Package: CooccurrenceAffinity 2.0.0

CooccurrenceAffinity: Affinity in Co-Occurrence Data

Computes a novel metric of affinity between two entities based on their co-occurrence (using binary presence/absence data). The metric and its maximum likelihood estimator (alpha hat) were advanced in Mainali, Slud, et al, 2021 <doi:10.1126/sciadv.abj9204>. Four types of confidence intervals and median interval were developed in Mainali and Slud, 2022 <doi:10.1101/2022.11.01.514801>. The `finches` dataset is bundled with the package.

Authors:Kumar Mainali [aut, cre], Eric Slud [aut]

CooccurrenceAffinity_2.0.0.tar.gz
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CooccurrenceAffinity_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CooccurrenceAffinity/json (API)

# Install 'CooccurrenceAffinity' in R:

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

Bug tracker:https://github.com/kpmainali/cooccurrenceaffinity/issues

Datasets:

finches - Darwin’s finches presence–absence data

On CRAN:

4.52 score 30 stars 22 scripts 357 downloads 18 exports 22 dependencies

Last updated from:9bb0d21807. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	130
source / vignettes	OK	181
linux-release-x86_64	OK	120
macos-release-arm64	OK	145
macos-oldrel-arm64	OK	220
windows-devel	OK	98
windows-release	OK	104
windows-oldrel	OK	86
wasm-release	OK	95

Exports:AcceptAffCI AcceptAffin affinity affinity2by2 AlphInts Bisect Covrg CovrgPlot dataprep EHypMidP EHypQuInt logLikExtHyp MaxX.Int midP.EHyp minmaxAlpha.pFNCH MinX.Int ML.Alpha plotgg

Dependencies:BiasedUrn cli cowplot cpp11 farver ggplot2 glue gtable isoband labeling lifecycle plyr R6 RColorBrewer Rcpp reshape rlang S7 scales vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Acceptability Interval	AcceptAffCI
Calculates the "Acceptability Function" used in defining Blaker's (2000) Acceptability Interval and computing the latter in the function AcceptAffCI().	AcceptAffin
Computes alpha, probability, expected co-occurence, median interval, various confidence intervals, other indices of affinity, etc.	affinity
Maximum likelihood estimate and intervals of alpha, null expectation, p-value and traditional indices from a 2x2 table	affinity2by2
Median interval, four confidence intervals, null expectation of cooccurrence count, and p-value	AlphInts
Bisections for finding a root of a function	Bisect
Coverage Probabilities for Confidence Intervals about alpha, for fixed true alpha	Covrg
Occurrence matrix (e.g., species by site) data preparation for affinity() function	dataprep
Quantile of the Extended Hypergeometric distribution approximated by the midP distribution function	EHypMidP
Interval of alpha values for which X is a specified q'th quantile	EHypQuInt
Darwin’s finches presence–absence data	finches
log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha)	logLikExtHyp
MaxX.Int computation	MaxX.Int
midP.EHyp computation	midP.EHyp
integer-endpoint of range for which BiasedUrn::pFNCHHypergeo() works without error	minmaxAlpha.pFNCH
MinX.Int computation	MinX.Int
Maximum likelihood estimate and intervals of alpha, null expectation and p-value of a 2x2 table	ML.Alpha
Heatmap plot of affinity() output	plotgg