Man pages for LocaTT
Geographically-Conscious Taxonomic Assignment for Metabarcoding
| 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... |
| 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... |
| 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 |
