Package: coralesce 1.0.1

Colin Shea

coralesce: Group Coral Colonies Based on Genetic Relatedness

Assigns coral colonies to clonal groups (genets) from single nucleotide polymorphism (SNP) data by comparing alleles at each locus across all pairwise combinations of colonies, and computes individual- and population-level mean kinship and gene diversity (excluding invariant loci). Wrapper functions read genotype CSV files from a 'Data' folder and write results to a 'Results' folder.

Authors:Colin Shea [aut, cre], Lauren Gentry [aut], Kristen Sauby [aut]

coralesce_1.0.1.tar.gz
coralesce_1.0.1.zip(r-4.7)coralesce_1.0.1.zip(r-4.6)coralesce_1.0.1.zip(r-4.5)
coralesce_1.0.1.tgz(r-4.6-any)coralesce_1.0.1.tgz(r-4.5-any)
coralesce_1.0.1.tar.gz(r-4.7-any)coralesce_1.0.1.tar.gz(r-4.6-any)
coralesce_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coralesce/json (API)

# Install 'coralesce' in R:

install.packages('coralesce', repos = c('https://colinpshea.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/colinpshea/coralesce/issues

Datasets:

IUPAC - IUPAC data

On CRAN:

2.60 score 23 exports 23 dependencies

Last updated from:f1dbeb3352. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	129
source / vignettes	OK	192
linux-release-x86_64	OK	160
macos-release-arm64	OK	84
macos-oldrel-arm64	OK	83
windows-devel	OK	91
windows-release	OK	89
windows-oldrel	OK	101
wasm-release	OK	115

Exports:calcPercentNotNull checkforAllowableData classifyAllelePairs classifyAllelePairsOthers collapseToGenets computeGenets computeKinship convertBasePairstoCodes determineAllAlleleMatches determineAllAlleleMatchesOthers find_dups groupByGenets handleError_allZeros handleError_ColumnContract handleError_ProhibitedData isolateAllNAColonies kinshipCalcs kinshipCalcsNoInvar omitInvariantLoci readGeneticData returnGenetIdentity runGenets runKinship

Dependencies:cli cpp11 dplyr generics glue igraph lattice lifecycle magrittr Matrix pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

coralesce Tutorial

Rendered fromcoralesce-tutorial.html.asisusingR.rsp::asis

Last update: 2026-07-10
Started: 2026-07-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate percent not null	calcPercentNotNull
Flag values that are valid IUPAC allele pairs	checkforAllowableData
Classify allele pairs at a single locus	classifyAllelePairs
Classify allele pairs at a single locus (excluding self-comparisons)	classifyAllelePairsOthers
Collapse colonies to one representative per genet	collapseToGenets
Assign colonies to genets from a genotype data frame	computeGenets
Compute kinship and gene diversity from a genotype data frame	computeKinship
Convert base-pair genotypes to single-letter IUPAC codes	convertBasePairstoCodes
Assess allele matches across all loci (self and other comparisons)	determineAllAlleleMatches
Assess allele matches across all loci (other comparisons only)	determineAllAlleleMatchesOthers
Stop if any colony has multiple rows of SNP data	find_dups
Assign colonies to genets from pairwise allele matches	groupByGenets
Identify colonies with no valid SNP data	handleError_allZeros
Validate the required input-column contract	handleError_ColumnContract
Report columns that do not hold valid SNP data	handleError_ProhibitedData
Separate colonies with no valid SNP data from the rest	isolateAllNAColonies
IUPAC data	IUPAC
Calculate pairwise kinship across all comparisons	kinshipCalcs
Population- and individual-level kinship and gene diversity	kinshipCalcsNoInvar
Remove invariant loci	omitInvariantLoci
Read and validate a genetic SNP data file	readGeneticData
Assign colonies to genets from clonal pairings	returnGenetIdentity
Assign genets for every data file in the working directory	runGenets
Run kinship calculations for every data file in the working directory	runKinship