adjust_taxonomies       Adjust Taxonomies
binomial_test           Binomial Test
blast_command_found     Check BLAST Installation
blast_version           Get BLAST Version
circle                  Draw Circle Polygon
contains_wildcards      Check Whether DNA Sequences Contain Wildcard
                        Characters
coordinates             Generate Circular Coordinates
cor2cov                 Convert Correlation to Covariance Matrix
dcopula                 Density of the Gaussian Copula
ddirmult                Density of the Dirichlet-Multinomial
                        Distribution
decode_quality_scores   Decode DNA Sequence Quality Scores
detection               Grouped Detection Plot
dissimilarity           Bray-Curtis Dissimilarity (Proportion Form)
diversity               Hill Diversity
djsdm                   Density of a Joint Species Distribution Model
dmWAIC                  WAIC for Dirichlet-Multinomial Regression
                        Models
dmpredict               Predictions for Dirichlet-Multinomial
                        Regression Models
dmreg                   Fitting Dirichlet-Multinomial Regression Models
dmvlogis                Density of the Multivariate Logistic
                        Distribution
expand_taxonomies       Expand Taxonomies
filter_sequences        Filter DNA Sequences by PCR Replicates
format_reference_database
                        Format Reference Databases
get_consensus_taxonomy
                        Get Consensus Taxonomy from Taxonomic Strings
get_taxonomic_level     Get Specified Taxonomic Level from Taxonomic
                        Strings
get_taxonomies.IUCN     Get Taxonomies from IUCN Red List Files
get_taxonomies.species_binomials
                        Get NCBI Taxonomies from Species Binomials
isolate_amplicon        Trim DNA Sequences to an Amplicon Region Using
                        Forward and Reverse Primer Sequences
local_taxa_tool         Perform Geographically-Conscious Taxonomic
                        Assignment
merge_pairs             Merge Forward and Reverse DNA Sequence Reads
mlWAIC                  WAIC for Multivariate Logistic Regression
                        Models
mlcoef                  Coefficients of Multivariate Logistic
                        Regression Models
mlcor                   Correlations of Multivariate Logistic
                        Regression Models
mlformat                Format Multivariate Logistic Regression Output
mlpredict               Predictions for Multivariate Logistic
                        Regression Models
mlreg                   Fitting Multivariate Logistic Regression Models
normalize               Normalize a Vector or Matrix
proportion              Grouped Proportion Plot
read.fasta              Read FASTA Files
read.fastq              Read FASTQ Files
reverse_complement      Get the Reverse Complement of a DNA Sequence
richness                Species Richness
sector                  Draw Sector Polygon
singular.detection      Singular Detection Plot
singular.proportion     Singular Proportion Plot
softmax                 The Softmax
substitute_wildcards    Substitute Wildcard Characters in a DNA
                        Sequence
summarize_quality_scores
                        Summarize Quality Scores
template                Initiate Template Plot
trim_sequences          Trim Target Nucleotide Sequence from DNA
                        Sequences
truncate_and_merge_pairs
                        Truncate and Merge Forward and Reverse DNA
                        Sequence Reads
truncate_sequences.length
                        Truncate DNA Sequences to Specified Length
truncate_sequences.probability
                        Truncate DNA Sequences at Specified Probability
                        that All Bases were Called Correctly
truncate_sequences.quality_score
                        Truncate DNA Sequences at Specified Quality
                        Score
waic                    Widely Applicable Information Criterion
write.fasta             Write FASTA Files
write.fastq             Write FASTQ Files
