add.below.LOD           Add in taxa that were not observed, assuming
                        this means they were zero-prevalence.
add.sig.descs           Add gene descriptions to significant results;
                        return in a tibble.
adjust.db               Clean up imported database.
alt.multi.enrich        An alternative way to get the enrichment table,
                        using a tbl of results instead of separate
                        inputs for significant results, effect signs,
                        etc.
calc.alpha.power        Calculate the FPR and (1 - FNR) for results of
                        a set of tests.
calc.ess                Main function to calculate environmental
                        specificity scores.
check.process.metadata
                        Check and process metadata
clean.pheno             Remove taxa from a phenotype that aren't in our
                        trees and gene matrices (usually only necessary
                        for testing).
do.clust.plot           Make a hybrid tree-heatmap plot showing the
                        taxon distribution of significant hits.
do.fisher               Wrapper around 'fisher.test' that starts with
                        string vectors instead of a contingency table.
gene.annot              Annotate genes using a gene-to-function table.
get.pheno.plotting.scales
                        Get phenotype plotting scales.
get.top.N               Return the significant hits with the N smallest
                        p-values.
get.vsearch.results     Read in results from vsearch.
gg.cont.tree            Plot continuous trait on a tree.
harmonize.abd.meta      Check metadata and abundance matrix against one
                        another
import.pz.db            Import the data necessary for *phylogenize*
                        analysis.
install_data            Copy and/or unzip downloaded data into the
                        Phylogenize2 database directory.
kable.recolor           Function to obtain HTML colors for a particular
                        value.
keep.tips               Keep some tips on a tree.
lm.fx.pv                Wrapper around _lm_ that returns just the
                        effect size and p-value.
logistic                Calculate inverse-logit of a value or vector of
                        values.
logit                   Calculate logit of a value or vector of values.
make.pos.sig            Get vectors of significant genes with positive
                        effect sizes.
make.results.matrix     Convert results into a long (vs. wide) format.
make.signs              Get effect sizes of genes from result tables.
make.sigs               Get vectors of significant genes from result
                        tables.
matrix.plm              Perform phylogenetic (or linear) modeling for a
                        single taxon.
multi.enrich            Given lists of significant genes (at different
                        thresholds), effect sizes, and gene set
                        mappings, assemble a tbl of results.
non.interactive.plot    A fall-back plotting option for when
                        'hack.tree.labels' fails, designed to produce
                        the same kind of output.
nonequiv.pos.sig        Get vectors of significant genes with positive
                        (or negative) effect sizes.
nonparallel.results.generator
                        Fit phylogenetic (or linear) models (single
                        core version, single taxon).
output.enr.table        Make a pretty enrichment table.
phylolm.fx.pv           Wrapper around _phylolm_ that returns just the
                        effect size and p-value.
plot.labeled.phenotype.trees
                        Edit a list of plotted trees to add fancy
                        highlight labels.
plot.pheno.distributions
                        Plot distributions of a phenotype across taxa.
plot.phenotype.trees    Plot a phenotype along a list of trees.
prepare.vsearch.input   Prepare input file for alignment
prev.addw               Main function to calculate taxon prevalences
                        with additive smoothing.
process.16s             Map denoised 16S sequence variants to MIDAS IDs
                        using vsearch.
pv1                     Fix p-values that are above 1.
pz.error                Throw an error and optionally log it in
                        errmsg.txt.
pz.message              Report a message and optionally log it in
                        errmsg.txt.
pz.options              Set and get options for phylogenize.
pz.warning              Report a warning and optionally log it in
                        errmsg.txt.
read.abd.metadata       Read in abundance and metadata file(s).
remove.allzero.abundances
                        Remove rows and columns of a matrix that are
                        all zero.
result.wrapper.plm      Fit phylogenetic (or linear) models, or perform
                        POMS.
results.report          Create a summary table giving how many tests
                        were significant.
retain.observed.taxa    Modify trees to retain only observed taxa (for
                        use with specificity only).
run.vsearch             Run vsearch analysis on a FASTA file of
                        sequences.
sanity.check.abundance
                        Sanity-check abundance data
sanity.check.metadata   Check that dataset, environment, and sample
                        columns all present
set_data_internal       Set data directory to internal
single.cluster.plot     Make a hybrid tree-heatmap plot showing the
                        taxon distribution of significant hits.
sum.nonunique.vsearch   Sum non-unique rows after vsearch mapping.
tax.annot               Annotate taxa using a taxonomy table.
tbl.result.qvs          Get q-values for results in tbl format.
threshold.pos.sigs      Filter out genes that are almost always present
                        or absent.
