# Geographically-Conscious Taxonomic Assignment for Metabarcoding

## Documentation for package ‘LocaTT’ version 1.3.0

- DESCRIPTION file
- Package README

## Help Pages

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
dmpredict | Predictions for Dirichlet-Multinomial Regression Models
dmreg | Fitting Dirichlet-Multinomial Regression Models
dmvlogis | Density of the Multivariate Logistic Distribution
dmWAIC | WAIC for Dirichlet-Multinomial Regression Models
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
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
mlWAIC | WAIC for 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