Pre-specified Tests

Hypothesis tests where the null, method, and significance threshold were committed before results were seen. Outputs are frozen after first execution — re-run a single analysis with make stats-<target>, then make stats to rebuild the site.

Analysis	Makefile target
Alpha diversity (Kruskal–Wallis)	`make stats-diversity`
Beta diversity (PERMANOVA × taxonomic level)	`make stats-permanova`
Symptoms × fungal composition (Spearman + PERMANOVA)	`make stats-symptoms`
Nutrients × diversity by disease group (Spearman)	`make stats-nutrients`
Diet + mycobiome PCA / clustering	`make stats-pca`
Evidence-ranking matrix (validation priority)	`make stats-evidence`

Mycobiome-Diet Relationship Exploration

mycobiome

diet

pre-specified

Statistical figures covering relationships between key dietary and mycobiome markers.

Nutrients vs fungal diversity by disease group (Spearman)

pre-specified

alpha-diversity

diet

nutrients

Spearman correlations between dietary nutrients and alpha diversity, overall and stratified by study group (Active IBD, Quiescent, Non-IBD).

PCA and clustering on combined diet and mycobiome profiles

pre-specified

pca

clustering

diet

genus

Participant-level PCA of scaled nutrient intake and genus relative abundance, with hierarchical clustering to explore diet–mycobiome groupings.

Evidence-ranking matrix for disease-group findings

pre-specified

synthesis

validation

Ranks the strongest diet, mycobiome, and symptom differences across Study_group_new to prioritize candidates for future validation.

Symptom scores vs fungal composition (Spearman and PERMANOVA)

pre-specified

alpha-diversity

beta-diversity

genus

symptoms

Survey symptom scores (HBI and related items) tested against alpha diversity (Spearman) and genus beta diversity (PERMANOVA on Bray–Curtis).

PERMANOVA phylum beta diversity by study group

permanova

beta-diversity

phylum

pre-specified

Bray–Curtis dissimilarity on phylum relative abundance; study-group effect tested with permutational MANOVA.

PERMANOVA genus beta diversity by study group

permanova

beta-diversity

genus

pre-specified

Bray–Curtis dissimilarity on genus relative abundance; study-group effect tested with permutational MANOVA.

PERMANOVA species beta diversity by study group

permanova

beta-diversity

species

pre-specified

Bray–Curtis dissimilarity on species relative abundance; group effect tested with permutational MANOVA.

Kruskal–Wallis alpha diversity by study group and fibre restriction

alpha-diversity

pre-specified

Non-parametric comparison of Shannon, richness, and other alpha metrics across study group and fibre-restriction levels.

PERMANOVA family beta diversity by study group

permanova

beta-diversity

family

pre-specified

Bray–Curtis dissimilarity on family relative abundance; study-group effect tested with permutational MANOVA.