Changes in Version 1.14.3 (2025-07-29)
=====================================

* Porting the changes of devel version 1.15.3 to release

Changes in Version 1.15.3 (2025-07-29)
=====================================

* Minor changes related to warn_prevalence and small_random_effects parameters in DA_maaslin3

Changes in Version 1.14.2 (2025-04-24)
=====================================

* Porting the changes of devel version 1.15.2 to release

Changes in Version 1.15.2 (2025-04-24)
=====================================

* Bug-fix: add 'microbiome' among Imports due to an error in some systems

Changes in Version 1.14.1 (2025-04-22)
=====================================

* Porting the changes of devel version 1.15.1 to release

Changes in Version 1.15.1 (2025-04-22)
=====================================

* New method: maaslin3
* Re-added mixMC

Changes in Version 1.15.0 (2025-04-15)
=====================================

* Bump x.y.z version to odd y following creation of RELEASE_3_21 branch

Changes in Version 1.14.0 (2025-04-15)
=====================================

* Published in Bioconductor release 3.21

Changes in Version 1.12.1 (2024-11-20)
=====================================

* Porting the changes of devel version 1.13.1 to release

Changes in Version 1.13.1 (2024-11-20)
=====================================

* Bug-fix: changed an internal parameter of DA_ANCOM() to make it works after the new release

Changes in Version 1.13.0 (2024-10-29)
=====================================

* Bump x.y.z version to odd y following creation of RELEASE_3_20 branch

Changes in Version 1.12.0 (2024-10-29)
=====================================

* Published in Bioconductor release 3.20

Changes in Version 1.10.1 (2024-09-23)
=====================================

* Porting the changes of devel version 1.11.1 to release

Changes in Version 1.11.1 (2024-09-23)
=====================================

* Bug-fix: getDA() function now correctly orders results
* Modify Maaslin2 feature names to match the original names

Changes in Version 1.11.0 (2024-04-30)
=====================================

* Bump x.y.z version to odd y following creation of RELEASE_3_19 branch

Changes in Version 1.10.0 (2024-04-30)
=====================================

* Published in Bioconductor release 3.19

Changes in Version 1.9.4 (2024-03-07)
=====================================

* Re-added corncob (due to its previous removal from CRAN)
* Bug-fix: correct DA_Seurat() due to changes of Seurat::FindMarkers()
* Computed DA direction for ANCOM method

Changes in Version 1.8.1 (2023-11-04)
=====================================

* Porting the changes of devel version 1.9.1 to release

Changes in Version 1.9.1 (2023-11-04)
=====================================

* Temporarily removed corncob (due to its removal from CRAN)

Changes in Version 1.9.0 (2023-10-24)
=====================================

* Bump x.y.z version to odd y following creation of RELEASE_3_18 branch

Changes in Version 1.8.0 (2023-10-24)
=====================================

* Published in Bioconductor release 3.18

Changes in Version 1.7.5 (2023-10-13)
=====================================

* Updated DA_Seurat() for the new version
* Waiting for bug-fix: DA_ANCOM() (random effects not working)
* Waiting for bug-fix: DA_mixMC() (multilevel analysis not working)
* Bug-fix: correct dataset name in unit tests
* Bug-fix: in DA_ALDEx2() replaced unlist() with as.vector()
* Minor documentation updates related to dependencies

Changes in Version 1.6.4 (2023-07-22)
=====================================

* Porting the changes of devel version 1.7.4 to release

Changes in Version 1.7.4 (2023-07-22)
=====================================

* Reducing the number of comparisons in vignette to reduce build time

Changes in Version 1.6.3 (2023-07-11)
=====================================

* Porting the changes of devel version 1.7.3 to release

Changes in Version 1.7.3 (2023-07-11)
=====================================

* Bug-fix: Minor changes in vignette

Changes in Version 1.6.2 (2023-07-09)
=====================================

* Porting the changes of devel version 1.7.2 to release

Changes in Version 1.7.2 (2023-07-09)
=====================================

* Bug-fix for DA_Maaslin2() function

Changes in Version 1.6.1 (2023-07-08)
=====================================

* Porting the changes of devel version 1.7.1 to release

Changes in Version 1.7.1 (2023-07-07)
=====================================

* New methods: linDA, Maaslin2, ZicoSeq
* New method: mixMC (temporarily unavailable)
* Add 'alpha' parameter in DA_ANCOM()

Changes in Version 1.7.0 (2023-04-25)
=====================================

* Bump x.y.z version to odd y following creation of RELEASE_3_17 branch

Changes in Version 1.6.0 (2023-04-25)
=====================================

* Published in Bioconductor release 3.17

Changes in Version 1.5.3 (2023-04-20)
=====================================

* Add CITATION file
* Update README.md file
* Add ORCID for authors
* Bug-fix for DA_MAST() function

Changes in Version 1.5.2 (2022-11-21)
=====================================

* Correct FDR description in vignette
* Add BiocParallel support for runMocks() and runSplits() functions
* Add example for ANCOMBC based methods in parallel

Changes in Version 1.5.1 (2022-11-14)
=====================================

* Add FDR computation in Type I Error Control analysis
* Add BiocParallel support for runMocks() and runSplits() functions
* Update vignette

