Solve conflicts

.github/workflows/biocbook.yml

@@ -123,13 +123,13 @@ jobs:
           clean: false
 
       - name: 💾 Upload package bundle artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: bundle
           path: ${{ env.bundle_path }}
 
       - name: 💾 Upload book artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: book
-          path: ${{ env.book_path }}
+          path: ${{ env.book_path }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OMA
 Title: Orchestrating Microbiome Analysis with Bioconductor
-Version: 0.98.32
-Date: 2024-11-26
+Version: 0.98.35
+Date: 2025-02-05
 Authors@R:
     c(
   person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0002-8563-8884")),
@@ -56,11 +56,12 @@ Suggests:
     glue,
     grid,
     gsEasy,
+    gt,
     gtools,
     igraph,
     IntegratedLearner,
     knitr,
-    Maaslin2,
+    maaslin3,
     mia,
     miaTime,
     miaViz,
@@ -102,9 +103,11 @@ Suggests:
     WGCNA,
     xgboost
 Remotes:
+    github::biobakery/maaslin3,
     github::microbiome/mia,
     github::microbiome/miaViz,
     github::microbiome/miaTime,
+    github::joey711/phyloseq,
     github::stefpeschel/NetCoMi,
     github::zdk123/SpiecEasi,
     github::GraceYoon/SPRING,

inst/assets/bibliography.bib

@@ -1,3 +1,66 @@
+@article{Hill1973,
+  title = {{Diversity and Evenness: A Unifying Notation and Its Consequences}},
+  volume = {54},
+  ISSN = {1939-9170},
+  url = {http://dx.doi.org/10.2307/1934352},
+  DOI = {10.2307/1934352},
+  number = {2},
+  journal = {{Ecology}},
+  publisher = {Wiley},
+  author = {Hill,  M. O.},
+  year = {1973},
+  month = mar,
+  pages = {427–432}
+}
+
+@article{Ma2019,
+  title = {Diversity-disease relationships and shared species analyses for human microbiome-associated diseases},
+  volume = {13},
+  ISSN = {1751-7370},
+  url = {http://dx.doi.org/10.1038/s41396-019-0395-y},
+  DOI = {10.1038/s41396-019-0395-y},
+  number = {8},
+  journal = {{The ISME Journal}},
+  publisher = {Oxford University Press (OUP)},
+  author = {Ma,  Zhanshan (Sam) and Li,  Lianwei and Gotelli,  Nicholas J},
+  year = {2019},
+  month = {mar},
+  pages = {1911–1919}
+}
+
+@article{Valles-Colomer2019GBMs,
+   author = {Valles-Colomer, Mireia and Falony, Gwen and Darzi, Youssef and Tigchelaar, Ettje F. and Wang, Jun and Tito, Raul Y. and Schiweck, Carmen and Kurilshikov, Alexander and Joossens, Marie and Wijmenga, Cisca and Claes, Stephan and Van Oudenhove, Lukas and Zhernakova, Alexandra and Vieira-Silva, Sara and Raes, Jeroen},
+   title = {The neuroactive potential of the human gut microbiota in quality of life and depression},
+   journal = {{Nature Microbiology}},
+   ISSN = {2058-5276},
+   DOI = {10.1038/s41564-018-0337-x},
+   url = {https://doi.org/10.1038/s41564-018-0337-x},
+   year = {2019},
+   type = {Journal Article}
+}
+
+@article{vandeputte2017quantitative,
+  title={Quantitative microbiome profiling links gut community variation to microbial load},
+  author={Vandeputte, Doris and Kathagen, Gunter and D’hoe, Kevin and Vieira-Silva, Sara and Valles-Colomer, Mireia and Sabino, Jo{\~a}o and Wang, Jun and Tito, Raul Y and De Commer, Lindsey and Darzi, Youssef and Vermeire, Séverine and Falony, Gwen and Raes, Jeroen},
+  journal={{Nature}},
+  volume={551},
+  number={7681},
+  pages={507--511},
+  year={2017},
+  publisher={{Nature Publishing Group UK London}}
+}
+
+@article{bastiaanssen2023bugs1,
+  title={Bugs as features (part 1): concepts and foundations for the compositional data analysis of the microbiome--gut--brain axis},
+  author={Bastiaanssen, Thomaz FS and Quinn, Thomas P and Loughman, Amy},
+  journal={{Nature Mental Health}},
+  volume={1},
+  number={12},
+  pages={930--938},
+  doi = {10.1038/s44220-023-00148-3},
+  year={2023},
+  publisher={{Nature Publishing Group US New York}}
+}
 
 @Article{Xu2023,
   author =	 {Shuangbin Xu and Li Zhan and Wenli Tang and Qianwen Wang and Zehan Dai and Lang Zhou and Tingze Feng and Meijun Chen and Tianzhi Wu and Erqiang Hu and Guangchuang Yu},
@@ -55,7 +118,7 @@ @Article{Martino2019
   volume =	 4,
   issue =	 1,
   doi =		 {},
-  year =	 2019 
+  year =	 2019
 }
 
 @Article{Gloor2017,
@@ -462,7 +525,7 @@ @Article{Faith1992
     volume = {61},
     number = {1},
     pages = {10},
-    doi = {https://doi.org/10.1016/0006-3207(92)91201-3},
+    doi = {10.1016/0006-3207(92)91201-3},
     url = {https://www.sciencedirect.com/science/article/pii/0006320792912013?via%3Dihub},
     year =	 {1992}
 }
@@ -1279,7 +1342,7 @@ @Article{Calgaro2020
     journal = {Genome Biology},
     url = {https://doi.org/10.1186/s13059-020-02104-1}
 }
-  
+
 @Article{Calgaro2022,
     title = {benchdamic: benchmarking of differential abundance
 methods for microbiome data},
@@ -2192,13 +2255,13 @@ @article{Rajaram2010
 }
 
 @misc{pelto2024,
-      title={Elementary methods provide more replicable results in microbial differential abundance analysis}, 
+      title={Elementary methods provide more replicable results in microbial differential abundance analysis},
       author={Juho Pelto and Kari Auranen and Janne Kujala and Leo Lahti},
       year={2024},
       eprint={2404.02691},
       archivePrefix={arXiv},
       primaryClass={stat.AP},
-      url={https://arxiv.org/abs/2404.02691}, 
+      url={https://arxiv.org/abs/2404.02691},
 }
 
 @article{Rahman2023,
@@ -2360,4 +2423,27 @@ @article{Logan2014nutritional
   pages={1--16},
   year={2014},
   publisher={Springer}
-}
+}
+@article{Marchesi2015,
+  title = {The vocabulary of microbiome research: a proposal},
+  volume = {3},
+  ISSN = {2049-2618},
+  url = {http://dx.doi.org/10.1186/s40168-015-0094-5},
+  DOI = {10.1186/s40168-015-0094-5},
+  number = {1},
+  journal = {Microbiome},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Marchesi,  Julian R. and Ravel,  Jacques},
+  year = {2015},
+  month = jul 
+}
+
+@article{Nickols2024,
+  title = {MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery},
+  url = {http://dx.doi.org/10.1101/2024.12.13.628459},
+  DOI = {10.1101/2024.12.13.628459},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Nickols,  William A. and Kuntz,  Thomas and Shen,  Jiaxian and Maharjan,  Sagun and Mallick,  Himel and Franzosa,  Eric A. and Thompson,  Kelsey N. and Nearing,  Jacob T. and Huttenhower,  Curtis},
+  year = {2024},
+  month = dec
+}