pommevilla / lamps_incubation

LAMPS Incubation

Project repo for analysis done on the crop priming data for the LAMPS incubation project.

File descriptions

• results
  • stats
    • n_anova_results.long.csv and n_anova_results.wide.csv: ANOVA results for NH4, NO3, CO2, and N2O (daily and cumulative), as well as mineralization and nitrification daily rates (absolute and relative), against Day, Treatment, Addition, and N Rate.
• figures
  • n_figures
    • n_line_plots.png - daily GHG and N by treatment.
    • n_line_plots_cumulative.png - cumulative GHG and N by treatment.
    • net_min_nitr_abs_rel.png - nitrification and mineralization rates (relative to previous sample and relative to initial sample) by treatment.

Repeating the analysis

After cloning the repo, restore the conda environment by doing:

mamba env create -f environment.yml

Then, activate the environment:

conda activate lamps_incubation

You can then run the pipeline with:

snakemake -c 1

(You can also do snakemake -c 2 or however many cores you'd like to use.)

This will restore the R environment, regenerate all the figures, and render the website.