Greenhouse gas concentrations from stabilization ponds at the Omo WWTP (Moquegua, Peru): dataset and reproducible analysis

This record contains the curated primary dataset, reproducible R and Python analysis code, derived statistical tables, and publication-quality figures supporting the manuscript by Valeriano-Zapana et al. (2026), submitted to Atmospheric Pollution Research. The primary dataset comprises 36 repeated temporal records collected during three monitoring campaigns conducted between August and October 2022 at the Omo Wastewater Treatment Plant in Moquegua, southern Peru, an arid Andean site located at approximately 1,410 m above sea level. Measurements were obtained from one sampled cell representing each of three stabilization-pond stages: anaerobic, facultative, and tertiary. Within each pond-cell × campaign deployment, observations were recorded at post-closure days 1, 3, 7, and 9. Each record includes chamber-headspace accumulation measurements for CH₄, N₂O, and CO₂, together with water temperature, pH, chemical oxygen demand (COD), and five-day biochemical oxygen demand (BOD₅). Chamber-headspace gas accumulation was measured in situ using an LGR-ICOS M-GGA-919 portable laser spectrometer. Water temperature and pH were measured in the field, whereas COD and BOD₅ were determined by INACAL-accredited laboratories using standardized analytical methods. The observations represent repeated temporal measurements from the sampled pond cells and should not be interpreted as independent spatial replicates of pond type. Original gas readings coded as zero denote observations below a single estimated operational threshold of approximately 0.05 ppm, rather than measured zero concentrations. In the primary analytical workflow, these left-censored observations were replaced with one-half of the threshold (0.025 ppm). The repository also includes sensitivity analyses using alternative substitution rules. The reproducible R workflow is organized through master.R and the modular scripts 00_setup.R to 09_supp_figures.R. The pipeline imports the curated CSV files, performs data validation and descriptive analyses, evaluates distributional assumptions and exploratory group comparisons, calculates Benjamini–Hochberg-adjusted Spearman correlations, fits and compares linear mixed-effects models, estimates marginal means and Tukey-adjusted contrasts, calculates concentration–time slopes, converts slopes to apparent chamber-footprint-normalized accumulation rates, and generates the main and supplementary tables and figures. Auxiliary Python scripts are included for selected figure and table production. Gas measurements were obtained after chamber closure intervals of 1, 3, 7, and 9 days. These intervals exceed the short-duration closure periods commonly recommended for steady-state chamber-flux measurements by two to three orders of magnitude. Consequently, the derived values are reported strictly as apparent chamber-footprint-normalized accumulation rates. They must not be interpreted as validated steady-state gas fluxes, whole-pond emission rates, or greenhouse-gas emission factors. Users of the dataset should preserve this methodological framing in any reuse, comparison, or secondary analysis. Data and documentation are released under the Creative Commons Attribution 4.0 International license (CC BY 4.0). Source code is released under the MIT License.