Geographically-Conscious Taxonomic Assignment for Metabarcoding

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Documentation for package ‘LocaTT’ version 1.3.0

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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