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66 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRS2013

Comparison of Four Precipitation Forcing Datasets in Land Information System Simulations over the Continental U.S.

This paper and poster presented a description of the current real-time SPoRT-LIS run over the southeastern CONUS to provide high-resolution, land surface initialization grids for local numerical model forecasts at NWS forecast offices. The LIS hourly output also offers a supplemental dataset to aid in situational awareness for convective initiation forecasts, assessing flood potential, and monitoring drought at fine scales. It is a goal of SPoRT and several NWS forecast offices to expand the LIS to an entire CONUS domain, so that LIS output can be utilized by NWS Western Region offices, among others. To make this expansion cleanly so as to provide high-quality land surface output, SPoRT tested new precipitation datasets in LIS as an alternative forcing dataset to the current radar+gauge Stage IV product. Similar to the Stage IV product, the NMQ product showed comparable patterns of precipitation and soil moisture distribution, but suffered from radar gaps in the intermountain West, and incorrectly set values to zero instead of missing in the data-void regions of Mexico and Canada. The other dataset tested was the next-generation GOES-R QPE algorithm, which experienced a high bias in both coverage and intensity of accumulated precipitation relative to the control (NLDAS2), Stage IV, and NMQ simulations. The resulting root zone soil moisture was substantially higher in most areas.

Case, Jonathan L.↗
DOE OSTI2025

Predicting weather impacts on corn production in a data-limited region using a transfer learning approach

The stability of food supply and prices may depend more on annual changes in yields from year-to-year variability in weather than on longer-term average changes from changing climatic conditions. However, the absence of high-quality data on crop yields at fine spatial resolutions in many regions of the world makes it challenging to statistically model their response to interannual variability in weather patterns. Therefore, there is a need for empirical methods that can project annual crop yield changes even in limited data regions. Here, we propose a transfer learning algorithm that uses high spatial resolution data from one region to project yields in another region with more limited data. The goal of our work is to understand what data types can be beneficial for transferring learning from a source region to a very different target region with more limited data. We utilize Long Short-Term Memory to develop a transfer learning model that is trained on historical county-level corn yield in the United States and predicts district-level corn yield variations in India. Even using smaller amounts of data in India, simulating a data-scarce region, we achieve an average root mean square error of 0.48 bu acre−1 in predicting interannual yield variations. Using Shapley values to interpret results, we explore the contribution of the different weather parameters to interannual yield variability and find a larger influence of precipitation-related variables. Our study demonstrates the usefulness of this method for transferring models of weather impacts on crop yields trained on a data-rich country to one with more limited data. It suggests the potential of applying the transfer learning model to mitigate the need for extensive raw data globally.

Vishwakarma, Srishti [ORNL] (ORCID:000000031674419↗
DOE OSTI2026

Unlocking plant-microbial interactions in deep Mollisols in the Midwestern US: Linking depth gradients in roots, microbial activity, and soil carbon in agroecosystems

Deep-rooted plants may build soil carbon (C) stocks, but most research has focused on shallow soils, leaving gaps in our understanding of how shifts in the balance between decomposition and C inputs drive soil C accumulation with depth. Thus, our objectives were to: (1) link depth gradients in root biomass with microbial activity and soil C stocks down to 1 m, and (2) examine the potential of simple C inputs to prime soil C across depths. To this end, we dug 5 quantitative soil pits in Argiudolls under mature perennial miscanthus plots in the SoyFACE Farm (Champaign-Urbana, IL). We added 13 C labeled glucose to our soils to determine the fate of simple C inputs with depth. We found that fine root biomass, total soil C, mineral-associated organic C (MAOC), particulate organic C (POC), and microbial activity (as measured by potential enzyme activity) declined with depth. POC declined more rapidly than MAOC, resulting in an increase in the ratio of MAOC-to-POC. Root biomass, enzyme activity (either acid phosphatase or n-acetyl-glucosaminadase) activity, and microbial respiration explained 74% and 38% of the variability in soil total C and MAOC, respectively, while POC was dependent on root biomass and microbial respiration (47%). Although the incorporation of simple 13 C inputs into MAOC was similar across depths, these inputs led to greater net MAOC losses in shallow soils than in deeper soils between 50 and 100 cm. The divergent impact of simple C inputs across depths may suggest that MAOC in shallow soils is more susceptible to priming losses, while C inputs into deep soils may instead be more persistent. Collectively, our results suggest that depth gradients in soil C stocks represents a balance between inputs, decomposition, and microbial necromass production and that increases in root C inputs by deep-rooted plants may have the potential to build stable MAOC.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2023

