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GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

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Package: Spectra
Commit: 424e9cedf36410ecdee446f492b823a011b644d9
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2024-10-15 22:15:22 +0200
Commit message:

 Merge pull request #335 from rformassspectrometry/jomain

feat: add new method backendRequiredSpectraVariables
Package: Spectra
Commit: 37d502933344ed5d9bc938f8cff2c5e189ac27d3
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-10-15 12:04:17 +0200
Commit message:

 feat: add new method backendRequiredSpectraVariables

- Add new method `backendRequiredSpectraVariables()` that allows a backend to
  specify which spectra variables are necessary to ensure proper
  functionality. Subsetting functions (like `selectSpectraVariables()`) should
  use these.
Package: glmGamPoi
Commit: 21e990894529ba874905fa09c6cdef8bddb10316
Author: Constantin <const-ae@users.noreply.github.com>
Date: 2024-07-22 10:53:54 +0200
Commit message:

 Merge pull request #64 from hpages/devel

Resync with recent developments in SparseArray/DelayedArray packages
Package: glmGamPoi
Commit: ace2c7e2c7c7940ef10afe88b2821dab8aaaa6e1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-07-15 14:00:01 -0700
Commit message:

 Resync with recent developments in SparseArray/DelayedArray packages
Package: cqn
Commit: 511115ef3e6ad1bbe3e419108c1c3867925fa8a2
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2024-10-15 13:00:40 -0400
Commit message:

 various import fixes caused by upstream changes
Package: MOSClip
Commit: 6bf20f24533ba505a8b62cf6e30bc5133c8a9c2a
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 18:32:20 +0200
Commit message:

 correct test
Package: MOSClip
Commit: 2131d2b41b28459d1e691038454be40fff344689
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 18:14:14 +0200
Commit message:

 change link in vignette and bump version
Package: MOSClip
Commit: 45c317be8550ecbefad0b5fdac7a7e4ba16e4fe1
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 18:13:43 +0200
Commit message:

 fix heatmaps
Package: CATALYST
Commit: 4ff7b0284710e81dd598d0a9dedf3e463bb191c1
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:20:49 +0200
Commit message:

 bump v1.29.1>.2
Package: CATALYST
Commit: 85ddee8580d26559378cb69ef46c6238a21dfdfa
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:20:18 +0200
Commit message:

 track changes v1.29.2
Package: CATALYST
Commit: d7007b85efcb458f57f898b64595e8f1f49d2ee2
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:20:00 +0200
Commit message:

 drop aes_string()
Package: CATALYST
Commit: 8d84e8cecd508dfe4c3245ff9a95a8cd799fbe57
Author: HelenaLC <helena@crowells.eu>
Date: 2024-10-15 18:19:50 +0200
Commit message:

 bug fix 'calculateDR' failure when in put is a 'table'
Package: philr
Commit: 1d4f2f3d25e277228b1050bb33075cbc5a1b26bb
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2024-10-15 11:48:49 -0400
Commit message:

 fix: bioconductor build error after mia function renaming
Package: gemma.R
Commit: 8882e11341ca5bed5a6f4e6f12826bc8ca9b78ef
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-10-15 08:36:04 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 2647536614fd2cfea9e3df6bf2ce1af580d24022
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-10-15 08:32:17 -0700
Commit message:

 get_platform_annotations fix
Package: MSnbase
Commit: 03e768f14bc5e6fe4fabf7f7077ee3b3bac2a29e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 16:32:23 +0200
Commit message:

 add pkgdown conf
Package: Rdisop
Commit: 1a7306945da577b5a2f461fca3c1b3eddef83b91
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 17:28:06 +0200
Commit message:

 adapt github actions
Package: seqsetvis
Commit: e4f659b458989a65fa98a6555c2f5cd945a68512
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2024-10-15 10:58:01 -0400
Commit message:

 v bump 1.25.5

within_clust_sort now respects "none" sort strategy. was bugged
Package: OmnipathR
Commit: 646d05410776d7c8a8c89e2ce44fd2e9d8c39e40
Author: deeenes <turei.denes@gmail.com>
Date: 2024-10-15 17:12:02 +0200
Commit message:

 Bump version: 3.13.27 → 3.13.28
Package: OmnipathR
Commit: 7edc1d855318cfe3bc051393d1d387a88a15d56e
Author: deeenes <turei.denes@gmail.com>
Date: 2024-10-15 17:09:41 +0200
Commit message:

 `oma`: missing variable declaration for R CMD check
Package: OmnipathR
Commit: fc69d6df82c374d16b025e041644a9bd21be3ee9
Author: deeenes <turei.denes@gmail.com>
Date: 2024-10-15 15:57:45 +0200
Commit message:

 `stitch_remove_prefix`: use `data.frame` instead of `tibble` in doctest
Package: Rdisop
Commit: 1f0e3db22f63fb35bd9c16d3bb8b41489f027992
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 17:05:18 +0200
Commit message:

 Remove compiled library
Package: Rdisop
Commit: 208c3e0b61a26ae1c9e3dbffdfc53d63937c5432
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 17:03:56 +0200
Commit message:

 Tiny cosmetic changes fixing version, generated files and new contributor
Package: Rdisop
Commit: 82df879d2ff2c7fa14ff24bdb05b3f3ca5250de5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-10-15 16:53:17 +0200
Commit message:

 Merge branch 'janlisec-master' into devel
Package: Rdisop
Commit: dfc0b430e8a165acc34b9584a81b4eb98739b192
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 14:15:58 +0200
Commit message:

 Ubuntu_dev excluded from GitHub action
Package: Rdisop
Commit: 78480d02c00d95093e22d400425961055ec7ddbb
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 14:05:07 +0200
Commit message:

 Put `rmarkdown` in Suggests.
Package: Rdisop
Commit: f0eff6b3ff4bcad081456722f1f9fee78d2b1da1
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:56:29 +0200
Commit message:

 GitHub Workflow fix
Package: Rdisop
Commit: 751c8309000acf55d2e4551236181989c8bd80eb
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:48:36 +0200
Commit message:

 GitHub Workflows fix
Package: Rdisop
Commit: e70c7a54bf6961ff7cc0dee92df901dca37aa5d6
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:39:51 +0200
Commit message:

 ReadMe fix
Package: Rdisop
Commit: f0169266c0460cfdcb9b005c12a6345092b006bc
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:21:21 +0200
Commit message:

 Vignette fix
Package: Rdisop
Commit: 3b49beab4304cf246edee65057b0c39a154bd5ab
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 13:08:06 +0200
Commit message:

 Rdisop-1.66.1 changes

Merge branch 'master' of https://github.com/janlisec/Rdisop

# Conflicts:
#	ChangeLog
#	DESCRIPTION
Package: Rdisop
Commit: 5d19de62b70375513e06b6499ea4ce3bc01445ae
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 12:39:16 +0200
Commit message:

 GitHub ReadMe set up.
Package: Rdisop
Commit: d80673fd5b03b286eddc6dc04c7cebbe59b97049
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 12:38:41 +0200
Commit message:

 Setting GitHub actions for PR and testing.
Package: Rdisop
Commit: c4c681276632586a35265fb014cac6fbd2a5d9fd
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:07:37 +0200
Commit message:

 - Namespace automized by roxygen2
- Description and Changelog revised
Package: Rdisop
Commit: 32afe37dde745ded3444cd2b25916c3f9366fe61
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:06:26 +0200
Commit message:

 several include statements out-commented (compose_f_gx_t) referencing deprecated functions
Package: Rdisop
Commit: 380e97b9138233db336c27764e0cf0aa41324fe1
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:05:50 +0200
Commit message:

 Rdisop.dll bound to R using R_useDynamicSymbols()
Package: Rdisop
Commit: ae58495dae92a9340c1bad90bceb89ac2ef63dd0
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:04:37 +0200
Commit message:

 `testthat` based testing environment set up
Package: Rdisop
Commit: 4897fe67055d0083372db7808baed78d1d032f6c
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 11:01:36 +0200
Commit message:

 - all R functions grouped to separate individual files
- all R functions documented using roxygen2
Package: Rdisop
Commit: e690014563d35d841c29773d3eef7d6dcd243a78
Author: janlisec <jan.lisec@bam.de>
Date: 2024-10-10 10:58:37 +0200
Commit message:

 Vignette format changed to Rmd. Minor corrections applied.
Package: Rdisop
Commit: 3e66e6d8141ceca7a58f1f4d0b0ebec582786120
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:14:22 +0200
Commit message:

 Bump version
Package: Rdisop
Commit: a75d7ba6a176318e0c118ba05059fbe1fcb14da6
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:09:45 +0200
Commit message:

 Merge branch 'yufree-master'
Package: Rdisop
Commit: 14300594ad8e37e14d372e9d6f0b35ab018c7766
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:07:06 +0200
Commit message:

 Merge branch 'master' of https://github.com/yufree/Rdisop into yufree-master
Package: Rdisop
Commit: 0907e7354efb5126367cd2cca7901c75802a4d5f
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-09-30 11:05:42 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/Rdisop
Package: Rdisop
Commit: 4939a2199daae72ce6e2105ab440e75647200f46
Author: yufree <yufree@live.cn>
Date: 2024-09-29 08:50:58 -0400
Commit message:

 remove unary_function
Package: Rdisop
Commit: d31cbbaeb7ec6926405f1d04fe0ccaa968e4e104
Author: yufree <yufree@live.cn>
Date: 2024-09-29 08:50:37 -0400
Commit message:

 remove binary_function
Package: Rdisop
Commit: 37d44575b7f2aa6530d79208c0fb05fcc7b84e19
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:21:07 +0200
Commit message:

 Merge branch 'master' of github.com:sneumann/Rdisop
Package: Rdisop
Commit: 700c83bb8715fe0c5c0210abcfcdd9c0ab108eae
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:14:25 +0200
Commit message:

 Fix merge conflict for two independent fixes for the same compile issue
Package: Rdisop
Commit: 880573120550e3c637a9a17271075cf01631f509
Author: yufree <yufree@live.cn>
Date: 2024-05-16 10:45:10 -0400
Commit message:

 Rf_error calls modified to include format string from @vjcitn
Package: Rdisop
Commit: 0bdf9fc4f82e794d9f5464655b75d815cc5dab43
Author: rickhelmus <37015911+rickhelmus@users.noreply.github.com>
Date: 2024-05-29 16:02:23 +0200
Commit message:

 Small if in case gcc's -Werror=format-security is enabled
Package: Rdisop
Commit: ed578481a01c10dce49b0a09c170a7a94a21de49
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:14:25 +0200
Commit message:

 Fix merge conflict for two independent fixes for the same compile issue
Package: Rdisop
Commit: 5fd08e7324becbeebe5a99d7bbfe2252d811b62e
Author: yufree <yufree@live.cn>
Date: 2024-05-16 10:53:12 -0400
Commit message:

 bump version with ChangeLog
Package: Rdisop
Commit: 64cde8fdad23d5e167730da5f71e71c71bbbbd29
Author: yufree <yufree@live.cn>
Date: 2024-05-16 10:45:10 -0400
Commit message:

 Rf_error calls modified to include format string from @vjcitn
Package: Rdisop
Commit: 74e8d34880c6e6d93cf8aad2c3fe9eac526adb60
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-04-30 10:17:29 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
Package: Rdisop
Commit: 9eeb38673870b3bf5a2eb29eafc9a9df7b8b8345
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-04-30 10:17:29 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
Package: Rdisop
Commit: a92d684e7bdb21a8f0912ccf65c735695dd52733
Author: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: 2023-10-24 09:39:07 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
Package: Rdisop
Commit: b06dc31e8bcfce146730cd0d7c995510d7bd064b
Author: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: 2023-10-24 09:39:07 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
Package: Rdisop
Commit: 711074b45991e3225b075a6cb25018ded294e83d
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2023-04-25 09:46:04 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
Package: Rdisop
Commit: 5a70ea6abfa4f542c01bd9ff45fe79a4d6d31b30
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2023-04-25 09:46:04 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
Package: Rdisop
Commit: edf079c84ebd7617865a26df83e53f657652ee1a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2024-05-29 16:10:47 +0200
Commit message:

 Merge pull request #26 from rickhelmus/Rf_error-fix

Small compilation fix
Package: Rdisop
Commit: 6bbc1df63b3f27a8ed4ed44ef82aced08f4ae784
Author: rickhelmus <37015911+rickhelmus@users.noreply.github.com>
Date: 2024-05-29 16:02:23 +0200
Commit message:

 Small if in case gcc's -Werror=format-security is enabled
Package: ClustIRR
Commit: 7fc41684bc3a45c065518021f7d08fb6281c6cb9
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2024-10-15 16:28:45 +0200
Commit message:

 Update README.md

Updated overview
Package: ClustIRR
Commit: e0191f8c62c6beb0756774ebd7b8b97d64bf68d7
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-15 16:18:48 +0200
Commit message:

 more bugfixes, tests and man files updates
Package: ClustIRR
Commit: 51c0f121d2ea01f2ef45e71c4f2e71c34061b85e
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-15 15:22:48 +0200
Commit message:

 major changes since 1.3.27, local clustering depreceated, will have to be implemented at different stage
Package: ATACCoGAPS
Commit: 8a0e634ee1b3c3f06e5f7462adc1c80f2c77ad42
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:45:29 -0400
Commit message:

 Deprecate

 - unresponsive
 - extended failure
Package: biodbKegg
Commit: 8f566c6ad90f9ac62dbc88100e24a6782471c579
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:44:28 -0400
Commit message:

 Deprecated

 - unresponsive
 - extended failure
Package: biodbExpasy
Commit: 07e10ca30eef157ab9374694700ffbc02416a582
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:43:11 -0400
Commit message:

 Deprecate

 - unresponsive
 - extended failure
Package: nanotatoR
Commit: e313e499974c9152a10ad6fc2d31fb74161fb844
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:41:45 -0400
Commit message:

 Deprecate

 - unresponsive
 - extended failure
Package: BRGenomics
Commit: acbd810498a9c9ac9ab15570ecdd414921756d7e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-15 09:37:58 -0400
Commit message:

 Deprecated

 - extended failure
Package: immunogenViewer
Commit: 7048e6206bd1334b74beb230691c22f4dbd4b102
Author: Waury <kwy700@login3.cm.cluster>
Date: 2024-10-15 15:10:43 +0200
Commit message:

 Version bump
Package: MSnbase
Commit: 6df777f0a9d89eb9c07e3913f34b4fa9b9428e48
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 14:30:46 +0200
Commit message:

 remove can email
Package: MSnbase
Commit: a1c80f6e2925371918e04d4be9387f630c69ce9a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:58:06 +0200
Commit message:

 fix pRolocdata dep version
Package: MSnbase
Commit: e113407cbb92072cb626b1499a2f29be8f2fc41a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:51:15 +0200
Commit message:

 suggest magick
Package: MSnbase
Commit: d886670e2788218a68d0bddd7573d1fb530053d9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 09:41:37 +0200
Commit message:

 install lgatto/pRolocdata
Package: MSnbase
Commit: 7df2372974b5e9a1a741bb247fa9c7441c93e8a9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 09:07:02 +0200
Commit message:

 latest pRolocdata
Package: pRolocdata
Commit: 857f96dd91a8631b8b16787776dfdf02cdc45057
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 14:29:32 +0200
Commit message:

