FUN-BioCROP with LIDET Parameters

Version of FUN-BioCROP model (https://github.com/BrzostekEcologyLab/FUN-BioCROP) with LIDET-derived litter decomposition parameters

Model name: “FUNBioCROP_LIDET Study.Rmd”

Creators: Stephanie Juice, Joanna Ridgeway, Melannie Hartman, William Parton, Danielle Berardi, Benjamin Sulman, Kara Allen, Edward Brzostek

Contact information: [email protected], [email protected]

Related publication:
Juice, S. M., Ridgeway, J. R., Hartman, M. D., Parton, W. J., Berardi, D. M., Sulman, B. N., et al. (2024). Reparameterizing litter decomposition using a simplified Monte Carlo method improves litter decay simulated by a microbial model and alters bioenergy soil carbon estimates. Journal of Geophysical Research: Biogeosciences, 129, e2023JG007625. https://doi.org/10.1029/2023JG007625

Software: R

Accompanying files:

1. CORPSE function code: CORPSE Functions_Bioenergy_V2.R

2. Data streams to load into the script:
   a. bulk.csv, bulk_till.csv, rhizo.csv, rhizo_till.csv, litter.csv: initial C and N (kg C or N/m²) pool values for each soil compartment, final values from spin up.
   

All five files have the same columns:

Column	Description	Units
uFastC	Unprotected fast decomposing carbon	kg carbon/m2
uSlowC	Unprotected slow decomposing carbon	kg carbon/m2
uNecroC	Unprotected necromass carbon	kg carbon/m2
pFastC	Protected fast decomposing carbon	kg carbon/m2
pSlowC	Protected slow decomposing carbon	kg carbon/m2
pNecroC	Protected necromass carbon	kg carbon/m2
livingMicrobeC	Carbon in living microbial biomass	kg carbon/m2
uFastN	Unprotected fast decomposing nitrogen	kg nitrogen/m2
uSlowN	Unprotected slow decomposing nitrogen	kg nitrogen/m2
uNecroN	Unprotected necromass nitrogen	kg nitrogen/m2
pFastN	Protected fast decomposing nitrogen	kg nitrogen/m2
pSlowN	Protected slow decomposing nitrogen	kg nitrogen/m2
pNecroN	Protected necromass nitrogen	kg nitrogen/m2
inorganicN	Inorganic nitrogen	kg nitrogen/m2
CO2	Carbon in carbon dioxide	kg carbon/m2
livingMicrobeN	Nitrogen in living microbial biomass	kg nitrogen/m2

​ b. FluxTower_AvgSoilT.csv: Average daily soil temperature (^oC) at 10 cm depth at University of Illinois Urbana-Champaign (UIUC) Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data)

​ c. FluxTower_AvgSoilVWC.csv: Average daily soil volumetric water content (VWC) at 10 cm depth at UIUC Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data)

​ d. input_CCS_LIDET Study.csv: This file has daily data to run FUN-BioCROP:

Column	Description	Units
yr	calendar year	year
doy	day of year (1 to 365) (no leap year)	day
anpp	aboveground NPP (DayCent)	kg C/m2/day
bnpp	belowground NPP (DayCent)	kg C/m2/day
aglivc	live aboveground biomass carbon (DayCent)	kg C/m2
bglivcj	live juvenile fine root biomass carbon (DayCent)	kg C/m2
bglivcm	live mature fine root biomass carbon (DayCent)	kg C/m2
aglivn	live aboveground biomass nitrogen (DayCent)	kg N/m2
bglivnj	live juvenile fine root biomass nitrogen (DayCent)	kg N/m2
bglivnm	live mature fine root biomass nitrogen (DayCent)	kg N/m2
nyr	simulation year	year
cult	indicates a cultivation event (0 or 1)
crop	indicates a new crop (0 or 1)
fert	indicates a fertilizer event (0 or 1)
frst	indicates the first day of the growing season (0 or 1)
harv	indicates a harvest event (0 or 1)
last	indicates the end of the growing season (0 or 1)
croptype	crop type (0=none; 1=alfalfa; 2=corn; 3=grass clover pasture; 4=soybean; 5=wheat)
cropsrl	crop specific root length	mm/g root
cultrhizmix	fraction of rhizosphere mixed with bulk soil during cultivation (0.0-1.0)	fraction
cultlitmix	fraction of litter mixed with bulk soil during cultivation (0.0-1.0)	fraction
harvremov	fraction of above ground biomass removed during harvest (0.0-1.0)	fraction
fertamt	fertilization amount	g N/m2
lifehist	plant life history (0 = annual, 1 = perennial)
froot_turnover_c	amount of C in fine root turnover	kg C/m2
froot_turnover_n	amount of N in fine root turnover	kg N/m2
agrd_turnover_c	amount of C in aboveground biomass turnover	kg C/m2
agrd_turnover_n	amount of N in aboveground biomass turnover	kg N/m2
leaf_litter_fastfrac	Fast decomposing fraction of leaf litter (0.0-1.0)	fraction
root_litter_fastfrac	Fast decomposing fraction of root litter (0.0-1.0)	fraction
root_diameter	root diameter	mm
root_length	root length	mm root/m2
rhizo_frac	fraction of total soil volume that is rhizosphere (0.0 - 1.0)	fraction
date	date in format YYYY-MM-DD