Fine particulate concentrations over East Asia derived from aerosols measured by the Advanced Himawari Imager using machine learning

Fine particulate matter with a diameter below 2.5 μm (PM 2.5 ) is deleterious to the cardiovascular and respiratory systems. It is often difficult to assess the effects of PM 2.5 on human health over regions with limited ground monitoring sites, especially in East Asia. As an alternative, we estimated near-surface PM 2.5 concentrations by analyzing Advanced Himawari Imager (AHI) Yonsei Aerosol Retrieval (YAER) products. This study incorporates daytime data for East Asia covering the Korean Peninsula, China, Japan, Southeast Asia, and southern Mongolia. We collocated AHI YAER product pixels with meteorological, land-cover, and other ancillary data for the period from March 2018 to February 2019. To estimate PM 2.5 concentrations over wide areas spanning many countries displaying various relationships between aerosol optical depth and PM 2.5 , monthly models were developed by considering both the spatial and temporal characteristics of ground-based PM 2.5 measurements. Random forest machine learning model estimated ground-level mass concentrations of PM 2.5 ; subsequent 10-fold cross validation (CV) yielded a CV R 2 value of 0.81 and a CV root mean squared error (RMSE) of 12.3 μg m -3 . We investigated the spatial pattern of PM 2.5 concentrations over multiple countries and seasonal variation in PM 2.5 concentrations. Diurnal variation of a severe PM 2.5 event in the Korean Peninsula was investigated as a case study. The model captured the extremely heterogeneous spatial distribution of PM 2.5 concentrations peaked around local noon. To measure the capability of the developed model to estimate PM 2.5 concentrations in areas with few in-situ data, its predictive performance was evaluated using a dataset independent of the training process with an R 2 of 0.60 and RMSE of 8.18 μg m −3 . This study demonstrates the potential for satellite-based PM 2.5 estimation for areas with insufficient measuring stations.

Pm2.5↗
NASA NTRS2011

Modeling the Height of Young Forests Regenerating from Recent Disturbances in Mississippi using Landsat and ICESat data

Many forestry and earth science applications require spatially detailed forest height data sets. Among the various remote sensing technologies, lidar offers the most potential for obtaining reliable height measurement. However, existing and planned spaceborne lidar systems do not have the capability to produce spatially contiguous, fine resolution forest height maps over large areas. This paper describes a Landsat-lidar fusion approach for modeling the height of young forests by integrating historical Landsat observations with lidar data acquired by the Geoscience Laser Altimeter System (GLAS) instrument onboard the Ice, Cloud, and land Elevation (ICESat) satellite. In this approach, "young" forests refer to forests reestablished following recent disturbances mapped using Landsat time-series stacks (LTSS) and a vegetation change tracker (VCT) algorithm. The GLAS lidar data is used to retrieve forest height at sample locations represented by the footprints of the lidar data. These samples are used to establish relationships between lidar-based forest height measurements and LTSS-VCT disturbance products. The height of "young" forest is then mapped based on the derived relationships and the LTSS-VCT disturbance products. This approach was developed and tested over the state of Mississippi. Of the various models evaluated, a regression tree model predicting forest height from age since disturbance and three cumulative indices produced by the LTSS-VCT method yielded the lowest cross validation error. The R(exp 2) and root mean square difference (RMSD) between predicted and GLAS-based height measurements were 0.91 and 1.97 m, respectively. Predictions of this model had much higher errors than indicated by cross validation analysis when evaluated using field plot data collected through the Forest Inventory and Analysis Program of USDA Forest Service. Much of these errors were due to a lack of separation between stand clearing and non-stand clearing disturbances in current LTSS-VCT products and difficulty in deriving reliable forest height measurements using GLAS samples when terrain relief was present within their footprints. In addition, a systematic underestimation of about 5 m by the developed model was also observed, half of which could be explained by forest growth that occurred between field measurement year and model target year. The remaining difference suggests that tree height measurements derived using waveform lidar data could be significantly underestimated, especially for young pine forests. Options for improving the height modeling approach developed in this study were discussed.