 Merge branch 'master' into devel
Package: pRolocdata
Commit: 9fcc9a13c8f0d4744bc4526695442b58cddb99d7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 14:29:04 +0200
Commit message:

 add hyperLOPIT-SIData-ms3-rep12-intersect.csv.gz
Package: iSEEde
Commit: c41c29eb3de88e7d7710adaaaccd9cece6cfe58b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-10-05 08:49:55 +0100
Commit message:

 update github action to use devel branch (#40)
Package: TrajectoryGeometry
Commit: 66c1cddc07369a2c0eb3fe3c595e634702fcae79
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-10-15 12:03:51 +0100
Commit message:

 updating citation
Package: pRolocdata
Commit: 219f1411e6400bb0e088b1fb1e8845ebd3e88185
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 12:52:37 +0200
Commit message:

 Merge branch 'master' into devel
Package: pRolocdata
Commit: a9860e412c55fe61e0dcb785d48281e82e89b00b
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 12:52:27 +0200
Commit message:

 add Dunkley2006
Package: CytoMDS
Commit: d013ba87910f1726ad4d872ecc93c68754a0f330
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 12:01:35 +0200
Commit message:

 Merge branch 'main' into devel
Package: CytoMDS
Commit: cd528f893b87eb0a05c0efb317e79321abdc1d25
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 11:30:00 +0200
Commit message:

 implemented `pkgdown` customization
Package: MOSClip
Commit: 5e54b2ee2943789cbcee9c58384319ff612ea2df
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 11:40:35 +0200
Commit message:

 version bump
Package: MOSClip
Commit: d4c1a5c7fdce332358a0b5cbc8ed671e61cd2687
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 11:17:04 +0200
Commit message:

 new readme
Package: MOSClip
Commit: 80480f2cdac0a92d031c402ea0fd8d1bc4252407
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-15 10:59:24 +0200
Commit message:

 citation file
Package: MOSClip
Commit: e31d08c298dd745295462c7d02ae963f39ee07e7
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-14 10:44:44 +0200
Commit message:

 format R code
Package: MOSClip
Commit: 685448b3cad4dca5e78d5d7969ff9a08008b9a4e
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-10 11:03:27 +0200
Commit message:

 remove suppressMessages from plots
Package: MOSClip
Commit: 8c2073399383f074b4713c12a06b6494bcdc6e84
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-09 10:40:29 +0200
Commit message:

 update readme
Package: MOSClip
Commit: 947745efb7b1fc6365fdb7ec9995e170add9a4ea
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-09 10:34:51 +0200
Commit message:

 Merge branch 'readme' of github.com:CaluraLab/MOSClip into readme
Package: MOSClip
Commit: 76836b1fad73a13571edb30c7b7ace637ecae3e3
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-10-08 17:30:23 +0200
Commit message:

 add documentation for MOSClip package
Package: MOSClip
Commit: 4eb6897ab07a3d3e2a5858c8470cddba3410713d
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:22:45 +0200
Commit message:

 Update README.md

add image
Package: MOSClip
Commit: eacccee342eef6697681f0f4d39a3fc85456c2e6
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:24:31 +0200
Commit message:

 update .Rbuildignore
Package: MOSClip
Commit: 01199fa46a17ad8580b428dd5ab9a51aba71d97f
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 15:50:30 +0200
Commit message:

 new readme
Package: MOSClip
Commit: 8820dcc76cfe3def5a96d0f9e9c46a1cbd5295ef
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:32:26 +0200
Commit message:

 Merge branch 'readme' of github.com:CaluraLab/MOSClip into readme
Package: MOSClip
Commit: a91d9550a871f47c1cadd9d393f10966c92099c9
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:24:31 +0200
Commit message:

 update .Rbuildignore
Package: MOSClip
Commit: 5b1ecfb4526e61b70fbb224870ca8758c028974b
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 16:22:45 +0200
Commit message:

 Update README.md

add image
Package: MOSClip
Commit: d384fe141613b25a2b58f1154b4748219f2b6c7b
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 15:50:30 +0200
Commit message:

 new readme
Package: MOSClip
Commit: d87335e1fbfbbecc3b11d4ed0f56a278c705d10b
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2024-09-26 15:33:16 +0200
Commit message:

 gitignore
Package: EnrichDO
Commit: 994ea179c4c26cd9fcbe2fc2e847d4e40e583e37
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-10-15 17:23:08 +0800
Commit message:

 modification
Package: CytoPipelineGUI
Commit: 4c5002f0f5dda5aa8a56fc7dbb16d602122a1a4b
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 11:16:12 +0200
Commit message:

 corrected typo in `.pkgdown` file
Package: ggsc
Commit: 6e006c6c95ded5bc42965d0dd5c126c72d99276b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-15 16:57:39 +0800
Commit message:

 update
Package: ggsc
Commit: f1b691cd8d9180ce54c3c3ff9bcce39833bd71c5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-15 16:53:40 +0800
Commit message:

 Merge pull request #39 from xiangpin/master

using sp_mat in c++ and adjust the levels of features in plot_lisa_feature
Package: ggsc
Commit: 2e586b41f84ba7c1f00ce0f586e0461d974965fc
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-15 12:07:08 +0800
Commit message:

 adjust features of plot_lisa_feature
Package: ggsc
Commit: 3580a1bd2f5c54987010c0f1abd898afa17fd26e
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-15 12:06:21 +0800
Commit message:

 keeping sp_mat
Package: ggsc
Commit: 13d96428779f1aa352bcdbed727fee4e5600c391
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-13 12:24:27 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggsc
Commit: e8b09e34f0b0b088b543dd216349aee17d27863c
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-10-13 12:24:21 +0800
Commit message:

 add levels of features
Package: ggsc
Commit: 7aa68ff8860a88a326540d1d3ad0b9b93f2e0095
Author: xushuangbin <xshuangbin@163.com>
Date: 2024-09-12 21:59:13 +0800
Commit message:

 plot_lisa_feature add levels for lisa result
Package: CytoPipelineGUI
Commit: 47e1ec5793f1a0d4137f374a54ad3fba5fd92c8f
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 09:42:56 +0200
Commit message:

 implemented `pkgdown` site customization
Package: CytoPipelineGUI
Commit: ab3cc954c0d4c73106b84bda5d4dd462a55d992a
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-28 09:31:17 +0200
Commit message:

 removed /pkgdown/_pkgdown.yml
Package: CytoPipelineGUI
Commit: cf350c04d3dea200f149dad0f713c0c7f1d7269e
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-14 14:37:03 +0200
Commit message:

 test with empty `_pkgdown/_pkgdown.yml`file
Package: CytoPipelineGUI
Commit: c6e1d4f08bdedd5b57be10e19292ebf25969ab9d
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-14 14:27:03 +0200
Commit message:

 test adding pkgdown/_pkgdown.yml
Package: CytoPipelineGUI
Commit: 009e22812964d8f1be2c1ea32b809b97c2d55b74
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-05-14 10:42:09 +0200
Commit message:

 test deployment in GHA
Package: pRolocdata
Commit: 71aad64eb43d998538bf8d32642d4373effb7ab2
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:57:06 +0200
Commit message:

 Merge branch 'master' into devel
Package: pRolocdata
Commit: d962a6dc851fcf8bd03a459a58fe51f5f7e9aeae
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-10-15 10:56:37 +0200
Commit message:

 add files back
Package: StabMap
Commit: 65f94a9965f8622cd3992266f333b1b086dbb8a7
Author: shazanfar <shazanfar@gmail.com>
Date: 2024-10-15 18:37:23 +1100
Commit message:

 add sparseMatrixStats to suggests
Package: CytoPipeline
Commit: 36efdd1ea24ad8e192495714144a70ff169846b2
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-15 09:00:47 +0200
Commit message:

 extended pkgdown set-up to allow customization - forced move to bootstrap5 by pkgdown (use of a _pkgdown.yml)
Package: CytoPipeline
Commit: 276c88b9c0e243334b37751ddc6089ddd6a34cdf
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-14 20:06:16 +0200
Commit message:

 added alternative texts for generated plots in main vignette
Package: CytoPipeline
Commit: d924f2a9caa163322c7144ca0c2887bb6766d904
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-10-14 17:30:28 +0200
Commit message:

 - updated unit test to account for flowAI version change
- now suggesting `CytoPipelineGUI` package
- bumped to version 1.5.2
Package: gemma.R
Commit: 7a88a9c1cfe048f99d5731523d99651cf78a3461
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-10-14 21:12:38 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 0d559a38a6d9d212507077845847f4d6b6b7137c
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-10-14 21:07:37 -0700
Commit message:

 fix get_platform_annotations file io
Package: chevreuldata
Commit: 9c45adfe663d5a0e3071313f62b94fc79e030c40
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 16:04:14 -0700
Commit message:

 bump version; fix nginx config on server
Package: EBImage
Commit: eb528bda72038be848cdc681c69bd16dedad4d32
Author: aoles <andrzej.oles@gmail.com>
Date: 2024-10-15 00:35:40 +0200
Commit message:

 Apply patch from Kurt Hornik
Package: chevreuldata
Commit: 48bb6b4ff1dc80bb838c0da963422faed60fabe0
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:23:06 -0700
Commit message:

 bump version
Package: chevreuldata
Commit: 2c7ede56310bb1fefb162c2c53c5013b59d73ab1
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:22:34 -0700
Commit message:

 fix coordinate column
Package: chevreuldata
Commit: 7afca9079e33f587b8140566d01bbe8a8f881ccd
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:04:48 -0700
Commit message:

 bump version
Package: chevreuldata
Commit: 461085a417774b1a230f4fe90a74c3324212b845
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-10-14 15:00:25 -0700
Commit message:

 add human fetal retina dataset
Package: Organism.dplyr
Commit: 60e43ae3b1f686db9e738235e23a23c0164930ca
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-14 17:09:19 -0400
Commit message:

 update 'mini' databases for new annotations
Package: multtest
Commit: 1d45f73c968f617b7b68dd4ce93be8bee662e1b9
Author: kspollard <kpollard@gladstone.ucsf.edu>
Date: 2024-10-14 12:58:24 -0700
Commit message:

 Change Calloc and Free to R_Calloc and R_Free
Package: multtest
Commit: bdb8df7739623d0475691f91709a726f3089e60c
Author: kspollard <kpollard@gladstone.ucsf.edu>
Date: 2024-10-14 12:32:08 -0700
Commit message:

 Changed Calloc and Free to R_Calloc and R_Free
Package: NormalyzerDE
Commit: aafd0fecf71d329fbe325e3e0194d6f50d95fb9a
Author: Jakob Willforss <jakob.willforss@hotmail.com>
Date: 2024-10-14 20:47:26 +0200
Commit message:

 Version bump
Package: NormalyzerDE
Commit: dd2d6eac7b5570c730a8679bdbcacc6e801a2966
Author: Jakob Willforss <jakob.willforss@hotmail.com>
Date: 2024-10-14 20:45:34 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/NormalyzerDE into devel
Package: NormalyzerDE
Commit: 6185ffd1a293780b84892cff5870933d5ba8bfb9
Author: Jakob Willforss <jakob.willforss@hotmail.com>
Date: 2024-10-14 20:38:55 +0200
Commit message:

 Disable varying p-value testthat
Package: S4Arrays
Commit: abdba2838565283c182c5e3c07c214f969900295
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-10-14 10:34:52 -0700
Commit message:

 S4Arrays 1.5.11

Replace is_sparse() methods for dg[C|R]Matrix and lg[C|R]Matrix objects
with methods for [C|R|T]sparseMatrix derivatives.
Package: S4Arrays
Commit: b07b09b5e0e04906fac3a8db55782883043eeaad
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-09-28 10:36:03 -0700
Commit message:

 small tweak to internal helper Mindex_row_is_repeated()
Package: HuBMAPR
Commit: 6da954fc3aabcdc575163858a0b0e751f573b39f
Author: christinehou11 <chou11@jh.edu>
Date: 2024-10-14 13:37:51 -0400
Commit message:

 bump up after first review
Package: HuBMAPR
Commit: fd33bd6e0ec583cc3be98de0b140b90e8c866ca6
Author: christinehou11 <chou11@jh.edu>
Date: 2024-10-13 01:04:28 -0400
Commit message:

 edit codes for review comments
Package: bugsigdbr
Commit: b9738478d6f863af586e0da8e1a72cad0555cc12
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2024-10-14 13:24:19 -0400
Commit message:

 getSignatures: fail when not specifiying tax.level with exact.tax.level=FALSE
Package: pgxRpi
Commit: bb7302a78d9001fe788cee4594f7eb510cb17b06
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2024-10-15 00:32:48 +0800
Commit message:

 version bump
Package: pgxRpi
Commit: 7dc7b01ccb55a2d8d87b08dbe1c60a9e804c3b82
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2024-10-15 00:31:57 +0800
Commit message:

 bug fix
Package: scrapper
Commit: ee1bcfd9a8d914ca4e634bdfa77be50d80b7d273
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-10-14 09:03:46 -0700
Commit message:

 Emit a warning if the number of neighbors is not as expected.

Also respect the user-supplied perplexity in t-SNE, don't try to infer
it from the number of neighbors - the R side already attempts to
synchronise the two, so if they're not consistent in the C++ side, we
assume that it was a deliberate choice of the user.
Package: scrapper
Commit: bcac405cb4e7f6fb0217917bd359d26b0ea0bfad
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-10-13 11:41:22 -0700
Commit message:

 Added Bioc badges to the README for prettiness.
Package: koinar
Commit: e5a8c69ae54b54c9080d5422d2599c4df40c1238
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-10-14 18:04:28 +0200
Commit message:

 Add mzR to suggests.
Package: GSEABase
Commit: e393a2722852b27d2f6aa32058fcaee440c16024
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-14 11:38:10 -0400
Commit message:

 version bump
Package: GSEABase
Commit: 16a0d20812183aa2ff70ce8e7ced64284a9b0ff0
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-14 11:37:47 -0400
Commit message:

 Merge branch 'axelklenk-devel' into devel

- closes #10
Package: GSEABase
Commit: 1d8b22faf769a19722992e1138a2602fcacec266
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-10-07 16:08:35 +0200
Commit message:

 fix misspelled argument in getGmt()
Package: SingleMoleculeFootprinting
Commit: 219a544dc897b26bf11967981d12715d45052cf8
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-14 16:44:33 +0200
Commit message:

 BiocCheck round
Package: SingleMoleculeFootprinting
Commit: d1bd58295c4c8a58d1f686765f10ca2d1ade60ed
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-14 16:05:43 +0200
Commit message:

 added Rproj to Rbuildignore
Package: SingleMoleculeFootprinting
Commit: 7fa55d76bdf86e8d85102eb1ab9358fcc0bb112e
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2024-10-14 15:55:15 +0200
Commit message:

 stopped tracking Rproj file
Package: PRONE
Commit: b680c2d74e00163be997cb8b8fb48ae2f7cbfea9
Author: lisiarend <lisiarend@me.com>
Date: 2024-10-14 13:57:25 +0200
Commit message:

 version changed
Package: smoppix
Commit: 4bcf3769264712272fca17949df0c1f0d001d567
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-14 12:33:16 +0200
Commit message:

 Try to find bug on server
Package: smoppix
Commit: 96b49688b2a185bc2eed731522244dc92baa8189
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-14 11:57:39 +0200
Commit message:

 With Biocodnuctor reviewr comments
Package: smoppix
Commit: 7bd8592ff5c294151b5a875a01987052a0d08617
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-10 21:14:30 +0200
Commit message:

 SYncing news and description
Package: smoppix
Commit: 8c129b323cd646cf42e42ff79d3bcb9deb9c8229
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-10 18:56:31 +0200
Commit message:

 return ggplot object
Package: smoppix
Commit: f74eaa3105946113d8be792ab8b41da2026b9825
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-10-10 18:47:40 +0200
Commit message:

