Files in biobakery/anpan
Quantifying Microbial Strain-Host Associations
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/clade_effects.R
R/filtering.R
R/genome_qc.R
R/imports.R
R/modelling.R
R/pglmm.R
R/pglmm_loo.R
R/pwy_ranef.R
R/read_in_data.R
R/visualization.R
R/zzz.R
README.Rmd
README.md
anpan.Rproj
inst/extdata/fake_metadata.tsv
inst/extdata/g__Madeuppy.s__Madeuppy_Fakerii.genefamilies.tsv.gz
inst/fsplit
inst/stan/.gitignore
inst/stan/base_ushoe.stan
inst/stan/bin_no_phylo_term.stan
inst/stan/bin_pglmm.stan
inst/stan/cont_no_phylo_term.stan
inst/stan/cont_pglmm.stan
inst/stan/cont_pglmm_noise_reg.stan
inst/stan/gaussian_ushoe.stan
inst/stan/logistic_ushoe.stan
inst/stan/pwy_ranef.stan
man/anpan.Rd
man/anpan_batch.Rd
man/anpan_pglmm.Rd
man/anpan_pglmm_batch.Rd
man/anpan_pwy_ranef.Rd
man/anpan_pwy_ranef_batch.Rd
man/anpan_repeated_measures.Rd
man/anpan_subjectwise_pglmm.Rd
man/anpan_vignette.Rd
man/compute_clade_effects.Rd
man/figures/1_overview.png
man/figures/logo.png
man/figures/logo.svgz
man/figures/logo_hi.png
man/filter_batch.Rd
man/filter_gf.Rd
man/get_cor_mat.Rd
man/get_genome_intersect_counts.Rd
man/olap_tree_and_meta.Rd
man/plot_cor_mat.Rd
man/plot_elpd_diff.Rd
man/plot_genome_intersection_histograms.Rd
man/plot_genome_intersections.Rd
man/plot_half_cor_mat.Rd
man/plot_lines.Rd
man/plot_outcome_tree.Rd
man/plot_p_value_histogram.Rd
man/plot_pwy_ranef.Rd
man/plot_pwy_ranef_intervals.Rd
man/plot_results.Rd
man/plot_tree_with_post.Rd
man/plot_tree_with_post_pred.Rd
man/read_and_filter.Rd
man/read_bug.Rd
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/test-pglmm.R
tests/testthat/test-pwy.R
vignettes/.gitignore
vignettes/anpan_tutorial.Rmd
vignettes/anpan_vignette_refs.bib
vignettes/leaf_pairs.PNG
vignettes/vignette_figs/cmat.png
vignettes/vignette_figs/fprau_ints.png
vignettes/vignette_figs/g__Madeuppy.s__Madeuppy_Fakerii_kmeans.png
vignettes/vignette_figs/g__Madeuppy.s__Madeuppy_Fakerii_labelled_lines.png
vignettes/vignette_figs/lines.png
vignettes/vignette_figs/pglmm_objects.RData
vignettes/vignette_figs/post.png
vignettes/vignette_figs/post_pred.png
vignettes/vignette_figs/scatter.png
vignettes/vignette_figs/tree1.png
vignettes/vignette_figs/tree2.png
vignettes/vignette_figs/tree_hcm.png
vignettes/wiki_figs/1_overview.png
vignettes/wiki_figs/advanced_pglmm_tree_result.png
vignettes/wiki_figs/ranef_data.png
vignettes/wiki_figs/ranef_ints.png
vignettes/wiki_figs/ranef_plots.png
vignettes/wiki_figs/tree_hcm.png