Changes in Version 1.5.0 (2022-11-01)
=====================================

* New devel version

Changes in Version 1.4.0 (2022-11-01)
=====================================

* New release version

Changes in Version 1.3.11 (2022-10-31)
=====================================

* Updated DA_ANCOM with the new ancombc2 method

Changes in Version 1.3.10 (2022-10-20)
=====================================

* Re-adapted p-values extraction from DA_ALDEx2() with test = "glm"

Changes in Version 1.3.9 (2022-09-18)
=====================================

* Re-added corncob after temporary removal in v1.3.5 

Changes in Version 1.3.8 (2022-09-18)
=====================================

* Bug-fix for table headers in chapter 3 of the vignette

Changes in Version 1.3.7 (2022-09-18)
=====================================

* Added more informations about the methods in chapter 3 of the vignette

Changes in Version 1.2.5 (2022-09-10)
=====================================

* Porting the changes of devel version 1.3.6 to release

Changes in Version 1.3.6 (2022-09-10)
=====================================

* Simplified the vignette 

Changes in Version 1.2.4 (2022-09-07)
=====================================

* Porting the changes of devel version 1.3.5 to release

Changes in Version 1.3.5 (2022-09-07)
=====================================

* Temporarily removed corncob. New version of detectseparation v0.3 broke it.
* Updated intro vignette accordingly. 

Changes in Version 1.2.3 (2022-09-07)
=====================================

* Porting the changes of devel version 1.3.4 to release

Changes in Version 1.3.4 (2022-09-07)
=====================================

* Updated intro vignette. 
* Removed HMP16SData chunks.
* Added conditional usage of kableExtra
* Removed dependency from HMP16SData and ffpe
* Implemented CAT function instead of using ffpe::CATplot

Changes in Version 1.2.2 (2022-09-06)
=====================================

* Porting the changes of devel version 1.3.3 to release

Changes in Version 1.3.3 (2022-09-06)
=====================================

* In DA_basic changed logFC calculation when paired = TRUE
* In intro vignette corrected the number of comparisons from 10 to 2

Changes in Version 1.2.1 (2022-09-03)
=====================================

* Porting the changes of devel version 1.3.2 to release

Changes in Version 1.3.2 (2022-09-03)
=====================================

* Changes after the first revision from the "Bioinformatics" journal
* Improved vignette with more descriptions, new methods, and more chapters
* Improved warning and error messages
* Support for TreeSummarizedExperiment object
* New function get_count_metadata() to access counts and metadata of a phyloseq or TreeSummarizedExperiment object.
* Added the "fitFeatureModel" implementation in DA_metagenomeSeq()
* "CSS" normalization factors are now returned as they are, not divided by a scaling factor
* Replaced "CSS_median" and "CSS_default" normalizations with "CSS"
* Added the "kw" and "glm" implementation in DA_ALDEx2()
* Added the "paired.test" option in DA_ALDEx2() for "t" and "wilcox" tests
* Added support for "CLR", "RC", and "none" normalization methods in DA_Seurat()
* Added support for "scale.factor" in DA_Seurat()
* Added more controls and verbosity regarding normalizations and DA methods
* Added the plotLogP() function for plottin the negative log p-values distribution
* Added DA_NOISeq(), DA_dearseq(), DA_ANCOM(), and DA_basic() to the pool of methods
* added detectseparation (<= 0.2.0) to the "Imports", new version 0.3 not compatible with corncob 0.2

Changes in Version 1.3.1 (2022-05-16)
=====================================

* Updated intro vignette
* Added more citations and authors
* Added figure captions and references

Changes in Version 1.3.0 (2022-04-26)
=====================================

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

Changes in Version 1.2.0 (2022-04-26)
=====================================

* Published in Bioconductor release 3.15

Changes in Version 1.1.1 (2022-03-21)
=====================================

* Corrected a bug in DA_ALDEx2 function
* Updated DA_ALDEx2 function manual
* Added more authors in the citation

Changes in Version 1.1.0 (2021-10-26)
=====================================

* Bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Changes in Version 1.0.0 (2021-10-26)
=====================================

* Published in Bioconductor release 3.14

Changes in Version 0.99.4 (2021-10-15)
=====================================

* Changed stats::coef to stats4::coef

Changes in Version 0.99.3 (2021-10-15)
=====================================

* Added the plotIt = FALSE option for plotRMSE function
* Added some more explanations into the "Goodness of Fit" chapter
* fitNB, fitZINB, fitHURDLE, fitZIG, and fitDM functions now work with both phyloseq object or count matrices

Changes in Version 0.99.2 (2021-10-11)
=====================================

* Changed dependency from R 4.0.0 to 4.1.0
* Added example for iterative_ordering() function
* Removed the usage of @ to access object's slot in the vignette
* Removed a suppressMessages() and a suppressWarnings() from createTIEC()
* Added verbosity to createTIEC() function
* Added NEWS file

Changes in Version 0.99.1 (2021-10-04)
=====================================

* Removed unnecessary files

Changes in Version 0.99.0 (2021-09-29)
=====================================

* Bumped version for submission to Bioconductor
* Added README.md file