 Avoid multiple return statements
Package: smoppix
Commit: f71459bcd940bafb4df373262a7ceaead9746317
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-09-04 17:34:32 +0200
Commit message:

 mistake in writetoxlsx
Package: tripr
Commit: cc5f0504236f4828d78466be214b3f3f65d3e130
Author: KonstantinosKardamiliotis <k.kardamiliotis@gmail.com>
Date: 2024-10-14 12:29:01 +0300
Commit message:

 Oct 24 Bioc 10.14 new push
Package: COTAN
Commit: 8588ed6f6e4137efaa8e57e165307f5e4767302c
Author: trinetra75 <marco.fantozzi@gmail.com>
Date: 2024-10-13 23:53:53 +0200
Commit message:

 Updated NEWS.md and bumped-up version
Package: COTAN
Commit: fa78f5fbf4c445ee4451a621daaa9b9a680b2ae0
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2024-10-13 19:01:24 +0200
Commit message:

 Exported existing utility functions about names arrays (#90)

The functions are: `conditionsFromNames()`,
`niceFactorLevels()`, `factorToVector()`
Package: RMassBank
Commit: 0df9d3bb10b18eb60fc216dac9585a5595edc2d9
Author: Michele <stravsmi@eawag.ch>
Date: 2024-10-14 07:09:11 +0000
Commit message:

 fixed flexAccessionBuilder
Package: BgeeDB
Commit: 9697b238cc0f896faac11e7e148885e4aca99be2
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-10-14 09:11:47 +0200
Commit message:

 use back the production release_v2.tsv file
Package: BgeeDB
Commit: 28921398d2bc9a3fd79c9621d5279ac72c3a2228
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-10-14 09:08:59 +0200
Commit message:

 add possibility to filter integrated calls based on anat. entity IDs
Package: PRONE
Commit: 5d3853136fc29b64c7d7d643ac3d7b291d4749b3
Author: lisiarend <lisiarend@me.com>
Date: 2024-10-14 08:30:41 +0200
Commit message:

 bioconductor installation + man pages changed
Package: Rsubread
Commit: d293f4b645963ffdb24ce41baae06b26652dfc39
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2024-10-14 08:15:43 +1100
Commit message:

 Disabled all code in and after cellCounts in the vignettes to see why the build crashed on BioC website.
Package: ClustIRR
Commit: 9aaaeade263f1f6f204c05d82d0421cca9297dbb
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-13 22:53:50 +0200
Commit message:

 update dac dco, minor changes, testing
Package: DuplexDiscovereR
Commit: 6df4e0ba303d15a37fcd90492035b176d253df1b
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 19:59:50 +0200
Commit message:

 vignette links version bump
Package: ontoProc
Commit: d620293177f50b7104c2f97944d41ff26a2d651e
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-10-13 13:59:10 -0400
Commit message:

 new bioregistry exploration
Package: DuplexDiscovereR
Commit: 1e2e5e22138ab230cd4325c525f28e664e0618aa
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 19:39:27 +0200
Commit message:

 vignette links
Package: ClustIRR
Commit: 7f902839ddd933543ac1538c09f3431a48f88c58
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2024-10-13 19:26:51 +0200
Commit message:

 bugfixes and vignette
Package: DuplexDiscovereR
Commit: 1a029cb3def8c381161dd9bbfc6e96956b4aefd6
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 18:35:42 +0200
Commit message:

 merge review branch and version bump
Package: DuplexDiscovereR
Commit: d75f3896a3977f66f1404ecf615aa0d0ef0d9332
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 18:33:57 +0200
Commit message:

 styling
Package: DuplexDiscovereR
Commit: 720bfecda352967aecd35fae780656f25af637f3
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-13 17:49:35 +0200
Commit message:

 fixed spelling and minot changes fir rev. request
Package: DuplexDiscovereR
Commit: ef96897996a113a67e5f1d50673e8e704629a0f5
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 21:23:55 +0200
Commit message:

 applied styler
Package: DuplexDiscovereR
Commit: 8224898d855cf7047df5b836014237b05930040f
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 21:16:52 +0200
Commit message:

 updated Sj and news
Package: DuplexDiscovereR
Commit: 337dbaa57267b2019ca6999a248a76fe6d4c4da0
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 20:28:55 +0200
Commit message:

 fixed text in vignettes
Package: DuplexDiscovereR
Commit: 1d782f53f52282b92200d4a8591a07f4f5676b2b
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 17:28:14 +0200
Commit message:

 merged res_class into review branch
Package: DuplexDiscovereR
Commit: b5a19321aea21140915bb67d93eb27fc545309a7
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 17:26:11 +0200
Commit message:

 added examples to results class
Package: DuplexDiscovereR
Commit: 6437e1cccf1c55818a7121d6702a6c4bd6d18034
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-11 13:25:39 +0200
Commit message:

 applied styler
Package: DuplexDiscovereR
Commit: 01dc675b30a490abdbe568fc4587ae2ea4ae4b46
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 19:08:04 +0200
Commit message:

 changed link in pkg R
Package: DuplexDiscovereR
Commit: 0add3495f11ab94cd8a3f6143808f61d186fa2ac
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 18:56:41 +0200
Commit message:

 changed output to result calss in code, tests and vignette
Package: DuplexDiscovereR
Commit: 5767a15103cbd5ac1c8d380020ee1d4630bbd5d6
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 18:03:23 +0200
Commit message:

 added class
Package: DuplexDiscovereR
Commit: 1651655d1e3d20203731757bbbf785ebc69033ab
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 16:35:38 +0200
Commit message:

 added all non-binds to globals pl one
Package: DuplexDiscovereR
Commit: 6f1436b1888b020450133d138944f6f4be079f13
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 16:34:36 +0200
Commit message:

 added all non-binds to globals
Package: DuplexDiscovereR
Commit: eee2a56c92b3e6033bb8cb90a89a745951d9dacf
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-10 14:35:56 +0200
Commit message:

 fixing cmd check note
Package: DuplexDiscovereR
Commit: 1e78d373c9859900f51dc48006d3310542b42027
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 18:19:29 +0200
Commit message:

 fixing NOTES in bindings and 2->4 tabs
Package: DuplexDiscovereR
Commit: 340b056d8a7eb5dd568c64c518213d62474051c2
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 17:11:11 +0200
Commit message:

 changed vignette name and added another note on RNAduplex
Package: DuplexDiscovereR
Commit: ef793090d4797d9a3dcba1b47703a1b4eb5cc600
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 17:01:50 +0200
Commit message:

 added warning for RNAduplex license
Package: DuplexDiscovereR
Commit: b04d63fbe43b1e152f9df36b144c5ef7daa296dd
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:51:52 +0200
Commit message:

 changed system to system2
Package: DuplexDiscovereR
Commit: 7b64b7d9e9539d8b7670be94bec2cce39f41bd3a
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:37:32 +0200
Commit message:

 restored tracking for test plots, file removed
Package: DuplexDiscovereR
Commit: 2325c2a94488c322151e1d5dcef89df3d78dd7d6
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:36:24 +0200
Commit message:

 removed tracking for test plots
Package: DuplexDiscovereR
Commit: 488c47629e4a04b6d5b5f04f913c2d5413e15caa
Author: Egors01 <yegor.smb@gmail.com>
Date: 2024-10-09 16:34:41 +0200
Commit message:

 removed for-loop for comps clustering
Package: DuplexDiscovereR
Commit: 36439e6b9c10a3ce691aacca671937724a851240
Author: Semenchenko <esemenc@cl-meyer18.mdc-berlin.net>
Date: 2024-10-08 11:42:46 +0200
Commit message:

 removed duplicate gitignore
Package: AlphaMissenseR
Commit: d90e937812bd72b0382acdd1755e732941d1267b
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-13 11:53:31 -0400
Commit message:

 update README, NEWS, and pkgdown for benchmarking vignette
Package: AlphaMissenseR
Commit: 562b2c466d31491decfc8cd21c3664c9ee1ba0d1
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-10-13 11:48:46 -0400
Commit message:

 Merge branch 'ccb-hms-ProteinGym' into devel
Package: AlphaMissenseR
Commit: 417b1cc61b5d5e9e2158bf5743ee103e99b74c13
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:44:07 +0000
Commit message:

 removed dplyr from `suggests`
Package: AlphaMissenseR
Commit: e529ffeec5758f86cd0debe76d39027d523ba94a
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:35:24 +0000
Commit message:

 bumped version
Package: AlphaMissenseR
Commit: 13397c5953684f7a03e478fcf8c9237baabd1920
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:34:31 +0000
Commit message:

 Issues vignette after D. Benchmarking
Package: AlphaMissenseR
Commit: 5735e70494369039f1bad312a6e718cb64952539
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:32:43 +0000
Commit message:

 dependencies for benchmarking in `Suggests`
Package: AlphaMissenseR
Commit: f451845ae5819aa28f5238d595e40f9baaaa370d
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-10-08 17:28:54 +0000
Commit message:

 vignette for benchmarking with ProteinGym
Package: bugsigdbr
Commit: 5b35f874f1ebc58594b7d2a8926bfc5ba1d76c9c
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2024-10-13 11:43:44 -0400
Commit message:

 importBugSigDB tests: check for different dimensions depending on source
Package: AlphaMissenseR
Commit: c6d478e446e4e6e27893f323e043257c2f5c7a6f
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-09-20 03:14:40 -0400
Commit message:

 refactor plot_granges() as gosling_plot()

- rename as gosling_plot(); renames files to Gosling.R / Gosling.Rd
- test for required packages as part of argument validation ('fail early')
- rename 'bars' option as 'bar', for consistency with gosling terminology
- separate compose_view_bar() and compose_view_lollipop() for code
  modularity
- separate gosling_app() for Shiny app creation. Only create app when
  create_app = TRUE (default when interactive()); facilitates running
  code in examples / vignettes during R CMD check
- revise example to maximize code run during R CMD check
- rename argument as `granges`, so users are less likely to puzzle over
  `gr_` meaning
- managing location of .gosling so that it is not created in the user
  working directory. Uses setwd() / on.exit() because shiny.gosling does
  not allow easy alternative specification
- link [`GenomicRanges::GRanges`] in man page to satisfy R CMD check
- version bump and NEWS update
Package: AlphaMissenseR
Commit: afe7401aaa0c3d0688a88a089f24339e00b2b1d8
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-09-20 02:08:32 -0400
Commit message:

 formatting changes so pull request follows package style

- run devtools::document() (renames man page to plot_granges.Rd, etc.)
- standardize roxygen documentation formatting
- update example argument 'mode = ' to 'plot_type = '
- use match.args() for plot_type argument validation
- avoid long lines and extra vertical spacing
- use standard code indentation in vignette
- do not use inline links []()
- wrap vignette text to 80 columns
- remove trailing whitespace
Package: AlphaMissenseR
Commit: 7191a7afd7727e5192d0755182ab905bd02d5f78
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2024-09-20 01:43:24 -0400
Commit message:

 minimize differences between pull request and devel

- retain original whitespacing in DESCRIPTION
- do not change vignette metadata order
- do not replace links [][] with inline links []()
- do not use shiny runtime in vignette
 </pre>
    </div>
  
    

      Package: AlphaMissenseR

      Commit: b22047e44330598b03e98f4771b590b155a6cb54

      Author:  Martin Morgan <mtmorgan.xyz@gmail.com> 

      Date: 2024-09-24 17:08:58 -0400

      Commit message:


	  
		
 Squash commit merges #6 'Add plot_granges` with the following commits:

Co-authored-by: lee-t <tyrone_lee@hms.harvard.edu>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Co-authored-by: lgeistlinger <ludwig.geistlinger@gmail.com>

commit aa46568508126ae8f31e3700040deb8e0e541818
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 14:25:40 2024 -0400

    change @details

commit b0b5a450a63edbeeecf85d6be07704fba63a445b
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:41:34 2024 -0400

    reformat DESCRIPTION

commit c65a35174a29a6cf53973307689ebfd696d0ccc5
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:30:56 2024 -0400

    format example

commit c9e90883a810e32127fdec3610f0cbcc6a3868d2
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:29:19 2024 -0400

    change to use `identical()`

commit 57cbc97d2903475f7edb802379ecf680cd7652c7
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:23:45 2024 -0400

    combine assertions into one `stopifnot()`, `plot_type` is already checked later in the plotting function at line192.

commit 73f173deacda4232a8a767b5802f1601008cdf59
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Sep 19 13:17:17 2024 -0400

    change function indentation and input granges name

commit a24edaa16d43d7f1f80d4537c86119e4524d2b36
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Sep 17 14:37:53 2024 -0400

    Rename plot_shinygosling to match function. Edit documentation wording. Change alphafold vignette to show images.

commit 916e254386cd918517477092ca9722115303279f
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date:   Wed Aug 21 17:00:43 2024 -0400

    some cosmetics to the gosling section

commit 48a05588655089c480718a209548d5ca15f27bfe
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 21 11:56:30 2024 -0400

    some message suppression and link fixes

commit e32322f4a10f43548f9b3c3dd7875ec6f4c12fdc
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 17:53:33 2024 -0400

    found the missing visual channel imports.

commit 008b5d6ba002d853c2a4702276627fd476aa00cd
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 17:36:31 2024 -0400

    reverting importFrom, cache order

commit 963a9ff7cc077a20ca6cc95244168e61190bdf9d
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 16:55:43 2024 -0400

    imports and cache creation reverted

commit 0c66dc92edf9719b9a0b2104a26b0595443f4f0c
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 15:18:16 2024 -0400

    fixing vignettes, trying to pass R CMD check

commit 00c57a76c297d5811113cb81ee72c5c3d78936f8
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 12:10:24 2024 -0400

    sync help page for plot_shinygosling.rd

commit c265cf240fa7ac38e4a915fd39c1f2289204808b
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 12:03:34 2024 -0400

    remove runtime from intro

commit b4a28bbcd90e3b22bd6ec33d21868234e88f1861
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 12:03:16 2024 -0400

    text and example changes to alphafold.Rmd; fix spelling of 'lollipop'

commit e6137b2e3715bfd352bd111a8af8f9d87c4da320
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed Aug 7 11:49:12 2024 -0400

    replace tabs with spaces (on Windows-1252)

commit 96fa7f52945231456c03ba0c344b17453d7cd0d1
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 17:52:38 2024 -0400

    'plot_type' selects between bars and lolipop plots

commit af48390b4ddbf8f011f49c4f070d0ddfbaaedc2a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 16:48:30 2024 -0400

    add tooltips to lolipop plot

commit b9b73887130b96f5006975a57b45d021d648728f
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 16:46:47 2024 -0400

    use cache for gosling dir

commit bbc4def826905eabbba01d864c78b802449cd16a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 16:30:31 2024 -0400

    add validation for input types

commit 6dfd4b288f8a9c1f960de17c2fbf1ae0e0faea1d
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue Aug 6 13:47:23 2024 -0400

    rename as_granges->gr, get_range - > g; fix GRanges accesssors in zoom view

commit 64e4de00de7e28f029ac2638c7b877c211d98c7a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Fri Aug 2 16:58:33 2024 -0400

    fixes for example

commit 7f445879c8c881310188779deb403f0c949a62f1
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Fri Aug 2 16:51:21 2024 -0400

    no `gosling` R package

commit 94837cffc54d1f03745036bb560a66e1191a0100
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:55:39 2024 -0400

    whitespace DESCRIPTION

commit a4a6785a04774e189aea48972f359f7484f88731
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:52:56 2024 -0400

    add contributors to DESCRIPTION

commit 70ca8d65bffcf32ac41179fc4ff79f0665948251
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:46:07 2024 -0400

    edit vignettes; remove gosling.shiny vis from intro, add to alphafold

commit 4eefe8728cc91cdbb470a69e2f3d5291adba6d09
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 16:36:59 2024 -0400

    modify function; change colormap, change example, fix categories

commit 424fe6b0182e7ce735a3443e9856dcf243b9b798
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date:   Mon Jul 29 19:43:15 2024 +0000

    checks for directory .gosling

commit 9e9170aa5cc90f23e14a692701dc11331a1af127
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:30:23 2024 -0400

