Package: CooccurrenceAffinity 1.0

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 MLE, alpha hat, were advanced in Mainali, Slud, et al, 2021 <doi:10.1126/sciadv.abj9204>. Various types of confidence intervals and median interval were developed in Mainali and Slud, 2022 <doi:10.1101/2022.11.01.514801>.

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

# 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

On CRAN:

4.39 score 26 stars 19 scripts 176 downloads 18 exports 33 dependencies

Last updated 2 years agofrom:37a2c58a18. Checks:3 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 15 2025
R-4.5-win	NOTE	Mar 15 2025
R-4.5-mac	NOTE	Mar 15 2025
R-4.5-linux	NOTE	Mar 15 2025
R-4.4-win	NOTE	Mar 15 2025
R-4.4-mac	NOTE	Mar 15 2025
R-4.4-linux	NOTE	Mar 15 2025
R-4.3-win	OK	Mar 15 2025
R-4.3-mac	OK	Mar 15 2025

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 colorspace cowplot fansi farver ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr R6 RColorBrewer Rcpp reshape rlang scales tibble utf8 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
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