Instructions:

1. Save the model code (“FUN-BioCROP_LIDET Study.Rmd”) and accompanything files (data streams and CORPSE function code) in the same folder.

2. In “Chunk 3: Load CORPSE Data Streams” set the working directory (setwd) to the folder with the files saved in step #1.

3. In "Chunk 5: Define LIDET parameter sets" select the litter decomposition parameter set to be used in the run, and comment out all other sets.

4. If changing any parameter values, edit them in “Chunk 6: Load parameters.”

5. Run all chunks up to and including “Chunk 10: Prepare Data for Export.”

6. In “Chunk 11: Export Output Data” edit data frames for export and filenames, as necessary.

7. “Chunk 12: Graph Total Soil C” makes a figure of C remaining over the model run period.

Description:

This model is a reparameterized version of the original FUN-BioCROP model (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms, and Protection, https://github.com/BrzostekEcologyLab/FUN-BioCROP). Leaf litter decomposition in the litter compartment was reparameterized using the Long-term Inter-site Decomposition Experiment Team dataset (LIDET) and a modified Monte Carlo simulation.

Description of each chunk:

1. Chunk 1: Remove all functions, clear memory. Removes all functions from R environment, clears the memory.

2. Chunk 2: Load Packages. Loads packages necessary to run the code.

3. Chunk 3: Load CORPSE Data Streams. Sets the working directory and loads the data files necessary to run CORPSE.

4. Chunk 4: Load CORPSE Functions. Loads the R script with CORPSE functions from the working directory, “CORPSE Functions_Bioenergy_V2.R”.

5. Chunk 5: Define LIDET parameter sets. Has ten different parameter sets for litter decomposition tested in this study: Baseline parameters, LIDET parameters, and the other 8 best performing parameter sets identified in the modified Monte Carlo. To run the model, all but one parameter set must be commented out.

6. Chunk 6: Load Parameters. Loads all fixed parameters to run the model. Data frame with definitions of parameters is in the CORPSE function script “CORPSE Functions_Bioenergy_V2.R”

7. Chunk 7: Prepare Data Streams. Takes data streams loaded in Chunk 3 and puts them in the format necessary to run the model. The model is coded to run at least two sites at a time, so if only one site is being run it must be run in duplicate. Individual data tables of daily values are created in this chunk from the input data file.

8. Chunk 8: Set Initial Conditions. Creates data tables of soil C and N pools for each soil compartment (rhizo_till, rhizo, bulk_till, bulk, litter) and loads initial values into the data tables. Creates lists for each soil compartment to hold model output.

9. Chunk 9: Load FUN Data and Set Up Matrices. Uses DayCent data to calculate FUN input data: root and leaf N demand, total N demand, plant CN, leaf N available for retranslocation, and litter production. Creates matrices for FUN model outputs.

10. Chunk 10: Run Model. Runs the model.

11. Chunk 11: Prepare Data for Export. Combines data from each day saved as lists into data frames for each soil compartment. Adds values from all soil compartments together to calculate total soil values, creates separate data frames for each soil C and N pool (e.g., protected slow C) for the total soil value. Adds different C and N pools together to calculate total soil C and N for all layers. Creates data frame of ratio of protected to unprotected SOC. Organizes FUN data for export.

12. Chunk 12: Export Results. Exports CSV files of model results to the working directory.

13. Chunk 13: Graph Total Soil C. Makes figure of C remaining over time.

Related Links:

Original FUN-BioCROP model: https://github.com/BrzostekEcologyLab/FUN-BioCROP
LIDET dataset: https://andlter.forestry.oregonstate.edu/data/abstract.aspx?dbcode=TD023