NEWS.md
In CharAnalysis: Peak Detection and Fire History from Sediment-Charcoal Records

CharAnalysis 2.0.3

Patch release with substantive vignette improvements and several factual corrections to the worked example. No changes to analytical behaviour or to any function signature.

The vignette now live-renders all worked-example figures from the bundled Code Lake dataset; the previous build showed only static code blocks. Figure chunks are gated on the availability of ggplot2, patchwork, and ggtext (all in Suggests) and skip cleanly if any is missing.
Two diagnostic figures, char_plot_raw() (Fig. 1) and char_plot_thresh_diag() (Fig. 2), are now included in the vignette alongside the analytical figures (Figs. 3, 5, 6, 7, 8).
A new bundled parameter file CO_compensated_charParams.csv (with companion CO_compensated_charData.csv) is shipped in inst/validation/. It is identical to the standard CO_charParams.csv except that the working threshold percentile (threshValues[4]) is lowered from 0.99 to 0.95 to compensate for language-induced drift in the Gaussian mixture model (GMM) noise estimation. The vignette uses this file for the worked example. With this compensation, R identifies 50 peaks for Code Lake (close to the published MATLAB v2.0 result of 48 peaks) and reproduces the significant decrease in fire-return intervals from Zone 1 to Zone 2 reported in Higuera et al. (2009). The strict 1-to-1 reference configuration remains available as CO_charParams.csv.
The vignette's Comparison with MATLAB v2.0 section gained a Threshold column in the validation table and a new "CO (compensated)" row; the narrative below the table was rewritten in terms of compensation for GMM drift rather than ad-hoc tuning.
Vignette factual corrections: Code Lake is in Alaska (not Colorado); the smoothing-method label for Code Lake in the validation table is Method 4 (moving median), not Method 1 (lowess); the discussion of smoothing-related differences was adjusted to identify Method 2 (robust lowess) as the only method that diverges between R and MATLAB.
Fixed a stale system.file() path in the vignette (extdata → validation) that would have returned an empty string if the chunk had been evaluated.

CharAnalysis 2.0.2

Patch release addressing the third round of CRAN reviewer feedback, plus a related rendering fix discovered during local testing. No changes to analytical behaviour.

Title field shortened to "Peak Detection and Fire History from Sediment-Charcoal Records" (62 characters) to satisfy the CRAN convention of titles under 65 characters.
char_write_results() and char_plot_all() no longer default out_dir to the working directory. out_dir is now required for char_write_results() and required when save = TRUE for char_plot_all(). This brings the package into compliance with the CRAN policy against writing to the user's home filespace by default. Users should pass an explicit path; tempdir() is acceptable for a transient location.
Vignette updated to write its example output to tempdir() instead of a Results/ directory in the user's working directory, with a note that real users would substitute their own path.
Fixed axis-label rendering in char_plot_peaks(), char_plot_fire_history() (peak-magnitude panel), and char_plot_zones() (CDF and box-plot panels). These labels were still using expression(paste(...)) (plotmath) syntax and rendered as raw text under the ggtext::element_markdown() axis-title theme introduced in 2.0.1. They now use the same conditional HTML-tag / plain-text pattern as the FRI and fire-frequency labels, so super- and subscripts render correctly when ggtext is available.

CharAnalysis 2.0.1

Patch release addressing CRAN reviewer feedback on the initial submission. No changes to analytical behaviour.

DESCRIPTION: condensed to a single paragraph and removed the paragraph separators that were rendering as double periods in CRAN metadata.
char_parameters() is now exported. Its help page previously contained an example for an unexported function.
Replaced \dontrun{} wrappers in all examples with \donttest{} (or unwrapped entirely, where the example runs in under 5 seconds). All examples now use the bundled validation dataset via system.file() and write any output to tempdir().

CharAnalysis 2.0.0

First R implementation of CharAnalysis, a direct translation of CharAnalysis v2.0 (MATLAB). Analytical outputs are validated against four benchmark datasets; user testing is ongoing. The package is in the experimental lifecycle stage: the API may change as user feedback is incorporated.

Please report issues at https://github.com/phiguera/CharAnalysis/issues.

Full R package with devtools::install_github() installation.
CharAnalysis() returns a named list with S3 class "CharAnalysis"; print(), summary(), and plot() methods are provided.
Eight publication-quality ggplot2 figures (char_plot_peaks(), char_plot_fire_history(), char_plot_cumulative(), char_plot_fri(), char_plot_zones(), char_plot_raw(), char_plot_thresh_diag(), char_plot_sni()); save all to PDF with char_plot_all().
char_write_results() writes the 33-column output matrix to CSV with column headers and numeric format matching the MATLAB output exactly.

Robust lowess background (smoothing method 2). MATLAB's Curve Fitting Toolbox smooth(..., 'rlowess') and the R char_lowess() port handle NaN gaps differently inside the bisquare robustness iteration, producing slightly different C_background series for records with missing values. For gap-free records the difference is negligible (< 0.001); for records with NaN gaps the maximum absolute difference across validated datasets is 0.267 (Chickaree Lake). Smoothing method 1 (plain lowess) is unaffected and agrees to within floating-point noise.

GMM peak counts. The Gaussian mixture model EM algorithm accumulates floating-point arithmetic differently in R and MATLAB, causing slightly different threshold values in some local windows. Peak counts differ by 10–20% across validated datasets, with the direction varying by dataset.

Figures 9 and 10. The threshold-sensitivity detail plot (Fig. 9) and multi-site comparison plot (Fig. 10) from the MATLAB interface are not implemented in this R package.

Smoothed FRI column (col 23). The R package computes smoothed fire-return intervals in this column; MATLAB v2.0 stores NaN.

| Dataset | Site | charBkg max\|diff\| | Peaks R | Peaks MATLAB | |---------|------|-------------------|---------|-------------| | CO | Code Lake, AK | ~5 × 10^-6^ | 39 | 48 | | CH10 | Chickaree Lake, CO | 0.267 | 59 | 50 | | SI17 | Silver Lake, CO | 0.130 | 25 | 31 | | RA07 | Raven Lake, AK | < 0.001 | 15 | 17 |

Full validation details are in inst/z_Validation_report_R_vs_MATLAB_V_2.0.md.

If you use CharAnalysis in published research, please cite:

Higuera, P.E., L.B. Brubaker, P.M. Anderson, F.S. Hu, and T.A. Brown. 2009. Vegetation mediated the impacts of postglacial climate change on fire regimes in the south-central Brooks Range, Alaska. Ecological Monographs 79:201–219. https://doi.org/10.1890/07-2019.1

If you used Version 2.0 specifically, please also cite the software:

Higuera, P.E. 2026. CharAnalysis: Diagnostic and analytical tools for peak analysis in sediment-charcoal records (Version 2.0). Zenodo. https://doi.org/10.5281/zenodo.19304064