Li, Ainong↗
NASA NTRS2015

Spatiotemporal Prediction of Fine Particulate Matter Using High-Resolution Satellite Images in the Southeastern US 2003-2011

Numerous studies have demonstrated that fine particulate matter (PM(sub 2.5), particles smaller than 2.5 micrometers in aerodynamic diameter) is associated with adverse health outcomes. The use of ground monitoring stations of PM(sub 2.5) to assess personal exposure, however, induces measurement error. Land-use regression provides spatially resolved predictions but land-use terms do not vary temporally. Meanwhile, the advent of satellite-retrieved aerosol optical depth (AOD) products have made possible to predict the spatial and temporal patterns of PM(sub 2.5) exposures. In this paper, we used AOD data with other PM(sub 2.5) variables, such as meteorological variables, land-use regression, and spatial smoothing to predict daily concentrations of PM(sub 2.5) at a 1 sq km resolution of the Southeastern United States including the seven states of Georgia, North Carolina, South Carolina, Alabama, Tennessee, Mississippi, and Florida for the years from 2003 to 2011. We divided the study area into three regions and applied separate mixed-effect models to calibrate AOD using ground PM(sub 2.5) measurements and other spatiotemporal predictors. Using 10-fold cross-validation, we obtained out of sample R2 values of 0.77, 0.81, and 0.70 with the square root of the mean squared prediction errors of 2.89, 2.51, and 2.82 cu micrograms for regions 1, 2, and 3, respectively. The slopes of the relationships between predicted PM2.5 and held out measurements were approximately 1 indicating no bias between the observed and modeled PM(sub 2.5) concentrations. Predictions can be used in epidemiological studies investigating the effects of both acute and chronic exposures to PM(sub 2.5). Our model results will also extend the existing studies on PM(sub 2.5) which have mostly focused on urban areas because of the paucity of monitors in rural areas.

PM2.5↗
DOE OSTI2024

Water foraging with dynamic roots in E3SM; The role of roots in terrestrial ecosystem memory on intermediate timescales (Final Technical Report)

Terrestrial ecosystems can show sustained responses to stress events that may last for years after the initial perturbation. This phenomenon is referred to as legacy or memory and it emerges from a set of ecosystem processes that are poorly captured by Earth System and Land Surface Models. Consequently, these models struggle to predict the impact that extreme climate events have on surface energy, carbon and hydrological exchange once a stressor such as drought has relaxed or in response to repeated exposure to stress. In this project, we set out to test how the addition of dynamic root profiles in land surface models impact the capacity for Earth System Models, such as the Department of Energy’s E3SM, to capture realistic legacy effects. Observations have shown that vegetation shifts their root profiles during stress events to forage for water and these altered root profiles may take years to relax back to the initial state. We hypothesized that the alteration of the belowground root structures may be a source of terrestrial ecosystem legacy that is missing from models. To test this idea we undertook three core activities. (1) We developed a global-scale analysis of the impact of dynamic roots on ecosystem legacy building from a recently developed dynamic root module. (2) We developed new root dynamics in the DOE’s Energy Land Model (ELM) that allowed not only root profiles to shift their profile but also simultaneously alter carbon allocation to fine root pools. We then tested the impact of these new dynamics with intensive sensitivity analysis at four long-term AmeriFlux sites. (3) We undertook detailed isotopic analysis of tree rings from these AmeriFlux sites to assess ecophysiological and ecohydrological legacy to stress events that can be used to benchmark the sensitivity experiments with ELM. From these core activities, we report the following key findings. Firstly, on a global scale, the addition of dynamic roots led to chronically water-stressed ecosystems recovering faster to climate stress while wetter ecosystem showed enhanced legacy. This is because across ecosystems, stress events were almost universally associated with water shortages that led to the development of deeper root profiles. These deeper root profiles proved beneficial for recovery from drought stress. While the root dynamics did not universally improve the modeled representation of legacy it showed complex transient dynamics that emerge from the addition of dynamic roots. Secondly, the sensitivity analysis illustrated long term shifts in rooting depths away from the prescribed default profile suggesting that initializing of root profiles could benefit from spin-up simulations that converge on locally optimized root profiles. In addition, by enabling dynamic allocation some of the sites predicted unrealistically low allocation to roots (and high allocation to leaves). While these changes did not dramatically alter modeled gross primary productivity, they illustrated that without more sophisticated root processes in models, there is little penalty to dramatically disinvest in roots. Thirdly, the isotopic analysis of tree rings showed highly distinct legacy responses across species and sites. For example, T. canadensis showed reduced transpiration the year after stress events illustrated by sustained elevated $\delta^{18}$O. In contrast, A saccharum displayed elevated $\delta^{13}$C associated with reduced stomatal conductance in response to the previous years’ stress event. These geochemical signatures of legacy were present despite tree growth returning to normal the year after the stress. The results show the importance of species-level dynamics in legacy that are absent in modeling that assumes common traits within plant functional types. In summary, the work here established new avenues to explore root dynamics in models while illustrating how additional root processes are needed before dynamic carbon allocation can be implemented. Lastly, this project provided mentorship to a postdoctoral fellow, training for an early career scientist and multiple undergraduate students recruited from a minority serving institution.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2013

