","after":"8312861bbd62de9500848e9cebfe9ba7f4587afb","ref":"refs/heads/devel","pushedAt":"2023-05-31T19:13:28.640Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"marouenbg","name":"Marouen","path":"/marouenbg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7914548?s=80&v=4"},"commit":{"message":"Add TIGER (#283)\n\n* Create TIGER.R\r\n\r\nadd TIGER.R\r\n\r\n* Add TIGER\r\n\r\n* compile TIGER\r\n\r\n1. change the TIGER example to fit LazyData=F mode\r\n2. document all the functions and required packages\r\n\r\n* DESCRIPTION depends\r\n\r\nAdd cmdstanr to DESCRIPTION depends\r\n\r\n* onLoad install cmdstan\r\n\r\n* Update puma.Rd\r\n\r\n* Add data document\r\n\r\n---------\r\n\r\nCo-authored-by: Marouen <marouenbg@users.noreply.github.com>","shortMessageHtmlLink":"Add TIGER (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1725016823\" data-permission-text=\"Title is private\" data-url=\"https://github.com/netZoo/netZooR/issues/283\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/netZoo/netZooR/pull/283/hovercard\" href=\"https://github.com/netZoo/netZooR/pull/283\">#283</a>)"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEEI535AA","startCursor":null,"endCursor":null}},"title":"Activity · netZoo/netZooR"}