    Fixes

commit 236aa27d454ac32acfcafeab20015c1c0c512cfa
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:10:34 2024 -0400

    Remove .RData

commit 1790d52a70e6b8df503a466dfc309e29c48c4c16
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:09:19 2024 -0400

    revert changes to ignores

commit ea6f464975ff2d97d8e13b7b5bb55b088995fe76
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:06:10 2024 -0400

    Remove .gosling repo

commit 75428d28da58803e38070d846653d5e4cf048216
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 15:00:35 2024 -0400

    Remove d_clinvar.R, fix DESCRIPTION

commit 4bac60a31896423625a2b1cd742b4a8be858d61c
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 14:28:26 2024 -0400

    Remove .Rproj

commit 123c788b894a7c9a96545878ffc3ad8bc2e7f2ce
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 14:26:31 2024 -0400

    Remove z_scratch.Rmd after consulting with Tram and Tyronne

commit 7fa695488c4b3a60df29ea23346e63f8db981a20
Merge: 2aba65e 1214ac9
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date:   Mon Jul 29 14:24:45 2024 -0400

    Merge branch 'devel' into vis_shinygosling

commit 2aba65ed4c56aefd713d1d86c2b832e6c6446cfc
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Mon Jul 29 10:56:41 2024 -0400

    wrap lolipop plotting in function "plot_shinygosling" examples and other plots in scratch Rmd

commit 224e5f2d27814b0aa1a8546ee3cd56860593ef1e
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Jun 20 14:56:02 2024 -0400

    fix knitting error: seperating track objects

commit b6a735822def4ca28a331cbd56b2cb968ff0ae4a
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Thu Jun 20 14:47:09 2024 -0400

    update b_vis vignette. take screenshots for presentation

commit 1886cb436018b612bfe8338bd0504f4ef759895d
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Wed May 29 13:59:10 2024 -0400

    update suggests w/shiny.gosling, fix runtime and library calls, update gitignore

commit b4c413650f9f14040443712c1acd33f3d7484661
Merge: f3dcd5a 199e755
Author: Tyrone Lee <tyrone_lee@hms.harvard.edu>
Date:   Tue May 28 16:40:29 2024 -0400

    Merge branch 'mtmorgan:devel' into vis_shinygosling

commit f3dcd5acb1e0477ce5a823bc64218f8ff9134d50
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Tue May 28 15:12:52 2024 -0400

    minor labels

commit ffbeac36f9ad7621aa6198b4054c6edbe1defc04
Author: lee-t <tyrone_lee@hms.harvard.edu>
Date:   Fri May 24 17:31:58 2024 -0400

    add integrated shiny.gosling plot embedded into vignette, first pass
 

    

  
    

      Package: ontoProc

      Commit: 07575140bde0d0d6d16e0c992c9f8ee5005cd2a7

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-13 08:24:30 -0400

      Commit message:


	  
		
 adding object caching in setup_entities2
 

    

  
    

      Package: SpaNorm

      Commit: fc96b27613996d3e01ba1259354079c11d903b6c

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 22:12:21 +1030

      Commit message:


	  
		
 Addressed bioc reviewer comments (triggering build)
 

    

  
    

      Package: SpaNorm

      Commit: 519192b6b1eaf5064231095df3357a52ea0047df

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 11:21:37 +0000

      Commit message:


	  
		
 bug fix in plotSpatial and doc update
 

    

  
    

      Package: SpaNorm

      Commit: 6668baa269ab2661faa28c6f35df0ef3294eb076

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 11:08:14 +0000

      Commit message:


	  
		
 changed isbio to wtype to represent covariate types more broadly
 

    

  
    

      Package: SpaNorm

      Commit: f2bc1ec948f9ea411f80101b38ef0b473950b0bf

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 20:22:03 +1030

      Commit message:


	  
		
 spell check in vignette and documentation
 

    

  
    

      Package: SpaNorm

      Commit: 57fecb05be2c74857b7b7547dbef16aa321d683c

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 14:49:52 +1030

      Commit message:


	  
		
 fixed warnings caused by setting lazydata to false
 

    

  
    

      Package: SpaNorm

      Commit: babfd815b55bebc9c0925ca69204ac9871e41c6e

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 14:26:11 +1030

      Commit message:


	  
		
 malformed authors field in description
 

    

  
    

      Package: SpaNorm

      Commit: 35168e10a401046ac0c88235bdda8637d983278f

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 14:17:28 +1030

      Commit message:


	  
		
 typo in description file
 

    

  
    

      Package: SpaNorm

      Commit: f3f3f23b0d0e3fe21ce56a36aba62d3675b5f209

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 02:50:24 +0000

      Commit message:


	  
		
 added spatial plotting function and swapped the previous function in the vignette
 

    

  
    

      Package: SpaNorm

      Commit: 9c92dcef8b2aaded8df4e1f90f07b4052f25d7c4

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:58:01 +0000

      Commit message:


	  
		
 Added citation file
 

    

  
    

      Package: SpaNorm

      Commit: 7a841d499f3f7eb89359a762c65f3dafe9d8ccbe

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:47:04 +0000

      Commit message:


	  
		
 changed dontrun to donttest in examples
 

    

  
    

      Package: SpaNorm

      Commit: 2145a76099906c6481740302fdb5631926dc72e9

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:39:54 +0000

      Commit message:


	  
		
 Added CellBiology to biocViews and set LazyData to false
 

    

  
    

      Package: SpaNorm

      Commit: 75844786de19c4f54262b5e3cfc213df6d7d4b9d

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:39:14 +0000

      Commit message:


	  
		
 changed loop from 1:... to seq_len
 

    

  
    

      Package: SpaNorm

      Commit: e437d612107ea2380b28a6defc9b845efd0b5dc5

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:09:35 +0000

      Commit message:


	  
		
 explicit call to str in show method for SpaNormFit
 

    

  
    

      Package: SpaNorm

      Commit: 48ad449963e21aa900965d3c14b1b6c162f62a94

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:07:21 +0000

      Commit message:


	  
		
 bug fix due to typo (W -> Wsub)
 

    

  
    

      Package: SpaNorm

      Commit: 0c43c108c2d1794dcec6ab4773f7ef18c66ac149

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:03:01 +0000

      Commit message:


	  
		
 explicit namespace import
 

    

  
    

      Package: SpaNorm

      Commit: 3384ab60c93f06cccaa7e7a20383f2faf2322be7

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:02:29 +0000

      Commit message:


	  
		
 added news file
 

    

  
    

      Package: SpaNorm

      Commit: 315b705708255b07608bca21191ede1f6ea5e77a

      Author:  Dharmesh Bhuva <dharmesh.bhuva@adelaide.edu.au> 

      Date: 2024-10-13 00:02:21 +0000

      Commit message:


	  
		
 removed unnecessary files
 

    

  
    

      Package: edgeR

      Commit: 9b2e2ea00b6fb4035dee7f71b5f8d1b21dc44c6d

      Author:  Yunshun Chen <yuchen@wehi.edu.au> 

      Date: 2024-10-13 15:05:31 +1100

      Commit message:


	  
		
 Update the edgeR user's guide
 

    

  
    

      Package: ggsc

      Commit: 86ac61edf63336c76a7e8c048a4a9cd2e4ce9595

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2024-10-13 11:18:28 +0800

      Commit message:


	  
		
 Merge pull request #37 from MingLi-929/devel

fix the function of features parameter 

    

  
    

      Package: ggsc

      Commit: 61bae901cc4e805708ca9ebc0e6498b3f8dc634a

      Author:  li ming <limiang929@gmail.com> 

      Date: 2024-10-13 10:37:37 +0800

      Commit message:


	  
		
 fix the function of features parameter
 

    

  
    

      Package: EpiDISH

      Commit: e107fce62c1e85b9b888f0885aed095acc9a6a20

      Author:  Shijie C. Zheng <shijieczheng@gmail.com> 

      Date: 2024-10-12 22:05:00 -0400

      Commit message:


	  
		
 Version bump after fixing cp
 

    

  
    

      Package: EpiDISH

      Commit: 38ef4b34046d0dc8cd41598e2a9563ad14ed5e8f

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-10-05 12:41:51 +0800

      Commit message:


	  
		
 Correct the DoCP function 

    

  
    

      Package: EpiDISH

      Commit: 9735edcc71b51b697101a56b9544c7758b9f0858

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 22:24:35 +0800

      Commit message:


	  
		
 Delete man/centCAB100i.Rd 

    

  
    

      Package: EpiDISH

      Commit: 0bcaedfc4c8bc5201a4f9f73e28f8009cec61940

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 22:08:42 +0800

      Commit message:


	  
		
 add 19 CT blood reference 

    

  
    

      Package: EpiDISH

      Commit: 6093187c0b8de9c1f2a00574e50b9c700142c2b3

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 22:08:00 +0800

      Commit message:


	  
		
 Delete man/centCAB100i.rda 

    

  
    

      Package: EpiDISH

      Commit: 509efee6053a3c9553bcdf839a17f70bcf42b42b

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 20:55:39 +0800

      Commit message:


	  
		
 add 19 blood CT reference 

    

  
    

      Package: EpiDISH

      Commit: a2039722bc7024d39a4782197a1b236a93ee873c

      Author:  xiaolong guo <85536994+tednb@users.noreply.github.com> 

      Date: 2024-09-02 20:52:53 +0800

      Commit message:


	  
		
 Add files via upload

add a 19 CT reference matrix 

    

  
    

      Package: SpliceWiz

      Commit: 2839410ea6b844e500fa86b4c65ee76fd2a66f6a

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2024-10-13 10:41:26 +1100

      Commit message:


	  
		
 Version bump 1.7.6

Fix uninformative message when gene ontology species not available
 

    

  
    

      Package: ontoProc

      Commit: c383cbf13b629aa6789f3bb75b721772eec57af4

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-12 12:45:01 -0400

      Commit message:


	  
		
 passes check on mac
 

    

  
    

      Package: ontoProc

      Commit: 13961bd3113f4108c727dab85cb80615332011ba

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-10 08:48:50 -0400

      Commit message:


	  
		
 conditioning owl2cache example
 

    

  
    

      Package: ontoProc

      Commit: 782024e36b4ca46a3ac7f62d4d25c2e170e16869

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-10 05:32:35 -0400

      Commit message:


	  
		
 various changes to condition on availability of owlready2
 

    

  
    

      Package: ontoProc

      Commit: 402590c5ac3d09922825c8469480a4d4cce7e025

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-09 11:19:18 -0400

      Commit message:


	  
		
 Merge branch 'devel' into with_pkgdown
 

    

  
    

      Package: ontoProc

      Commit: f1bc01126fded9776b1a1063129004c81db3c9c2

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2024-10-09 05:50:43 -0400

      Commit message:


	  
		
 update action workflow
 

    

  
    

      Package: mzR

      Commit: fe18e32ad24fc9cdffbc3eca88f63a362dc5e2a6

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2024-10-12 08:48:22 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: mzR

      Commit: 4507e04c00ab6d6bbe34a2dffe2bdea230f7f2ae

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2024-10-12 08:46:48 +0200

      Commit message:


	  
		
 Merge pull request #299 from rdhale92/patch-1

Improve grammar of `openMSfile` manpage 

    

  
    

      Package: mzR

      Commit: f7ea9b3e8d5ee903c27fdb789a1fe02e74360828

      Author:  rdhale92 <75230021+rdhale92@users.noreply.github.com> 

      Date: 2024-10-11 22:54:13 -0400

      Commit message:


	  
		
 Improve grammar of `openMSfile` manpage

I found the previous structures of two sentences confusing. I believe these new changes more clearly communicate the intent of the `openMSfile` and `openIDfile` constructors. 

    

  
    

      Package: sccomp

      Commit: e664088d6d86340940f7663253c0814a73add6fe

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-12 14:13:00 +1100

      Commit message:


	  
		
 pull

Merge branch 'master' of github.com:stemangiola/sccomp

# Conflicts:
#	DESCRIPTION
 

    

  
    

      Package: sccomp

      Commit: fe49259cc4f420997ef411b0bdb5b253b920df0a

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-12 14:12:13 +1100

      Commit message:


	  
		
 rename man files
 

    

  
    

      Package: sccomp

      Commit: f19730364336e8d749d92fb8a299fa6002ebc7c4

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-12 14:10:41 +1100

      Commit message:


	  
		
 update version

Merge branch 'master' of git.bioconductor.org:packages/sccomp

# Conflicts:
#	DESCRIPTION
 

    

  
    

      Package: sccomp

      Commit: b680e8a43a832816a30bd957ec3728506995c53f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-12 12:29:16 +1030

      Commit message:


	  
		
 fix Vignette
 

    

  
    

      Package: sccomp

      Commit: 1ca8e35ce253cd99f70c2fd25a6e806c6ee4bacd

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-12 12:12:47 +1030

      Commit message:


	  
		
 Update README
 

    

  
    

      Package: sccomp

      Commit: d670de3e201dead89fa72cf9c287ce5fe80a0330

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 22:24:45 +1030

      Commit message:


	  
		
 Merge pull request #126 from MangiolaLaboratory/proportions

Proportions 

    

  
    

      Package: sccomp

      Commit: 4adf0361961dd6b071eb9cb89fe5674a80747d3c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 21:40:26 +1030

      Commit message:


	  
		
 Merge branch 'proportions' of https://github.com/MangiolaLaboratory/sccomp into proportions
 

    

  
    

      Package: sccomp

      Commit: 3de029f6824fac18225a8908320afc2af62b7040

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 21:40:08 +1030

      Commit message:


	  
		
 add docs
 

    

  
    

      Package: sccomp

      Commit: f4bc4ef3d0fb543d8e0ae40fb10fad1216813436

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 21:26:56 +1030

      Commit message:


	  
		
 Merge branch 'master' into proportions 

    

  
    

      Package: sccomp

      Commit: 2cbc33e0769f25f8e815e87e35521debe7d85022

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 21:23:07 +1030

      Commit message:


	  
		
 fix Vignette
 

    

  
    

      Package: sccomp

      Commit: 755734a507f9b0ce1e456cce47c06e0b54bc9643

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 21:21:44 +1030

      Commit message:


	  
		
 Merge pull request #124 from MangiolaLaboratory/change-residuals

Change residuals 

    

  
    

      Package: sccomp

      Commit: feb7be9b1c2b27d240c3dde6daf2f89363996f85

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 19:50:04 +1030

      Commit message:


	  
		
 fix tests and documentation
 

    

  
    

      Package: sccomp

      Commit: 2bdc69135cb9a209b1bffbfd4f016252d1fe926c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 17:00:29 +1030

      Commit message:


	  
		
 rebase master
 

    

  
    

      Package: sccomp

      Commit: e5b55668771ad6a284a59978d49eb4cb46278213

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:57:00 +1030

      Commit message:


	  
		
 Merge branch 'master' into change-residuals 

    

  
    

      Package: sccomp

      Commit: ed6e6698b709ecec8a089e4c898094af13afedcb

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:54:33 +1030

      Commit message:


