Links updated in DAA page (#855)

Co-authored-by: jepelt <jepelt@users.noreply.github.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi>

Author: jepelt

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OMA
 Title: Orchestrating Microbiome Analysis with Bioconductor
-Version: 1.1.0
-Date: 2026-04-20
+Version: 1.1.1
+Date: 2026-05-07
 Authors@R:
     c(
   person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", comment = c(ORCID = "0000-0002-8563-8884")),

inst/pages/differential_abundance.qmd

@@ -756,7 +756,9 @@ comparison, but it can also incorporate covariates (and interaction terms)
 
 As there does not currently exist a good implementation of ORM for
 DAA one must use a custom function. Such custom function with application
-examples is given in [@sec-extra_daa]. We also note that, in contrast to
+examples is given in
+[extra materials](https://microbiome.github.io/OMA-extras/docs/devel/pages/extra_daa.html#sec-orm).
+We also note that, in contrast to
 `Maaslin2()` function, the custom function provides confidence intervals and
 q-values (calculated for the variable of interest) automatically in its output.
 
@@ -770,7 +772,7 @@ statistical power, we recommend using a version of logistic regression
 introduced by @Firth1993. As there currently exists no convenient
 implementation of Firth logistic regression for DPA, one needs to use a custom
 function. Such custom function with application examples is given in the
-[@sec-extra_daa].
+[extra materials](https://microbiome.github.io/OMA-extras/docs/devel/pages/extra_daa.html#sec-firth).
 
 ::: {.callout-tip icon=false}
 
@@ -808,7 +810,8 @@ with interactions.
 of positive abundances with your data.
 
 10. Bonus 2: Try to run DAA and DPA with ordinal regression model and Firth 
-logistic regression with the custom functions provided in the extra materials.
+logistic regression with the custom functions provided in the
+[extra materials](https://microbiome.github.io/OMA-extras/docs/devel/pages/extra_daa.html#sec-orm).
 See how the results differ from the results obtained with `Maaslin2()` and
 `maaslin3()`.
 

oma_packages/oma_packages.csv

@@ -1,87 +1,44 @@
-ALDEx2
-ANCOMBC
 ape
-biclust
 BiocBook
 BiocManager
-BiocParallel
 BiocStyle
-Biostrings
 bluster
-caret
-circlize
-cluster
-cobiclust
 ComplexHeatmap
-corpcor
-cowplot
 curatedMetagenomicData
-dada2
 dendextend
-devtools
-DirichletMultinomial
 dplyr
 DT
 factoextra
-fido
-forcats
 ggdag
 ggExtra
 ggplot2
 ggpubr
 ggtree
-glmnet
 glue
-grid
-gsEasy
 gt
-gtools
-igraph
-IntegratedLearner
 knitr
-limma
-logistf
-Maaslin2
 maaslin3
 mediation
 mia
 miaTime
 miaViz
-microbiome
 microbiomeDataSets
-MicrobiomeStat
 mikropml
-MMUPHin
 MOFA2
-multiview
 NbClust
-NetCoMi
 NMF
 patchwork
 philr
 phyloseq
-plotly
-purrr
 qgraph
-RColorBrewer
 rebook
-reshape2
-reticulate
-rgl
-rms
 scales
 scater
 scuttle
 sechm
 sessioninfo
 shadowtext
-SpiecEasi
-SPRING
 stats
-stringr
-SuperLearner
 tidySingleCellExperiment
 tidyverse
 vegan
-WGCNA
-xgboost (== 1.7.7.1)