v2.0.3

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 v2.0.0 (R) — beta release

CharAnalysis 2.0.0 (beta)

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.

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

New features relative to MATLAB v2.0

• 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.

Known differences from MATLAB v2.0

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.

Validation summary

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.

Citation

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

CharAnalysis Version 2.0

Since the mid-2000s, CharAnalysis has been used in dozens of published studies, with applications to sediment-charcoal records from across the globe. Version 2.0 is the first major update to the program, focusing entirely on modernizing the MATLAB codebase: eliminating legacy patterns, removing toolbox dependencies, and improving computational efficiency. The analytical methods are unchanged from Version 1.1.

CharAnalysis Version 1.1

Updates from CharAnalysis 1.0:

(1) Integrates SNI from Kelly et al. (2011)
(2) Compiled version (CharAnalysis*.exe) for Window 7, 64 bit machine.