	  
		
 fix documentation
 

    

  
    

      Package: sccomp

      Commit: 4e5f36aa469a0c162688ee5bc2d7fdb63944f2d9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:41:00 +1030

      Commit message:


	  
		
 Merge pull request #155 from MangiolaLaboratory/improve-remove_unwanted_variation-arguments

deprecate argument 

    

  
    

      Package: sccomp

      Commit: 5645d787a2224ebbac95207f83e6049e78106227

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:40:44 +1030

      Commit message:


	  
		
 rebase master

Merge branch 'master' into proportions

# Conflicts:
#	R/utilities.R
#	README.md
#	inst/figures/unnamed-chunk-10-1.png
#	inst/figures/unnamed-chunk-11-1.png
#	inst/figures/unnamed-chunk-12-1.png
#	inst/figures/unnamed-chunk-13-1.png
#	inst/figures/unnamed-chunk-19-1.png
#	inst/figures/unnamed-chunk-20-1.png
#	inst/figures/unnamed-chunk-21-1.png
#	inst/stan/glm_multi_beta_binomial.stan
#	man/fragments/intro.Rmd
 

    

  
    

      Package: sccomp

      Commit: 76e964a1fb06837fc1fdc953944aef2740c60413

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:16:52 +1030

      Commit message:


	  
		
 adapt test to cmdstanr
 

    

  
    

      Package: sccomp

      Commit: b7e2c950a6c88e0a16dc91d60ca8490108e68948

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:14:19 +1030

      Commit message:


	  
		
 add test
 

    

  
    

      Package: sccomp

      Commit: 99c2306111d94e8cebbfb3796e21304b79060f41

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 14:04:32 +1030

      Commit message:


	  
		
 fix tests
 

    

  
    

      Package: sccomp

      Commit: 2e93084d24b234b4686eb1ce5f7ab3bccfa74b4a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 11:24:53 +1030

      Commit message:


	  
		
 rebase master

Merge branch 'master' into change-residuals

# Conflicts:
#	DESCRIPTION
#	R/methods.R
#	README.Rmd
#	tests/testthat/test-sccomp_.R
 

    

  
    

      Package: sccomp

      Commit: 8445816ca40baa209d8d27079f57cab0e2e4122f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 11:16:20 +1030

      Commit message:


	  
		
 change to current model
 

    

  
    

      Package: sccomp

      Commit: 2883910cf796307338e85ad1ff016a41b3adbffd

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-11 11:03:39 +1030

      Commit message:


	  
		
 deprecate argument
 

    

  
    

      Package: sccomp

      Commit: a81bc86ed02ff7572657fd9d3670ba9a4b783936

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-07 10:38:51 +1030

      Commit message:


	  
		
 Merge pull request #84 from MangiolaLaboratory/cmdstanr

Cmdstanr 

    

  
    

      Package: sccomp

      Commit: 1c192582ac870dc3327a1755a3ad8100ca8f4334

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-02 20:58:50 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: sccomp

      Commit: 667abcc5f14ae0346d40f546ccc9fe5f51246e22

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-02 18:50:25 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: sccomp

      Commit: fae0401e975e1f7352ece2d0df0ca8f858ce8283

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-02 18:38:43 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: sccomp

      Commit: c4eda42d9dd97af7d87bd8bc3e321e30f67dd5dd

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-02 18:37:32 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: sccomp

      Commit: 0dc12929266bc3a947e2240749e9763d486467c2

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-10-01 10:46:09 +0200

      Commit message:


	  
		
 fix code execution
 

    

  
    

      Package: sccomp

      Commit: 19bd106ef45ff40255f22e45658ab9ba41f018c3

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-27 15:57:33 +0200

      Commit message:


	  
		
 fix vignette
 

    

  
    

      Package: sccomp

      Commit: 2df7a171085ec1f2f90c6b1701eb2bd5cc7b402c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-27 15:50:07 +0200

      Commit message:


	  
		
 clear model if cmdstanr is uninstalled because give error
 

    

  
    

      Package: sccomp

      Commit: 1394d0b581fe57856ce80f14618c18a6aeddc536

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-27 15:34:59 +0200

      Commit message:


	  
		
 fix vignettes
 

    

  
    

      Package: sccomp

      Commit: ec575598df7f633623bf577e1d8d7fc0adcdb34d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-25 10:41:20 +0200

      Commit message:


	  
		
 typos
 

    

  
    

      Package: sccomp

      Commit: 3e2336376d9c79e64601b53a7bc7517e5b68ba06

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-25 09:34:57 +0200

      Commit message:


	  
		
 update dependency instantiate
 

    

  
    

      Package: sccomp

      Commit: f511f02ccb1ddef72790c1591df40593ad4b4247

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 22:49:38 +0200

      Commit message:


	  
		
 drop actions
 

    

  
    

      Package: sccomp

      Commit: 0c7fc0a0473ae42264dedf878cf126b5589284ee

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 22:31:37 +0200

      Commit message:


	  
		
 fix tests
 

    

  
    

      Package: sccomp

      Commit: 5f143a8b91f7c6ef03a76b2a47da0aca9beb4063

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 22:17:29 +0200

      Commit message:


	  
		
 fix vignette
 

    

  
    

      Package: sccomp

      Commit: 5607c7c882987e4282b7beb36e0b7297887d68aa

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 22:08:22 +0200

      Commit message:


	  
		
 Merge branch 'cmdstanr' of https://github.com/MangiolaLaboratory/sccomp into cmdstanr
 

    

  
    

      Package: sccomp

      Commit: a5f9105f256a4972e657ad04a62f58ae2305875b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 22:08:08 +0200

      Commit message:


	  
		
 add rworkflows back
 

    

  
    

      Package: sccomp

      Commit: a88a928cea9e445d0c30eeab7a8682fe2f10a43f

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-24 06:04:44 +1000

      Commit message:


	  
		
 Merge branch 'cmdstanr' of github.com:stemangiola/sccomp into cmdstanr
 

    

  
    

      Package: sccomp

      Commit: f716bdc20066fc00acb0d98ad937ae3dfb2b8d07

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-24 06:04:03 +1000

      Commit message:


	  
		
 fix second grouping initialisation
 

    

  
    

      Package: sccomp

      Commit: e8901ca910e45f2dbb1e1264e3f8d3a86839bf6d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 22:01:06 +0200

      Commit message:


	  
		
 reintentation
 

    

  
    

      Package: sccomp

      Commit: df9ca5cc63b604537a47bec5abc9e2e129759830

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-24 05:50:50 +1000

      Commit message:


	  
		
 pull

Merge branch 'cmdstanr' of github.com:stemangiola/sccomp into cmdstanr

# Conflicts:
#	NAMESPACE
 

    

  
    

      Package: sccomp

      Commit: 08403b6ff2d0c55a33f305858f65a616dab5be05

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-24 05:49:25 +1000

      Commit message:


	  
		
 dummy
 

    

  
    

      Package: sccomp

      Commit: d462912e86c68fe3cd1ff5a8fdbb632d1a658146

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 20:47:02 +0200

      Commit message:


	  
		
 try fix github action
 

    

  
    

      Package: sccomp

      Commit: 9e09330c100625c4bf2c574d6d369104d39f1e8d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 20:37:51 +0200

      Commit message:


	  
		
 drop zzz
 

    

  
    

      Package: sccomp

      Commit: 1c8a74d7c88d1ddc5712fdeddf21c8ce8850741f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 20:31:06 +0200

      Commit message:


	  
		
 fix workflows
 

    

  
    

      Package: sccomp

      Commit: 56522972e4b8a848ba75fab070d90f28446c01bb

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 19:42:18 +0200

      Commit message:


	  
		
 pull conflicts

Merge branch 'master' of https://github.com/MangiolaLaboratory/sccomp into cmdstanr

# Conflicts:
#	R/methods.R
#	R/stanmodels.R
#	README.md
#	inst/figures/unnamed-chunk-12-1.png
#	inst/figures/unnamed-chunk-14-1.png
#	inst/figures/unnamed-chunk-15-1.png
#	inst/figures/unnamed-chunk-19-1.png
 

    

  
    

      Package: sccomp

      Commit: 1648cbb00e857471116a0cf6ad996cc967469e4f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 19:22:52 +0200

      Commit message:


	  
		
 fix BiocCheck
 

    

  
    

      Package: sccomp

      Commit: bd34533e7728763f6c3ff608a827a3a957b1d558

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-23 18:31:34 +0200

      Commit message:


	  
		
 fix simulation
 

    

  
    

      Package: sccomp

      Commit: 68b8614bfb58f34c672c6f06e40b1886c6127dde

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-22 11:56:30 +0200

      Commit message:


	  
		
 fix bug in censoring function
 

    

  
    

      Package: sccomp

      Commit: d2bf04a80a9dcd5a16f873842bd1c8d4da3d097d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 23:18:25 +0200

      Commit message:


	  
		
 fix model loading
 

    

  
    

      Package: sccomp

      Commit: 41551a3009d65146fa2e81dd7c115867c3b5011d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 22:37:32 +0200

      Commit message:


	  
		
 fix repo
 

    

  
    

      Package: sccomp

      Commit: 708a03da8ab865954cd8f3462236337ef086f0d6

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 22:19:28 +0200

      Commit message:


	  
		
 temp fixes
 

    

  
    

      Package: sccomp

      Commit: 7fca94da98ac2bc4138ee0cc7db49a06fd9f0d93

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 21:07:47 +0200

      Commit message:


	  
		
 drop loading message
 

    

  
    

      Package: sccomp

      Commit: 00f4a868955009f3b4eb6d0f480eea4305b2941a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 21:02:14 +0200

      Commit message:


	  
		
 Merge pull request #153 from MangiolaLaboratory/cmdstanr_nested_grouping

Cmdstanr nested grouping 

    

  
    

      Package: sccomp

      Commit: ecd1119cf15a55d1b753e525dc97285382278331

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 21:01:50 +0200

      Commit message:


	  
		
 Merge pull request #152 from MangiolaLaboratory/refactor-model-functions

Refactor model functions 

    

  
    

      Package: sccomp

      Commit: c116e597402b2af27e0c940412ea203e5678fc8b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 20:59:53 +0200

      Commit message:


	  
		
 drop dependency from cmdstanr
 

    

  
    

      Package: sccomp

      Commit: de99f75871b05fb5f430d44f131004aa7a010b07

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 19:04:20 +0200

      Commit message:


	  
		
 fix CHECK
 

    

  
    

      Package: sccomp

      Commit: 297e78fdb182d0aea7602c05d62e3b8c7cdb3dcb

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 18:02:46 +0200

      Commit message:


	  
		
 Merge pull request #151 from MangiolaLaboratory/cmdstanr_nested_grouping

Cmdstanr nested grouping 

    

  
    

      Package: sccomp

      Commit: 48886f869958b719725b09a89d868b2ff461bc5b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 18:00:41 +0200

      Commit message:


	  
		
 Merge pull request #150 from MangiolaLaboratory/refactor-model-functions

Refactor model functions 

    

  
    

      Package: sccomp

      Commit: 593f489852f3b0dcfcc611cb569ee7766ee6db58

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 17:58:52 +0200

      Commit message:


	  
		
 restructure tests for cmdstanr, from https://github.com/ethan-alt/hdbayes/tree/main
 

    

  
    

      Package: sccomp

      Commit: db2937887a089bc92b80647865dbec6e7636d961

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 17:38:02 +0200

      Commit message:


	  
		
 put back LOO in the model
 

    

  
    

      Package: sccomp

      Commit: 7c034b929253132f31c814dacb8420d23dc8e749

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 16:08:04 +0200

      Commit message:


	  
		
 fix tests
 

    

  
    

      Package: sccomp

      Commit: b999b447cda7b15d9476fe9dff8b3810d452b608

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 11:55:15 +0200

      Commit message:


	  
		
 Merge branch 'refactor-model-functions' of https://github.com/MangiolaLaboratory/sccomp into refactor-model-functions
 

    

  
    

      Package: sccomp

      Commit: f85da0de35f327851ff94c4b487bbf891f5e9faa

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 11:55:05 +0200

      Commit message:


	  
		
 fix truncation
 

    

  
    

      Package: sccomp

      Commit: c4df4259d330a60af6f5596ec5acd6bb339c1d7d

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-21 19:53:55 +1000

      Commit message:


	  
		
 fix inits
 

    

  
    

      Package: sccomp

      Commit: b28bd76a624bba032086b59564322da7bf29deb9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-19 10:48:41 +0300

      Commit message:


	  
		
 one multivariate per cell type
 

    

  
    

      Package: sccomp

      Commit: a0b7379827c752bd19151445bfefa6661305860a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-14 12:32:55 +0200

      Commit message:


	  
		
 update vignette
 

    

  
    

      Package: sccomp

      Commit: 39cfe101d37dd9fdfc17508a705e290d3b849410

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-11 12:27:54 +0200

      Commit message:


	  
		
 Merge branch 'refactor-model-functions' of https://github.com/MangiolaLaboratory/sccomp into refactor-model-functions
 

    

  
    

      Package: sccomp

      Commit: 01550df5a621196370fd25bc916137c61d0975aa

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-11 12:27:48 +0200

      Commit message:


	  
		
 add ellipse
 

    

  
    

      Package: sccomp

      Commit: dbce014ea10843da20b84aa15d53b4d1a536e8d3

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-05 11:49:49 +0100

      Commit message:


	  
		
 fix generated data 2
 

    

  
    

      Package: sccomp

      Commit: e327a4608e650ba4f03d85e60ba0182ecd911217

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-05 11:49:22 +0100

      Commit message:


	  
		
 fix generate_data
 

    

  
    

      Package: sccomp

      Commit: 9826ef4c209c22b94610d4ba22902b16f3bdf2f6

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-05 18:38:05 +1000

      Commit message:


	  
		
 Merge branch 'refactor-model-functions' of github.com:stemangiola/sccomp into refactor-model-functions
 

    

  
    

      Package: sccomp

      Commit: a5f6d2f36d9cf6c1b75230bc2d66631f5daaff95

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-05 18:37:50 +1000

      Commit message:


	  
		
 docs
 

    

  
    

      Package: sccomp

      Commit: 3a195845aa2aba64909d70783abbb11ff0cfc24c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-03 21:46:27 +0200

      Commit message:


	  
		
 parallelise based on samples
 

    

  
    

      Package: sccomp

      Commit: 49ada52cb0672b7cab715bdacafd133deb8376f6

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-04 01:59:24 +1000

      Commit message:


	  
		
 add create mu function
 

    

  
    

      Package: sccomp

      Commit: d8ab42a5c890daa746da744cd6a2d341aa1998a7

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-09-04 01:57:50 +1000

      Commit message:


	  
		
 add custom draw directory
 

    

  
    

      Package: sccomp

      Commit: 71f2e1a7358e5679a1fd3a7e0c44c450bcc0b6b9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-29 08:40:10 +0930

      Commit message:


	  
		
 Merge pull request #148 from MangiolaLaboratory/add_test_messaging

add message 

    

  
    

      Package: sccomp

      Commit: 8f54a93ec1cd32409e72bf6c1ebe8db1941ab5b7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 20:33:52 +0930

      Commit message:


	  
		
 add message
 

    

  
    

      Package: sccomp

      Commit: ad3d099e612824dfdb28481d78bd8a73d8aa8224

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 20:15:29 +0930

      Commit message:


	  
		
 Merge branch 'add_test_messaging' of https://github.com/MangiolaLaboratory/sccomp into add_test_messaging
 

    

  
    

