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v0.7.0#31

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ethanbass merged 60 commits intomasterethanbass/chromatographR:masterfrom devethanbass/chromatographR:devCopy head branch name to clipboardJan 26, 2024

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Commits

Commits on Dec 10, 2023

• fix: correct_peaks

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• fix: "use.cor" option in get_peaktable

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• remove 'load_chroms' function

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• fix: plot.peak_table to allow numeric lambdas

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• remove load_chroms from namespace

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• docs: suggest numeric lambdas in vignette

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• added option for summing split peaks with combine_peaks

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• added option for fixing peak order in reshape_peaktable

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• fix: error message for clicking with ggplot engine

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• docs: update NEWS.md

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• tests: rearrange tests

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• fix: merge_peaks error, add test

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Commits on Dec 11, 2023

• ci: set null device cairo

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• fix: extraneous warning from attach_ref_spectra

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• Merge branch 'dev' of https://github.com/ethanbass/chromatographR into dev

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• Revert "ci: set null device cairo"

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• Refactor: cluster_spectra

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• style: whitespace in get_peaktable

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• docs: very -> always

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• test: add back cluster_spectra test

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• Update NEWS.md

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• fix: bug in correct_peaks

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• fix: get_peaktable new bug

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Commits on Dec 14, 2023

• ui, docs: changed index argument to idx

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Commits on Dec 18, 2023

• standardized arguments by deprecating chr and replacing with idx

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• fix: bug in reshape_chroms (empty metadata column)

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• added tests

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• Update NEWS.md

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• tests: remove offending test

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• fix: use modified times for peak start and end

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Commits on Dec 23, 2023

• fix: bug in correct_rt ui (erroneous error with 1D chromatograms)

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• docs: update readme

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• docs: small changes to vignette

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• docs: write_peaktable

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• test: comment out problematic test

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Commits on Dec 24, 2023

• add subset.peak_table function with test

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• feat: add peak title to spectrum_plot

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• docs: rearranged utils.R, added more comments

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• style: whitespace

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• docs: updated news

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• Update NEWS.md

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Commits on Dec 25, 2023

• docs: added example for write_peaktable

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• feat: added collapse argument to get_peaks

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Commits on Jan 19, 2024

• feat: added "what" argument to plot_all_spectra

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• Update NEWS.md

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• Update cran-comments.md

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• docs: update docs

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• docs: fix read_chroms docs so it links to chromconverter

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• rename load_chroms.R to read_chroms.R

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• docs: edited package help page

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• Update WORDLIST

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• docs: fix scan_chrom example

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• docs: removed docs for unexported functions

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• docs: update data documentation

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• style: cosmetic changes to vignette

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• style: reshape_chroms

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• style: attach_metadata whitespace

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• refactor: use seq_len instead of 1:x

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• added back necessary purity functions to namespace

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Commits on Jan 26, 2024

• Merge branch 'master' into dev

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