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recruitlag: Can Episodic Recruitment be a Delayed Consequence of Continuous Reproduction?

Tests whether an episodic recruitment record can be the delayed consequence of a reproductive record, under any distributed lag. A delay is a convolution, and a convolution is a weighted average, so the concentration in time of expected recruitment can never exceed that of reproduction: reproduction's own concentration is a ceiling. The package computes that ceiling by searching families of lag weights (pure delays, windows, geometric decay and Dirichlet draws), calibrates the pooled comparison against negative-binomial counts to show what it can and cannot refute, and runs the host-level (replicate-unit) test in which the null is the lag hypothesis exactly as it is asserted: expected recruitment on each unit is that unit's own lagged reproduction, scaled to its own total. Uncertainty on the exceedance comes by three routes, a cluster bootstrap over units, a Bayesian bootstrap (Rubin 1981 <doi:10.1214/aos/1176345338>) and a negative-binomial model of the counts fitted with 'Stan' through 'cmdstanr'; recruit_triage() asks whether a first sighting is a recruit or a plant returning from dormancy. Plotting functions draw the ceiling strip, the lag profiles against the observed counts, the calibration and a forest plot of the intervals. The census data on the epiphytic orchid Lepanthes eltoroensis analysed in the companion paper are included.

Version: 0.1.0
Depends: R (≥ 4.1)
Imports: ggplot2, rlang, stats, tibble, tools, utils
Suggests: testthat (≥ 3.0.0), knitr, rmarkdown, dplyr, tidyr, cmdstanr (≥ 0.6.0), posterior
Published: 2026-10-15
DOI: 10.32614/CRAN.package.recruitlag (may not be active yet)
Author: Raymond L. Tremblay ORCID iD [aut, cre, cph]
Maintainer: Raymond L. Tremblay <raymond.tremblay at gmail.com>
BugReports: https://github.com/RaymondLTremblay/recruitlag/issues
License: MIT + file LICENSE
Copyright: see file COPYRIGHTS
URL: https://github.com/RaymondLTremblay/recruitlag
NeedsCompilation: no
Additional_repositories: https://stan-dev.r-universe.dev
Language: en-GB
Citation: recruitlag citation info
Materials: NEWS
CRAN checks: recruitlag results

Documentation:

Reference manual: recruitlag.html , recruitlag.pdf
Vignettes: Reading the intervals: confidence, credible, and the four ways to cut one (source, R code)
Invented records: where the test has power and where it does not (source, R code)
The Lepanthes eltoroensis analysis (source, R code)
The mathematics behind the test, and the functions that implement it (source, R code)
Introduction to recruitlag: a worked analysis, step by step (source, R code)

Downloads:

Package source: recruitlag_0.1.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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