      Package: sccomp

      Commit: 87ae47c3a92079bacc3f09d0d1d0f182694c607d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 19:56:55 +0930

      Commit message:


	  
		
 add message
 

    

  
    

      Package: sccomp

      Commit: f0f83149378daa8d5a15188507a4dffaecdca907

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 20:14:16 +0930

      Commit message:


	  
		
 Merge pull request #147 from MangiolaLaboratory/calculate_proportion_difference

Calculate proportion difference 

    

  
    

      Package: sccomp

      Commit: fea9518d699e27dc7006e5701347db755ad8a4c0

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 20:13:34 +0930

      Commit message:


	  
		
 merge master

Merge branch 'master' of https://github.com/MangiolaLaboratory/sccomp into calculate_proportion_difference

# Conflicts:
#	README.md
#	inst/figures/unnamed-chunk-19-1.png
 

    

  
    

      Package: sccomp

      Commit: afaec6e5be2119ebe9098fbc42c9f4e6cd06bfcd

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 19:56:55 +0930

      Commit message:


	  
		
 add message
 

    

  
    

      Package: sccomp

      Commit: 22acf87b977e3ff5232e4c7b8b48f05318e1b3d7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-27 19:49:03 +0930

      Commit message:


	  
		
 add models
 

    

  
    

      Package: sccomp

      Commit: cb426f93f74d0018eeccf86609a6a7a778ec038b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-14 20:09:12 +0930

      Commit message:


	  
		
 fix after merging with nested random effect
 

    

  
    

      Package: sccomp

      Commit: 385d12aaa11b647e1d1b9d8392a73a644bb9c1c7

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-13 00:14:52 +1000

      Commit message:


	  
		
 fix the merge
 

    

  
    

      Package: sccomp

      Commit: c3611570268d38b8b6b052428ff4bc0873d79964

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-12 23:16:24 +1000

      Commit message:


	  
		
 merge

Merge branch 'nested-grouping' into cmdstanr_nested_grouping

Conflicts:
	R/methods.R
	R/stanmodels.R
	R/utilities.R
	inst/stan/glm_multi_beta_binomial.stan
	inst/stan/glm_multi_beta_binomial_generate_date.stan
	man/sccomp_estimate.Rd
	man/sccomp_remove_outliers.Rd
	tests/testthat/test-sccomp_.R
 

    

  
    

      Package: sccomp

      Commit: 5e371863c4f8de6aa9c008224061e483a7b40c78

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-12 23:05:31 +1000

      Commit message:


	  
		
 pull

Merge branch 'cmdstanr' of github.com:stemangiola/sccomp into cmdstanr

Conflicts:
	tests/testthat/test-sccomp_.R
 

    

  
    

      Package: sccomp

      Commit: ef5e8f14088dcfe0bdf9fb67de5a490ca712c532

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-12 22:19:09 +1000

      Commit message:


	  
		
 change one test
 

    

  
    

      Package: sccomp

      Commit: 6b9c341fa9433f947abdc3086a132128acc00783

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-12 21:46:02 +1000

      Commit message:


	  
		
 solve current tests, missing 2+1 grouping
 

    

  
    

      Package: sccomp

      Commit: ea10d785894cc621caa0f88a0f21c2b1248616f0

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-11 09:51:08 +1000

      Commit message:


	  
		
 fix argument size
 

    

  
    

      Package: sccomp

      Commit: 02ef388bed2551432d355a46414f7396fbe116e6

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-07 23:06:23 +1000

      Commit message:


	  
		
 update model and scripts to accommodate 2 hierarchies
 

    

  
    

      Package: sccomp

      Commit: 24de3f5057d23c9903e2b7a9e88800ebe69be889

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-08-06 16:16:26 +1000

      Commit message:


	  
		
 update models script
 

    

  
    

      Package: sccomp

      Commit: 7d3850603d3ee018eac273d0678d771e7f31bce1

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-03 12:35:22 +0930

      Commit message:


	  
		
 update docs
 

    

  
    

      Package: sccomp

      Commit: 2839d62a7b493500c0f7e53c62302dc04ece47c3

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-03 12:16:57 +0930

      Commit message:


	  
		
 merge master

Merge branch 'master' into proportions

# Conflicts:
#	README.md
#	inst/figures/unnamed-chunk-10-1.png
#	inst/figures/unnamed-chunk-11-1.png
#	inst/figures/unnamed-chunk-12-1.png
#	inst/figures/unnamed-chunk-19-1.png
#	inst/figures/unnamed-chunk-20-1.png
#	inst/figures/unnamed-chunk-21-1.png
#	man/fragments/intro.Rmd
 

    

  
    

      Package: sccomp

      Commit: 290cf466df49d7a822b71466d4a79ab725548a32

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-03 12:12:37 +0930

      Commit message:


	  
		
 update figures
 

    

  
    

      Package: sccomp

      Commit: 07802a6755542d11b5ab82ed6df99f24a30dcf8b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-03 12:12:11 +0930

      Commit message:


	  
		
 update docs
 

    

  
    

      Package: sccomp

      Commit: 3e1daa113f8424b1833a9b128cb627c29ff97421

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-02 09:34:19 +0930

      Commit message:


	  
		
 fold back to HMC as default
 

    

  
    

      Package: sccomp

      Commit: d13e0c34f1eb828ec8fc9176bdbdf1e9386b6bd9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-01 16:52:14 +0930

      Commit message:


	  
		
 update tests
 

    

  
    

      Package: sccomp

      Commit: 19c55722a3e24251cb68af80745684b72b695ed4

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-01 11:55:56 +0930

      Commit message:


	  
		
 rebuild model if not compiled
 

    

  
    

      Package: sccomp

      Commit: 827a6812efb420ebcb399621cc15fd90f89f3655

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-07-01 10:02:07 +0930

      Commit message:


	  
		
 Merge pull request #142 from MangiolaLaboratory/drop-env-from-quotes-and-formula

drop environment from formula and quotes 

    

  
    

      Package: sccomp

      Commit: 393f1a5a9322ba766a92ef994d4ea3492a4c0a2d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 23:13:46 +0930

      Commit message:


	  
		
 rebase

Merge branch 'master' into cmdstanr

# Conflicts:
#	.Rbuildignore
#	.gitignore
#	NAMESPACE
#	R/functions_dirichlet_multinomial.R
#	R/functions_multi_beta.R
#	R/utilities.R
#	README.md
#	inst/figures/unnamed-chunk-10-1.png
#	inst/figures/unnamed-chunk-11-1.png
#	inst/figures/unnamed-chunk-12-1.png
 

    

  
    

      Package: sccomp

      Commit: 1a91bb46f04c9d6283a9e3083aa936e750040076

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 23:02:11 +0930

      Commit message:


	  
		
 drop environment from formula and quotes
 

    

  
    

      Package: sccomp

      Commit: ff735d730841f8783fbbdcaf8fd1a5dc8881bf60

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 22:27:48 +0930

      Commit message:


	  
		
 Merge pull request #141 from MangiolaLaboratory/pass-foldchange

update README and vignette 

    

  
    

      Package: sccomp

      Commit: e16c1cfbf43da2a906521f8eaa4bbddf8cf35479

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 20:56:36 +0930

      Commit message:


	  
		
 fix tests
 

    

  
    

      Package: sccomp

      Commit: 58d0bf5b3878e18770aaea1cf7c5240c59394f4d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 19:35:08 +0930

      Commit message:


	  
		
 update README and vignette
 

    

  
    

      Package: sccomp

      Commit: 50e0f8faed6c9613f2d66c5336113d94dc836b84

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 16:18:34 +0930

      Commit message:


	  
		
 Merge pull request #140 from MangiolaLaboratory/pass-foldchange

pass the attribute 

    

  
    

      Package: sccomp

      Commit: a217890163da447d2fc12f8594fcea70c9f27f6d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 14:51:35 +0930

      Commit message:


	  
		
 warning fixes
 

    

  
    

      Package: sccomp

      Commit: cc1f0f67c306a4f409a259f94cfe8ba845fb0717

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-30 12:24:46 +0930

      Commit message:


	  
		
 fix CRAN NOTEs
 

    

  
    

      Package: sccomp

      Commit: e1468a9e98fdcc892e56ee19365e7199fd3e7533

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-29 14:41:42 +0930

      Commit message:


	  
		
 Merge branch 'pass-foldchange' of https://github.com/MangiolaLaboratory/sccomp into pass-foldchange
 

    

  
    

      Package: sccomp

      Commit: 88ae26cd1139f6c490f20fe71f678420643e8a78

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-29 14:41:36 +0930

      Commit message:


	  
		
 pass foldchange from attribute
 

    

  
    

      Package: sccomp

      Commit: bf10c01686db6f8a7fdb88f37f0c8b168b840213

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-29 12:42:09 +0930

      Commit message:


	  
		
 update git ignore
 

    

  
    

      Package: sccomp

      Commit: 4d0c61e45cf8f8f3159c6261306127d7ebc442bc

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-29 12:40:28 +0930

      Commit message:


	  
		
 pass the attribute
 

    

  
    

      Package: sccomp

      Commit: f1a7e9fe1b60c2ac741382e8bd81b480bb9c8e4c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-29 12:40:28 +0930

      Commit message:


	  
		
 pass the attribute
 

    

  
    

      Package: sccomp

      Commit: 22e02d4e9b4292ee6c7facdc01b40090bf80cc5c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-29 12:27:35 +0930

      Commit message:


	  
		
 Merge pull request #139 from MangiolaLaboratory/export-plotting-functions

update functions to be exposed 

    

  
    

      Package: sccomp

      Commit: 7e10c333d3879416d06ca9b250de2ea31004c6a9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-28 12:12:10 +0930

      Commit message:


	  
		
 Merge branch 'master' into export-plotting-functions 

    

  
    

      Package: sccomp

      Commit: db2a51c2ce34c066cda664016c828220273d800a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-28 12:07:38 +0930

      Commit message:


	  
		
 expose the functions with significance threshold
 

    

  
    

      Package: sccomp

      Commit: 525efcd8f1351d8d4db37e26c5f199ffc42355ad

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-28 11:36:44 +0930

      Commit message:


	  
		
 fix browser() and version UP
 

    

  
    

      Package: sccomp

      Commit: 1bc84ede231a2c3f3ddbc4949e7a1073195952fb

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-28 11:30:21 +0930

      Commit message:


	  
		
 update functions to be exposed
 

    

  
    

      Package: sccomp

      Commit: 20f61e88d17851a4d0758ea0dd46aa103b6b08cf

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-28 10:13:09 +0930

      Commit message:


	  
		
 version UP 

    

  
    

      Package: sccomp

      Commit: 6a5f46e0cbb26ad22337897e65abc2adbf5ed358

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-28 09:45:58 +0930

      Commit message:


	  
		
 fix threshold to 0.1
 

    

  
    

      Package: sccomp

      Commit: 6332499ba112be751d262b2edafc8ed6b23fdc4a

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-20 10:52:47 +1000

      Commit message:


	  
		
 remove seed
 

    

  
    

      Package: sccomp

      Commit: 7dfe52dd3b030ca56e807e33ddac657abd3f2d2c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-19 13:59:48 +0930

      Commit message:


	  
		
 fix hmc init
 

    

  
    

      Package: sccomp

      Commit: db009538ee645febf33ff883c09b9a29daf5ab62

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-18 23:54:40 +0930

      Commit message:


	  
		
 upgrade pathfinder with more chains
 

    

  
    

      Package: sccomp

      Commit: 40cdf2d9a3f17cb5cfdc144111fb3319567d53e8

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-18 23:21:37 +0930

      Commit message:


	  
		
 Merge pull request #137 from MangiolaLaboratory/allow-vb-output-samples

allow custom output samples for vb 

    

  
    

      Package: sccomp

      Commit: 02ee364c7fee0dd8ca64cd52893fa1e10372d731

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-18 11:48:47 +0930

      Commit message:


	  
		
 allow arbitrary samples
 

    

  
    

      Package: sccomp

      Commit: 9288b3a75389b05427d5563a93132c92361b4ba6

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-17 22:29:12 +0930

      Commit message:


	  
		
 allow custom output samples for vb
 

    

  
    

      Package: sccomp

      Commit: 7b1651073810d92fd8c959ad0fed48d46d2fd33d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-17 21:48:21 +0930

      Commit message:


	  
		
 fix old framework tests
 

    

  
    

      Package: sccomp

      Commit: 0eae6694b69bab2f219f98141a0ce58a73ae0c4e

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-17 20:54:28 +0930

      Commit message:


	  
		
 fix test errors
 

    

  
    

      Package: sccomp

      Commit: cef2e2c9dd8f5f57373e0891f30d659f0578e659

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 22:17:09 +0930

      Commit message:


	  
		
 put model into inst
 

    

  
    

      Package: sccomp

      Commit: b9e229531291b5d6b0506757f3736a0cb609d8b6

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 14:30:51 +0930

      Commit message:


	  
		
 merge master

Merge branch 'master' into cmdstanr

# Conflicts:
#	R/functions_multi_beta_binomial.R
 

    

  
    

      Package: sccomp

      Commit: fe98bd3b0a04a0c892477e8a73adb8bdb5e88188

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 14:56:44 +1000

      Commit message:


	  
		
 delete R file package
 

    

  
    

      Package: sccomp

      Commit: b801fecdf543ca451f73e00628ba5d7e12aa4002

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 14:03:55 +0930

      Commit message:


	  
		
 Merge branch 'cmdstanr' of https://github.com/MangiolaLaboratory/sccomp into cmdstanr
 

    

  
    

      Package: sccomp

      Commit: db22459c7d1321c3495cf877d8e1870d6d22c826

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 14:00:48 +0930

      Commit message:


	  
		
 Merge pull request #136 from MangiolaLaboratory/instantiate

Instantiate 

    

  
    

      Package: sccomp

      Commit: 07c6db87a14d692048b8018aaab16e2105235358

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 14:30:10 +1000

      Commit message:


	  
		
 update files
 

    

  
    

      Package: sccomp

      Commit: e4930664ae33878b7f938c16a10d7920a4b5bb53

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-15 11:28:02 +1000

      Commit message:


	  
		
 update scripts
 

    

  
    

      Package: sccomp

      Commit: 2bd208c2c7420e71218c2f0dc37609adf2613b39

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-14 18:10:12 +1000

      Commit message:


	  
		
 update scripts
 

    

  
    

      Package: sccomp

      Commit: a3158af03976ee024052a56ace2d5c88a7ce147f

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-14 01:13:52 +1000

      Commit message:


	  
		
 update decription
 

    

  
    

      Package: sccomp

      Commit: 6956d3d517b5ff507ab212a9d0155d86f2ca8934

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-13 19:38:22 +1000

      Commit message:


	  
		
 pull

Merge branch 'cmdstanr' of github.com:stemangiola/sccomp into cmdstanr

Conflicts:
	.gitignore
	DESCRIPTION
	R/functions_multi_beta_binomial.R
	R/methods.R
	R/utilities.R
	inst/stan/glm_multi_beta_binomial.stan
	man/sccomp_glm.Rd
 

    

  
    

      Package: sccomp

      Commit: e00675aedf7cd092eb19ba56c167cbacc16f4827

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-07 16:09:58 +0930

      Commit message:


	  
		
 make variable dynamic
 

    

  
    

      Package: sccomp

      Commit: d24bc9801aa4cf66e76ddedce74da4976b2cb1f0

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-06 21:40:10 +0930

      Commit message:


	  
		
 add man
 

    

  
    

      Package: sccomp

      Commit: b787beac63925942b71e4e13521eed982f229023

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-06 17:37:00 +0930

      Commit message:


	  
		
 Update vignette and README
 

    

  
    

      Package: sccomp

      Commit: be933ec561c804b5ca0ae13985b10a49030c8ec4

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-06 14:56:21 +0930

      Commit message:


	  
		
 add function
 

    

  
    

      Package: sccomp

      Commit: 85f2e2c041efbe0327de7d74775069ef9c701e85

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-05 18:12:39 +0930

      Commit message:


	  
		
 add parallelisation
 

    

  
    

      Package: sccomp

      Commit: 510b04add1e6d3aa6fe01e2e95a3e95c552aeab1

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-05 17:52:03 +0930

      Commit message:


	  
		
 fix pathfinder
 

    

  
    

      Package: sccomp

      Commit: f77c9cd14fe69ff0cc8f62902904aedbe615f3c9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-05 16:43:31 +0930

      Commit message:


	  
		
 tweak pathfinder
 

    

  
    

      Package: sccomp

      Commit: effd4910dbfd4956862a39ce714dc25a51057027

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-06-03 13:08:34 +0930

      Commit message:


	  
		
 fix number of draws
 

    

  
    

      Package: sccomp

      Commit: 0018ea1759c29ef682dfc39d62158cdce57a0101

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-05-31 12:35:41 +0930

      Commit message:


	  
		
 modify inference method argument to include pathfinder as well
 

    

  
    

      Package: sccomp

      Commit: 8856924ee586f0a002209648844d879f15b3bedb

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-05-17 14:08:56 +1000

      Commit message:


	  
		
 update backend
 

    

  
    

      Package: sccomp

      Commit: 84cb1a029d01c310dc41c81e3e887ffad35d3f77

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-05-07 16:17:50 +1000

      Commit message:


	  
		
 change default threshold
 

    

  
    

      Package: sccomp

      Commit: f705eb9244056c18edb7a59f33f2c80d4a6ce42f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-05-06 10:39:49 +1000

      Commit message:


	  
		
 lower the logit threshold to test significance as we observed across studies that is much sensitive threshold
 

    

  
    

      Package: sccomp

      Commit: 5d9e1cdff5c4d289e6b1571a400b5dd078f2062d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-05-06 10:23:04 +1000

      Commit message:


	  
		
 adapt rng
 

    

  
    

      Package: sccomp

      Commit: 743cc4ce61e79344cd7dff9c77b6b0f0c79c0e6d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-04-29 13:20:56 +0930

      Commit message:


	  
		
 update with master

Merge branch 'master' into cmdstanr

# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	R/data.R
#	R/functions_multi_beta_binomial.R
#	R/methods.R
#	R/utilities.R
#	README.Rmd
#	README.md
#	inst/figures/unnamed-chunk-11-1.png
#	inst/figures/unnamed-chunk-12-1.png
#	inst/figures/unnamed-chunk-14-1.png
#	inst/figures/unnamed-chunk-15-1.png
#	inst/stan/glm_multi_beta_binomial.stan
#	inst/stan/glm_multi_beta_binomial_generate_date.stan
 

    

  
    

      Package: sccomp

      Commit: f5e59cda80479615ed3963b70675375370344b4f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-04-27 22:19:39 +0930

      Commit message:


	  
		
 fix iterative variational
 

    

  
    

      Package: sccomp

      Commit: 865924e49f674ef6f4b9faf39de13090913f12e7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-04-27 22:19:19 +0930

      Commit message:


	  
		
 update README and improve checks

Merge branch 'master' into proportions

# Conflicts:
#	README.md
#	inst/figures/unnamed-chunk-11-1.png
#	inst/figures/unnamed-chunk-12-1.png
#	inst/figures/unnamed-chunk-13-1.png
#	man/fragments/intro.Rmd
 

    

  
    

      Package: sccomp

      Commit: 2d296f42fde58cedbc53ad0d6871389fc232cd71

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-03-29 09:47:49 +1100

      Commit message:


	  
		
 update tests
 

    

  
    

      Package: sccomp

      Commit: ce0d13d00ea6aa9155345993b7a64096c9aa7943

      Author:  Mangiola Laboratory <mangiolastefano@gmail.com> 

      Date: 2024-03-27 00:36:40 +1100

      Commit message:


	  
		
 Merge pull request #128 from stemangiola/master_for_merge

rebase master 

    

  
    

      Package: sccomp

      Commit: 7083bf079b561a0377d6bcff6b2daf0a5ab75b58

      Author:  Mangiola Laboratory <mangiolastefano@gmail.com> 

      Date: 2024-03-27 00:36:10 +1100

      Commit message:


	  
		
 Merge branch 'proportions' into master_for_merge 

    

  
    

      Package: sccomp

      Commit: 7d8d674655f3676a580d58562b3d2faa8addd084

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-03-14 17:28:17 +1030

      Commit message:


	  
		
 update script and README to proportions
 

    

  
    

      Package: sccomp

      Commit: 3278cd354d4a30a2a72b3b2461a6b471645737d7

      Author:  Mangiola Laboratory <mangiolastefano@gmail.com> 

      Date: 2024-03-14 13:32:04 +1030

      Commit message:


	  
		
 Merge pull request #125 from stemangiola/master_suitable_to_proportions

rebase 

    

  
    

      Package: sccomp

      Commit: f1e0128c126374a1b7935ac9f661a080ce4bfdd8

      Author:  Mangiola Laboratory <mangiolastefano@gmail.com> 

      Date: 2024-03-14 13:31:14 +1030

      Commit message:


	  
		
 Merge branch 'proportions' into master_suitable_to_proportions 

    

  
    

      Package: sccomp

      Commit: a207c229b61cf7721e2da665158a8bf52b47709c

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-03-14 13:56:46 +1100

      Commit message:


	  
		
 update model
 

    

  
    

      Package: sccomp

      Commit: 79cb50620d4d76a8d3d8c144aa30d21d04cb9d47

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-02-14 09:54:46 +1100

      Commit message:


	  
		
 fix typo
 

    

  
    

      Package: sccomp

      Commit: 4bd1c3fece9a86cccedb0bf3acccc99ff1addeb0

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-02-14 00:01:08 +1100

      Commit message:


	  
		
 fix bug
 

    

  
    

      Package: sccomp

      Commit: a268c5a4ee8fc18f8301251acbf69a157614571d

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2024-02-13 23:52:15 +1100

      Commit message:


	  
		
 fix sum to zero
 

    

  
    

      Package: sccomp

      Commit: 6e16a04885818381108ad8b680e73fe8120e0bd9

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-02-12 17:46:10 +1100

      Commit message:


	  
		
 change residuals to be calculated on the proportion scale, not the logit scale

and add residual method
 

    

  
    

      Package: sccomp

      Commit: faab8f8dae3baf4188968bd1884ec62c6230cc3a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2024-01-20 10:25:42 +1100

      Commit message:


	  
		
 start proportion version
 

    

  
    

      Package: sccomp

      Commit: 75949e11dbae473dd439d90800e6d7f6885f8623

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-08-12 09:45:43 +1000

      Commit message:


	  
		
 rebase

Merge branch 'master' into cmdstanr

Conflicts:
	.gitignore
	R/functions_multi_beta_binomial.R
	R/methods.R
	README.md
	inst/figures/unnamed-chunk-11-1.png
	inst/figures/unnamed-chunk-12-1.png
	inst/figures/unnamed-chunk-14-1.png
	inst/figures/unnamed-chunk-15-1.png
	inst/stan/glm_multi_beta_binomial.stan
 

    

  
    

      Package: sccomp

      Commit: 891ef1f0018a63edcbb3a4c813609d6c9dd7af56

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-08-12 09:45:43 +1000

      Commit message:


	  
		
 rebase

Merge branch 'master' into cmdstanr

Conflicts:
	.gitignore
	R/functions_multi_beta_binomial.R
	R/methods.R
	README.md
	inst/figures/unnamed-chunk-11-1.png
	inst/figures/unnamed-chunk-12-1.png
	inst/figures/unnamed-chunk-14-1.png
	inst/figures/unnamed-chunk-15-1.png
	inst/stan/glm_multi_beta_binomial.stan
 

    

  
    

      Package: sccomp

      Commit: 71dfe33ff4c2acab058acbed77e719f270b42a26

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-22 20:23:13 +1100

      Commit message:


	  
		
 fix if NA are present in generated quantities
 

    

  
    

      Package: sccomp

      Commit: 6b4abc3c5e899756b2f60dea894c2f23be5dbf25

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-22 20:23:13 +1100

      Commit message:


	  
		
 fix if NA are present in generated quantities
 

    

  
    

      Package: sccomp

      Commit: f0b4347f45437dd156ee1bf012b9c086e0a72169

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-11 00:02:17 +1100

      Commit message:


	  
		
 merge master

Merge branch 'master' into parallel-chains

Conflicts:
	DESCRIPTION
	R/utilities.R
 

    

  
    

      Package: sccomp

      Commit: 3945ff5c8df2e262aa29dc9ef62b506da8961df3

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-11 00:02:17 +1100

      Commit message:


	  
		
 merge master

Merge branch 'master' into parallel-chains

Conflicts:
	DESCRIPTION
	R/utilities.R
 

    

  
    

      Package: sccomp

      Commit: c9ac0b4cac846b3b536f9ceb794c549ce0ca70c4

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 23:59:33 +1100

      Commit message:


	  
		
 Merge branch 'parallel-chains' of github.com:stemangiola/sccomp into parallel-chains
 

    

  
    

      Package: sccomp

      Commit: e842c94bc88432763f2f28aa7317243509e28b18

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 20:37:30 +1100

      Commit message:


	  
		
 make algorithm more stable
 

    

  
    

      Package: sccomp

      Commit: 294e9136c8446f3b9490ffaee840c97fd8083351

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 20:37:30 +1100

      Commit message:


	  
		
 make algorithm more stable
 

    

  
    

      Package: sccomp

      Commit: daf46513def6aff06482315bdc8ca5b856df8f5a

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 02:47:01 +1100

      Commit message:


	  
		
 fix description
 

    

  
    

      Package: sccomp

      Commit: 3d06066eaa2a89603b3320b7edfcb15c993082bb

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 02:47:01 +1100

      Commit message:


	  
		
 fix description
 

    

  
    

      Package: sccomp

      Commit: b2d35bf6cb7cf345e1d907112e4476768b9e2dd5

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 01:08:19 +1100

      Commit message:


	  
		
 fix and update README
 

    

  
    

      Package: sccomp

      Commit: 36c54a8702fae522e5f8e2dccc62cba974a40fdf

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-10 01:08:19 +1100

      Commit message:


	  
		
 fix and update README
 

    

  
    

      Package: sccomp

      Commit: 167140c1091b6a43de1e28e2b83378939c92e47b

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 21:46:54 +1100

      Commit message:


	  
		
 update git ignore
 

    

  
    

      Package: sccomp

      Commit: c7be6ba2d619473429571c47936d0a8d8b737da8

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 21:46:54 +1100

      Commit message:


	  
		
 update git ignore
 

    

  
    

      Package: sccomp

      Commit: 74fb425c39480e0636b40ea525ecbeb2bf9b5156

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 21:46:23 +1100

      Commit message:


	  
		
 merge master

Merge branch 'master' into parallel-chains

Conflicts:
	R/utilities.R
	README.md
	inst/figures/unnamed-chunk-10-1.png
	inst/figures/unnamed-chunk-11-1.png
	inst/figures/unnamed-chunk-12-1.png
	inst/figures/unnamed-chunk-14-1.png
	inst/figures/unnamed-chunk-15-1.png
 

    

  
    

      Package: sccomp

      Commit: bb3c64f1a3a05e1e6f375b768f606ee9e9404d18

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 21:46:23 +1100

      Commit message:


	  
		
 merge master

Merge branch 'master' into parallel-chains

Conflicts:
	R/utilities.R
	README.md
	inst/figures/unnamed-chunk-10-1.png
	inst/figures/unnamed-chunk-11-1.png
	inst/figures/unnamed-chunk-12-1.png
	inst/figures/unnamed-chunk-14-1.png
	inst/figures/unnamed-chunk-15-1.png
 

    

  
    

      Package: sccomp

      Commit: a18242c21db003597057c1dd64b01a0ef13cbc8d

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 04:54:55 +1100

      Commit message:


	  
		
 save fit into local path for cmdstanr
 

    

  
    

      Package: sccomp

      Commit: 9dbecd970797a87d6ec87d4dddbd37b7086dfe0c

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 04:54:55 +1100

      Commit message:


	  
		
 save fit into local path for cmdstanr
 

    

  
    

      Package: sccomp

      Commit: af10595df9091427e4f37ff6a00f0f6c3024bb27

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 00:13:40 +1100

      Commit message:


	  
		
 fix bug
 

    

  
    

      Package: sccomp

      Commit: bb207668b00a9341259a759bb58f5c7514248d92

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-09 00:13:40 +1100

      Commit message:


	  
		
 fix bug
 

    

  
    

      Package: sccomp

      Commit: 2a4b1ad2718a8b7b981bf1b4ea4c0ae1a84a096c

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-08 21:38:43 +1100

      Commit message:


	  
		
 update scripts for fixes
 

    

  
    

      Package: sccomp

      Commit: 15925a736c8bb4dcb0c37965815f28835872b4d2

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-08 21:38:43 +1100

      Commit message:


	  
		
 update scripts for fixes
 

    

  
    

      Package: sccomp

      Commit: 83eb72845aebe8453de797d77e14126942c92952

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-07 02:21:00 +1100

      Commit message:


	  
		
 merge master

Merge branch 'master' into parallel-chains

Conflicts:
	R/utilities.R
	inst/stan/glm_multi_beta_binomial.stan
 

    

  
    

      Package: sccomp

      Commit: 49080e7cfbe104a073f066b6ee7823cd29d844cb

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-07 02:21:00 +1100

      Commit message:


	  
		
 merge master

Merge branch 'master' into parallel-chains

Conflicts:
	R/utilities.R
	inst/stan/glm_multi_beta_binomial.stan
 

    

  
    

      Package: sccomp

      Commit: 3fafeab2aea7ce4782c64e22e83d8a2876eb2d72

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 09:42:40 +1100

      Commit message:


	  
		
 edit model very inefficient
 

    

  
    

      Package: sccomp

      Commit: 017666095a8154e277164caa507cdea8bc06f556

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 09:42:40 +1100

      Commit message:


	  
		
 edit model very inefficient
 

    

  
    

      Package: sccomp

      Commit: 22bc4c3debeee25c5291137ab2805582a8683d41

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 08:42:41 +1100

      Commit message:


	  
		
 fix model
 

    

  
    

      Package: sccomp

      Commit: 0da9b1b120a50372b164fed810d2dccb93c7b818

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 08:42:41 +1100

      Commit message:


	  
		
 fix model
 

    

  
    

      Package: sccomp

      Commit: 84f30b1f61d3b3c3a085940c6ae37b5f9b79b320

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 07:35:02 +1100

      Commit message:


	  
		
 update script, now it does not work
 

    

  
    

      Package: sccomp

      Commit: b7c679ddffb03e45e500717b4e3b8c5415431342

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 07:35:02 +1100

      Commit message:


	  
		
 update script, now it does not work
 

    

  
    

      Package: sccomp

      Commit: 78f700ba3d8f32fcb19477bf25ca5e82b790eba7

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 07:05:15 +1100

      Commit message:


	  
		
 update model

Merge branch 'master' into parallel-chains

Conflicts:
	inst/stan/glm_multi_beta_binomial.stan
 

    

  
    

