Decomposing the gut community of hybrid house mice identifies host genetics and spatial effects
R/1_filtering.R --> quality filtering ASVs per amplicon and merging. Removing ASVs with less than 0.005% abundance and removing samples with less than 100 reads Removing taxonomic handlers from silva (e.g. g__; s__). Total sum scaling per amplicon (relative abundances) Merge into one phyloseq object. Relable and merge Eimeria spp. as in Ferreira et al. 2023, resulting in 3 combined ASVs (cASVs) for E. ferrisi, E. falciformis and E. vermiformis Small adjustments to metadata. Correlation co-occurrence networks for all known parasite genera. Is network modular? Only Oxyurida. We do phylogenetic analysis as done for Eimeria in Ferreira et al. 2023. Readjust genera names Merge ASVs into cASV that are likely from the same taxa: Co-occurrence networks with only positive edges of ASV abundace per genus. Merge ASVs that cluster together.
final phyloseq object for further analysis is "tmp/PS.TSS_filtered.rds"
R/2_dyadicMCMC_full.R --> prepare dyadic data and do distance-based model for all the taxa (full model) with brms. model checks plotting figure 1
R/3_dyadicMCMC_groups.R --> prepare data and do distance based model for parasites, plants, fungi and bacteria plotting figure 2 and 3 and 4ab
R/4_Networl.R Co-occurrence network of Fungi, Parasites and Bacteria