Data and code for: Biogenic aggregation mediates indirect pathways of soil carbon storage across integrated agricultural systems

# Data and code for: Biogenic aggregation mediates indirect pathways of soil carbon storage across integrated agricultural systems Vanolli, B.S., Lloyd, G., Franco, A.L.C., Cherubin, M.R. Deposit supporting the article submitted to *Agriculture, Ecosystems & Environment*.Everything reported in the article and its supplementary material is reproduced fromthese files by a single script. --- ## Files | File | Content ||---|---|| `DATA_SPREADSHEET.xlsx` | 144 rows. One row per plot × land-use system, 0–30 cm depth. Soil chemistry and texture, bulk density, aggregate-size fractions, biogenic and physicogenic aggregates, SOC and its fractions, SOC stock, macrofauna abundance and Shannon diversity. || `POCMAOC.xlsx` | 432 rows. Intra-macroaggregate organic carbon by depth increment (0–0.1, 0.1–0.2 and 0.2–0.3 m). Source of Supplementary Figures S6–S8. || `analise_AGEE.R` | Complete analysis. Reads the two spreadsheets and writes every figure and table. | ## How to reproduce 1. Place the three files in one folder.2. Open `analise_AGEE.R` and set `PASTA` to that folder.3. Run the whole script. Missing packages are installed automatically. Outputs are written to `outputs/figuras` (TIFF), `outputs/figuras_pdf` (vector PDF)and `outputs/tabelas` (CSV). The console prints a version stamp and every quality-controlcheck. Tested with R 4.6.1, ggplot2 4.0.3 and piecewiseSEM 2.3.1. The script stops with anexplicit message if ggplot2 is older than 3.4.0. ## Variable names `CS` SOC stock (Mg C ha⁻¹, equivalent soil mass) · `SOC` bulk soil organic carbon ·`MAOM` and `POM` mineral-associated and particulate organic carbon of the whole soil(dag kg⁻¹; the script converts to g kg⁻¹ by a factor of 10) · `MAOM_ma`, `POM_ma`,`MAOM_mi`, `POM_mi` the same fractions within macro- and microaggregates ·`MacroAGG`, `MicroAGG`, `Sil_ClayAGG` aggregate-size fractions (%) ·`BioAGG`, `PhysioAGG` biogenic and physicogenic aggregates (g g⁻¹) ·`WMD` mean weight diameter (mm; renamed `MWD` in the script and in the article). ## Known data issue Three samples from the Clay8 site (rows 129, 130 and 136 of `DATA_SPREADSHEET.xlsx`)have `MicroAGG` and `Sil_ClayAGG` values outside the physically possible range. All othervariables measured on those samples fall within the normal range for the site and wereretained. The three rows are excluded only from analyses in which microaggregates enter,that is, the principal component analysis and the microaggregate structural equationmodels. No value was imputed. The script identifies these rows automatically and writesthem to `outputs/tabelas/QC_valores_impossiveis.csv`. ## Licence Data and code: CC BY 4.0. ## Citation Please cite the article. If you use the data or code independently, please also citethis deposit.