      Package: sccomp

      Commit: c40e9c4dfa4a5f3c91cf9db1199860721468452e

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 07:05:15 +1100

      Commit message:


	  
		
 update model

Merge branch 'master' into parallel-chains

Conflicts:
	inst/stan/glm_multi_beta_binomial.stan
 

    

  
    

      Package: sccomp

      Commit: 0e562ec5c434b8bde4ec155f2c2bc9a17b24af1b

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 01:57:33 +1100

      Commit message:


	  
		
 first attempt parallelisation
 

    

  
    

      Package: sccomp

      Commit: 1cf99c6326dca76cd58ca31937bfc082efdc2c81

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 01:57:33 +1100

      Commit message:


	  
		
 first attempt parallelisation
 

    

  
    

      Package: sccomp

      Commit: db1d004b5a74903cf9b266b28f9aa59cf3a7ed58

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 01:34:43 +1100

      Commit message:


	  
		
 rstan 2.26
 

    

  
    

      Package: sccomp

      Commit: cef2220cedeaff6bfe1844739d0a0c626134bd61

      Author:  stemangiola <mangiolastefano@gmail.com> 

      Date: 2022-02-05 01:34:43 +1100

      Commit message:


	  
		
 rstan 2.26
 

    

  
    

      Package: ClustIRR

      Commit: a63df4dd5a2327ba8928f1065269caa641216a9e

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2024-10-12 00:29:39 +0200

      Commit message:


	  
		
 bugfixes, renaming, fixing unused code and params
 

    

  
    

      Package: ClustIRR

      Commit: 8788901d91fb021b8ebd180315c25af62b76314c

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2024-10-12 00:23:38 +0200

      Commit message:


	  
		
 bugfixes, renaming, fixing unused code and params
 

    

  
    

      Package: lefser

      Commit: 5630d8fc2381d4803562b34b07519781ed9b6106

      Author:  Sehyun Oh <shbrief@hotmail.com> 

      Date: 2024-10-11 18:05:09 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: lefser

      Commit: 83819712d8b8f052c091ba39865aa949fb3345bd

      Author:  Sehyun Oh <shbrief@hotmail.com> 

      Date: 2024-10-11 18:04:46 -0400

      Commit message:


	  
		
 fix the errors in the examples
 

    

  
    

      Package: lefser

      Commit: 5152e999dbebf6ea8d6ba13abc113a48d80fe922

      Author:  Sehyun Oh <shbrief@hotmail.com> 

      Date: 2024-10-09 12:46:21 -0400

      Commit message:


	  
		
 correct wrong reference
 

    

  
    

      Package: visiumStitched

      Commit: 7792530a9a6e86d65e284e90f8f3bf8272aa4f69

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-03 10:16:47 -0400

      Commit message:


	  
		
 Add missing package name to function calls in an example
 

    

  
    

      Package: visiumStitched

      Commit: fc6c65b38daffbf45627f8c0e5a35cd95ebabc2a

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-02 14:01:14 -0400

      Commit message:


	  
		
 Add missing dependency
 

    

  
    

      Package: visiumStitched

      Commit: d3405df233cd405bc57971fe7e6ef74cf12a31d7

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-02 08:48:35 -0400

      Commit message:


	  
		
 Resolve a NOTE about missing function definition
 

    

  
    

      Package: visiumStitched

      Commit: 50ac8fa2369fc53e7e76d51c03286a4514fba681

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-02 08:46:38 -0400

      Commit message:


	  
		
 Resolve a NOTE about undefined variables
 

    

  
    

      Package: visiumStitched

      Commit: 080f0d32ea8981f2a5cabf4cb1735c17ef9b0589

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-02 08:44:13 -0400

      Commit message:


	  
		
 Prepend package names to functions in examples to fix an error
 

    

  
    

      Package: visiumStitched

      Commit: 0a4676ef4f4fd4cc0018e1ce04aaf2f5ea3f89f7

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-01 16:20:05 -0400

      Commit message:


	  
		
 Fix a test
 

    

  
    

      Package: visiumStitched

      Commit: 706c9b6f73859aaf60bdec4721da18674d9dffd9

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-10-01 15:39:34 -0400

      Commit message:


	  
		
 Eliminate warnings by more carefully creating an example object
 

    

  
    

      Package: visiumStitched

      Commit: 82f1ebc70633a0303bc08107fe1cb80170bbcc12

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-30 16:42:33 -0400

      Commit message:


	  
		
 Add a section in the vignette to explain the purpose of the merge_overlapping() function
 

    

  
    

      Package: visiumStitched

      Commit: 9e67f9388d8992deca3bc9e418716c166e97d286

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-30 15:52:53 -0400

      Commit message:


	  
		
 Add a couple tests for merge_overlapping()
 

    

  
    

      Package: visiumStitched

      Commit: 034aee1ef72a62cc98a51f3c14edf1249db767f9

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-30 15:06:29 -0400

      Commit message:


	  
		
 Add missing dependencies
 

    

  
    

      Package: visiumStitched

      Commit: 5137c84b66f789e57fc769e5f7681b2c3f067ebb

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-30 15:05:08 -0400

      Commit message:


	  
		
 Add an example
 

    

  
    

      Package: visiumStitched

      Commit: 4cd9059e4a155a64bcb6e47559eae6f3ae9d466c

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-30 12:43:50 -0400

      Commit message:


	  
		
 Add comments, improve variable names, and complete the function
 

    

  
    

      Package: visiumStitched

      Commit: 2b105f927780e550fb3772bf23dd7b0e201082f6

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-30 12:29:08 -0400

      Commit message:


	  
		
 Add much of the code for a new function to merge expression of overlapping spots
 

    

  
    

      Package: visiumStitched

      Commit: 93844e8527663fcf3c4ce70d11fa606903256551

      Author:  Nick-Eagles <nick.eagles@libd.org> 

      Date: 2024-09-10 15:03:24 -0400

      Commit message:


	  
		
 Add a section explaining and exploring error metrics when computing array coordinates
 

    

  
    

      Package: DeconvoBuddies

      Commit: eca461aca3c0023bb8499284c5bb7c9867b248c0

      Author:  Louise Huuki <lahuuki@gmail.com> 

      Date: 2024-10-11 13:45:56 -0400

      Commit message:


	  
		
 Bump Version to 0.99.1
 

    

  
    

      Package: DeconvoBuddies

      Commit: 0d8ea7dd50069b7873e23d86c4a267aec32cb7d4

      Author:  Leonardo Collado-Torres <lcolladotor@gmail.com> 

      Date: 2024-10-11 13:14:05 -0400

      Commit message:


	  
		
 Use release version of pkgdown 

    

  
    

      Package: DeconvoBuddies

      Commit: a21a4344c89e10f98c3966a3df22f23051469b6b

      Author:  Louise Huuki <lahuuki@gmail.com> 

      Date: 2024-10-10 14:34:30 -0400

      Commit message:


	  
		
 Merge updates by Leo

Merge branch 'devel' of github.com:LieberInstitute/DeconvoBuddies into devel

# Conflicts:
#	README.md
 

    

  
    

      Package: DeconvoBuddies

      Commit: 6ae3da136a6ffb1a3e9bd003c24473ea51aa174e

      Author:  Louise Huuki <lahuuki@gmail.com> 

      Date: 2024-10-10 14:14:20 -0400

      Commit message:


	  
		
 Add BioC note to README
 

    

  
    

      Package: BatchQC

      Commit: 4b8f224a1e11db79ff830d9fb0e7e0b3fcaeefeb

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-10-11 13:30:14 -0400

      Commit message:


	  
		
 Update version and date
 

    

  
    

      Package: BatchQC

      Commit: 33ae88a7eba73f642ebff4375f3b3638b6147c7e

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-10-11 12:56:46 -0400

      Commit message:


	  
		
 Merge pull request #101 from jessmcc22/devel

Option to select multiple variables to include in nb analysis 

    

  
    

      Package: BatchQC

      Commit: 36b882219c9d69314406de2574374cde9991cfb7

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-10-11 12:55:48 -0400

      Commit message:


	  
		
 Updated example to have coldata as factors
 

    

  
    

      Package: BatchQC

      Commit: a40966920f750fd8a06ba4ffbfb227d5ed449afb

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-10-09 16:31:46 -0400

      Commit message:


	  
		
 Corrected error where only first other varaible was used in the DESeq analysis
 

    

  
    

      Package: BatchQC

      Commit: c296ec68cfa9308e7c23c59ce69db4f4497230f5

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-10-08 17:04:51 -0400

      Commit message:


	  
		
 Updated nb check to be more dynamic and accept multiple other variables. Currently only works with the first provided variable
 

    

  
    

      Package: BatchQC

      Commit: 6e09b615b4ab29fef35e7e68b5cbc278ca6fb05c

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-10-03 09:54:58 -0400

      Commit message:


	  
		
 Merge pull request #100 from jessmcc22/devel

Added DeSeq2 Negative Binomial check for more than 20 samples 

    

  
    

      Package: BatchQC

      Commit: a0300ce10bd6248253e1acbad5b866c7715134bb

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-09-20 09:35:31 -0400

      Commit message:


	  
		
 Updated threshold to be 1/1000th for large datasets, it is now only optional for small data sets; updated recommendation language
 

    

  
    

      Package: BatchQC

      Commit: 8e07c13d29eb810e9b866b77f3c7b18cef875707

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-09-18 16:28:18 -0400

      Commit message:


	  
		
 Added "advanced features" check box
 

    

  
    

      Package: BatchQC

      Commit: 7d43ac380156c13432f4ec8cfabb6e8e00dc5779

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-09-16 17:02:51 -0400

      Commit message:


	  
		
 remove na row before analysis; add a numeric input to select number of genes to use when down sampling
 

    

  
    

      Package: BatchQC

      Commit: 710613cedff4e82789e79d0699c343bbf8d19670

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-09-13 16:08:03 -0400

      Commit message:


	  
		
 Update recommendations to be based only on condition variables and to count variables only once.
 

    

  
    

      Package: BatchQC

      Commit: 599d0e6e3e426067c310b324461f6767428a8d1d

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-09-11 16:46:55 -0400

      Commit message:


	  
		
 Update negative binomial test to include a test for more than 20 samples
 

    

  
    

      Package: BatchQC

      Commit: a1b9a89059640128cf56bb41824cca9e51f7bdf1

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-08-09 12:52:30 -0400

      Commit message:


	  
		
 Remove type 2 langauge from variation analysis
 

    

  
    

      Package: BatchQC

      Commit: f742601d584096bf81614223bbafe862648b83f7

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-07-29 16:33:24 -0400

      Commit message:


	  
		
 Merge pull request #98 from jessmcc22/devel

Update DESeq2 nb check to only allow datasets with 20 or fewer samples 

    

  
    

      Package: BatchQC

      Commit: e74f9540dffd8d00e71f373caa5d1a9dcc316b88

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-07-29 16:32:51 -0400

      Commit message:


	  
		
 Merge branch 'wejlab:devel' into devel
 

    

  
    

      Package: BatchQC

      Commit: e7c374b3be6fe7167668f86e8c6396f990d1b489

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-29 16:31:37 -0400

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 

    

  
    

      Package: BatchQC

      Commit: 6eea5ced2b2089f2aac84228e3fd29b4aa44b991

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-29 16:31:29 -0400

      Commit message:


	  
		
 Added warning message if using the DESeq nb check when the sample size is greater than 20
 

    

  
    

      Package: BatchQC

      Commit: fef2c37f526b04fbe1bf437a298494b2d08f4b36

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-07-24 15:51:11 -0400

      Commit message:


	  
		
 Merge pull request #97 from jessmcc22/devel

Added bladderbatch warning message if not installed 

    

  
    

      Package: BatchQC

      Commit: 54e8db814b5ab484f600ca739277b1d4cdbbb1a9

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-07-24 15:50:31 -0400

      Commit message:


	  
		
 Merge branch 'wejlab:devel' into devel
 

    

  
    

      Package: BatchQC

      Commit: df1b774906866e269857147de2311d7f2e1cb648

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-24 15:28:15 -0400

      Commit message:


	  
		
 Add warning message to bladderbatch data set when bladderbatch is not installed
 

    

  
    

      Package: BatchQC

      Commit: 71c1d18c30a2c1c796a36b8b0e334bdd0aeece6c

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-24 15:27:47 -0400

      Commit message:


	  
		
 Correct spacing
 

    

  
    

      Package: BatchQC

      Commit: 705c4871600773ee685028da31a033c40109b8f0

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-24 12:58:26 -0400

      Commit message:


	  
		
 Converted proportion to a percentage; added a space to the sentence
 

    

  
    

      Package: BatchQC

      Commit: a833656d8acb9b9157ab59774b67d1f71f2984a4

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-24 12:57:10 -0400

      Commit message:


	  
		
 Update R dependency
 

    

  
    

      Package: BatchQC

      Commit: 1ed3318e958668c2e764d534526508d3a935cf10

      Author:  Jessica <102758461+jessmcc22@users.noreply.github.com> 

      Date: 2024-07-16 16:48:48 -0400

      Commit message:


	  
		
 Merge pull request #96 from jessmcc22/devel

Added NB check; added some user error messages; Updated Variationi Ratios to convert data to factors 

    

  
    

      Package: BatchQC

      Commit: 8c4f9f694ab8e7993ed1c2b7918ef41836bb4dab

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-16 15:00:31 -0400

      Commit message:


	  
		
 Updated De_analyze to provide a user error messafe when non-integer or negative values are provided to DESeq2
 

    

  
    

      Package: BatchQC

      Commit: ae618c191f747ba26594eda07578617601793a3b

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-07-12 15:21:04 -0400

      Commit message:


	  
		
 Convert variables into factors to run variation analysis
 

    

  
    

      Package: BatchQC

      Commit: 4088bcdc1991be8219c6277cfeea6d6797059b8d

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-28 14:29:05 -0400

      Commit message:


	  
		
 Spacing for lint free; added bladderbatch installation instructions to the bladderbatch example vignette
 

    

  
    

      Package: BatchQC

      Commit: f3f75eaa21fcf28d6fbc0335a9c4b6948dfacef7

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-26 16:23:20 -0400

      Commit message:


	  
		
 Added function to provide information on the proportion of features above a threshold to determine if DESeq2 is an appropriate analysis tool
 

    

  
    

      Package: BatchQC

      Commit: 1e1758049542bcaa5756796fc11873e4e6978f49

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-25 17:49:19 -0400

      Commit message:


	  
		
 Added histograms to the nb_test
 

    

  
    

      Package: BatchQC

      Commit: 66dc9cff673f6b8e627171deaa4426a0e6be0a68

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-21 17:45:27 -0400

      Commit message:


	  
		
 Removed examlpe since it is an internal function; fixed lintr errors
 

    

  
    

      Package: BatchQC

      Commit: c6703514ab0e94b701ae320a919ba8a66c441f97

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-21 16:06:42 -0400

      Commit message:


	  
		
 Corrected spelling error "ID" to "Id"; added rendertable details when calling nb function
 

    

  
    

      Package: BatchQC

      Commit: 5e7d422026d44654ee3be32d52cd879e8329b51c

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-21 16:05:42 -0400

      Commit message:


	  
		
 Update the input to include the se object and to call the actual values within the function to mirror other functions
 

    

  
    

      Package: BatchQC

      Commit: 05e947233c95c02cc53a846796303d2966032468

      Author:  jessmcc22Mac <jessmcc@bu.edu> 

      Date: 2024-06-20 15:34:28 -0400

      Commit message:


	  
		
 Added negative binomial check
 

    

  
  


</div>

</div>