Estimating Ground-Level PM(sub 2.5) Concentrations in the Southeastern United States Using MAIAC AOD Retrievals and a Two-Stage Model

Previous studies showed that fine particulate matter (PM(sub 2.5), particles smaller than 2.5 micrometers in aerodynamic diameter) is associated with various health outcomes. Ground in situ measurements of PM(sub 2.5) concentrations are considered to be the gold standard, but are time-consuming and costly. Satellite-retrieved aerosol optical depth (AOD) products have the potential to supplement the ground monitoring networks to provide spatiotemporally-resolved PM(sub 2.5) exposure estimates. However, the coarse resolutions (e.g., 10 km) of the satellite AOD products used in previous studies make it very difficult to estimate urban-scale PM(sub 2.5) characteristics that are crucial to population-based PM(sub 2.5) health effects research. In this paper, a new aerosol product with 1 km spatial resolution derived by the Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm was examined using a two-stage spatial statistical model with meteorological fields (e.g., wind speed) and land use parameters (e.g., forest cover, road length, elevation, and point emissions) as ancillary variables to estimate daily mean PM(sub 2.5) concentrations. The study area is the southeastern U.S., and data for 2003 were collected from various sources. A cross validation approach was implemented for model validation. We obtained R(sup 2) of 0.83, mean prediction error (MPE) of 1.89 micrograms/cu m, and square root of the mean squared prediction errors (RMSPE) of 2.73 micrograms/cu m in model fitting, and R(sup 2) of 0.67, MPE of 2.54 micrograms/cu m, and RMSPE of 3.88 micrograms/cu m in cross validation. Both model fitting and cross validation indicate a good fit between the dependent variable and predictor variables. The results showed that 1 km spatial resolution MAIAC AOD can be used to estimate PM(sub 2.5) concentrations.

aerosol optical depth↗
NASA NTRS2017

Full-Coverage High-Resolution Daily PM(sub 2.5) Estimation using MAIAC AOD in the Yangtze River Delta of China

Satellite aerosol optical depth (AOD) has been used to assess population exposure to fine particulate matter (PM (sub 2.5)). The emerging high-resolution satellite aerosol product, Multi-Angle Implementation of Atmospheric Correction(MAIAC), provides a valuable opportunity to characterize local-scale PM(sub 2.5) at 1-km resolution. However, non-random missing AOD due to cloud snow cover or high surface reflectance makes this task challenging. Previous studies filled the data gap by spatially interpolating neighboring PM(sub 2.5) measurements or predictions. This strategy ignored the effect of cloud cover on aerosol loadings and has been shown to exhibit poor performance when monitoring stations are sparse or when there is seasonal large-scale missngness. Using the Yangtze River Delta of China as an example, we present a Multiple Imputation (MI) method that combines the MAIAC high-resolution satellite retrievals with chemical transport model (CTM) simulations to fill missing AOD. A two-stage statistical model driven by gap-filled AOD, meteorology and land use information was then fitted to estimate daily ground PM(sub 2.5) concentrations in 2013 and 2014 at 1 km resolution with complete coverage in space and time. The daily MI models have an average R(exp 2) of 0.77, with an inter-quartile range of 0.71 to 0.82 across days. The overall Ml model 10-fold cross-validation R(exp 2) (root mean square error) were 0.81 (25 gm(exp 3)) and 0.73 (18 gm(exp 3)) for year 2013 and 2014, respectively. Predictions with only observational AOD or only imputed AOD showed similar accuracy.Comparing with previous gap-filling methods, our MI method presented in this study performed bette rwith higher coverage, higher accuracy, and the ability to fill missing PM(sub 2.5) predictions without ground PM(sub 2.5) measurements. This method can provide reliable PM(sub 2.5)predictions with complete coverage that can reduce biasin exposure assessment in air pollution and health studies.

