Release 1.3 0#167

Merged

jchiquet merged 18 commits into

Jun 18, 2026

Commits on Jun 18, 2026

Merge the two devlog files into a single continuous journal

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Change default backends: PLN -> nlopt, PLNnetwork -> builtin

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Document default-backend revision in devlog

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Suppress benign glm.fit warnings in ZIPLN ZI-component init

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Convert README.Rmd to an executed README.qmd with live illustrations

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Document README.qmd conversion in devlog
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Ignore quarto local cache/notebook artifacts

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Add ZIPLN vignette covering ZIPLN and ZIPLNnetwork

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Document ZIPLN vignette in devlog

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Switch ZIPLNnetwork default backend to builtin

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Fix ZIPLN vignette coefficient heatmaps and declare pheatmap dependency

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Fix spurious igraph warning when plotting networks

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Re-render README after the igraph warning fix

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Document ZIPLN vignette fixes and igraph warning fix in devlog

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Strip internal benchmark numbers from user-facing roxygen docs

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add genetic covariance in oaks_tree
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Pre-release documentation audit: fix missing @return, clean WORDLIST

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Compress NEWS.md unreleased entry into higher-level grouped bullets

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