PM2.5↗
DOE OSTI2024

Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open-source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Simulated plant-mediated oxygen input has strong impacts on fine-scale porewater biogeochemistry and weak impacts on integrated methane fluxes in coastal wetlands

Methane (CH 4 ) emissions from wetland ecosystems are controlled by redox conditions in the soil, which are currently underrepresented in Earth system models. Plant-mediated radial oxygen loss (ROL) can increase soil O 2 availability, affect local redox conditions, and cause heterogeneous distribution of redox-sensitive chemical species at the root scale, which would affect CH 4 emissions integrated over larger scales. In this study, we used a subsurface geochemical simulator (PFLOTRAN) to quantify the effects of incorporating either spatially homogeneous ROL or more complex heterogeneous ROL on model predictions of porewater solute concentration depth profiles (dissolved organic carbon, methane, sulfate, sulfide) and column integrated CH 4 fluxes for a tidal coastal wetland. From the heterogeneous ROL simulation, we obtained 18% higher column averaged CH 4 concentration at the rooting zone but 5% lower total CH 4 flux compared to simulations of the homogeneous ROL or without ROL. This difference is because lower CH 4 concentrations occurred in the same rhizosphere volume that was directly connected with plant-mediated transport of CH 4 from the rooting zone to the atmosphere. Sensitivity analysis indicated that the impacts of heterogeneous ROL on model predictions of porewater oxygen and sulfide concentrations will be more important under conditions of higher ROL fluxes or more heterogeneous root distribution (lower root densities). Despite the small impact on predicted CH 4 emissions, the simulated ROL drastically reduced porewater concentrations of sulfide, an effective phytotoxin, indicating that incorporating ROL combined with sulfur cycling into ecosystem models could potentially improve predictions of plant productivity in coastal wetland ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

FUN-BioCROP model with litter decomposition parameters derived from the LIDET dataset

This repository contains the code and data necessary to run the FUN-BioCROP (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms, and Protection) model with litter decomposition parameters derived from a modified Monte Carlo simulation that used the Long-term Intersite Decomposition Experiment Team dataset. Related publication:Juice, S.M., Ridgeway, J.R., Hartman, M.D., Parton, W.J., Berardi, D.M., Sulman, B.N., Allen, K.E., & Brzostek, E.R. Reparameterizing litter decomposition using a simplified Monte Carlo method improves litter decay simulated by a microbial model and alters bioenergy soil carbon estimates. Description of Files: FUNBioCROP_LIDET Study.Rmd R code with FUN-BioCROP model that can be run with 10 different sets of parameters for litter decomposition (Baseline, LIDET, or eight other best parameter sets identified in the modified Monte Carlo simulation. CORPSE Functions_Bioenergy_V2.R Code with CORPSE model functions, called by FUNBioCROP_LIDET Study.Rmd Model Input Data: 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 Model Input Data: 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) Model Input Data: 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) Model Input Data: 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: Save the model code ("FUN-BioCROP_LIDET Study.Rmd") and accompanything files (data streams and CORPSE function code) in the same folder. In model code "Chunk 3: Load CORPSE Data Streams" set the working directory (setwd) to the folder with the files saved in step #1. 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. If changing any parameter values, edit them in "Chunk 6: Load parameters." Run all chunks up to and including "Chunk 10: Prepare Data for Export." In "Chunk 11: Export Output Data" edit data frames for export and filenames, as necessary. "Chunk 12: Graph Total Soil C" makes a figure of C remaining over the model run period. Description of each model chunk (in file FUN-BioCROP_LIDET Study.Rmd): Chunk 1: Remove all functions, clear memory. Removes all functions from R environment, clears the memory. Chunk 2: Load Packages. Loads packages necessary to run the code. Chunk 3: Load CORPSE Data Streams. Sets the working directory and loads the data files necessary to run CORPSE. Chunk 4: Load CORPSE Functions. Loads the R script with CORPSE functions from the working directory, "CORPSE Functions_Bioenergy_V2.R". 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. 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" 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. 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. 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. Chunk 10: Run Model. Runs the model. 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. Chunk 12: Export Results. Exports CSV files of model results to the working directory. 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

Juice, Stephanie↗