new spatial structure, outputs, and other updates for CALAND.r

[msimmond]

This topic branch adds the following new features and functionality to CALAND.r:

1. (issue #7) Updates model structure to accommodate new input files (carbon_input and scenario files). Input files have a new spatial delineation column (Eco-Region) for the land categories, an increase in number of land categories (45 to 935), and some formatting differences. Therefore, the new structure includes the following: (1) updates to all commands that read in files or specifically subset data frames by column number or something related to old file structure; (2) increases generality of simulations to account for additional possible outcomes and interactions among land categories and scenarios for each stage in the simulation (e.g. all available area in a given region-ownership combination can be in restoration which freezes land cover conversions, or there are missing land types in a given region), which would otherwise cause errors (e.g. due to negative new areas); (3) updates the final summary section to include new outputs based on the new spatial structure of input files (i.e. each summary output sheet in the .xls file now includes summary rows that aggregate across regions (all land), land types (all regions) and all California land).

2. Adds a test that checks if all management areas in scenario file exist in initial areas, and stops CALAND.r if not true prints an error message for user.

3. Partitions net C emission from wood decay in landfills into CO2-C and CH4-C (previously only CO2-C) based on (1) fraction of C emissions from anaerobic decay (0.71) from IPCC waste model; (2) CH4 production from anaerobic decay (0.5) from IPCC; (3) CH4 emissions based on ARB equation 89, using C filter technology; and (4) CO2-C emissions is the difference between net C emissions and CH4-C emissions.

4. Updates routine that partitions C emissions from biomass burning for bioenergy to include California-specific boiler emission data, as well as data on C concentrations in particulate matter (PM) which is the source of black carbon (BC) emissions (previously based on Liu et al. 2014). Specifically, the proportion of CO2, CH4, and PM2.5 and PM10 emissions are now based on normalized California-specific emissions factors for forest biomass boilers (Carreras-Sospedra, 2015), and BC-C% in each PM fraction based on small pile burn data (Jenkins, 1996).

   CO2C_energy_frac <- 0.9994 CH4C_energy_frac <- 0.0001 BCC_energy_frac <- 0.0005

5. Updates emission factors for CO2, CH4, and BC for pile burns and wildfire (previously Liu et al, 2014) based on small pile burn date from Jenkins et al (1996).

   CO2C_fire_frac <- 0.9952 CH4C_fire_frac <- 0.0021 BCC_fire_frac <- 0.0027

6. Adds additional output sheets to .xls file that further breaks down and/or aggregates annual and cumulative GHG outputs. Specifically, there are now the following output sheets for land-atmosphere C gas exchange: Total C Emissions

   • Eco_CumGain_C_stock
   • Total_Atmos_CumGain_C_stock
   • Manage_Atmos_CumGain_C_stock
   • Fire_Atmos_CumGain_C_stock
   • LCC_Atmos_CumGain_C_stock
   • Wood_Atmos_CumGain_C_stock
   • Total_CumEnergy2Atmos_C_stock
   • (same as above for annual) C Emissions by source:
   • Manage_Atmos_CumGain_FireC
   • Manage_Atmos_CumGain_EnergyC
   • Manage_Atmos_CumGain_NonBurnedC
   • Fire_Atmos_CumGain_BurnedC
   • Fire_Atmos_CumGain_NonBurnedC
   • LCC_Atmos_CumGain_EnergyC
   • LCC_Atmos_CumGain_NonBurnedC
   • (same as above for annual) C Emissions by source and GHG species:
   • Eco_CumCO2
   • Eco_CumCH4eq
   • ManEnergy_CumCO2
   • ManEnergy_CumCH4eq
   • ManEnergy_CumBCeq
   • ManFire_CumCO2
   • ManFire_CumCH4eq
   • ManFire_CumBCeq
   • ManNonBurned_CumCO2
   • LCCEnergy_CumCO2
   • LCCEnergy_CumCH4eq
   • LCCEnergy_CumBCeq
   • LCCNonBurned_CumCO2
   • TotalEnergy_CumCO2
   • TotalEnergy_CumCH4eq
   • TotalEnergy_CumBCeq
   • Wildfire_CumCO2
   • Wildfire_CumCH4eq
   • Wildfire_CumBCeq
   • Wood_CumCO2
   • Wood_CumCH4eq
   • (same as above for annual) Total GWP Emissions by GHG species:
   • Total_CumCO2
   • Total_CumCH4eq
   • Total_CumBCeq
   • (same as above for annual) Total GWP Emissions:
   • TotalWood_CumCO2eq_all
   • TotalEnergy_CumCO2eq_all
   • TotalFire_CumCO2eq_all
   • TotalBurn_CumCO2eq_all
   • TotalNonBurn_CumCO2eq_all
   • Total_CumCO2eq_all
   • (same as above for annual)

(continued below)

[msimmond]

Addendum to new features added to this topic branch:

7. (issue #5) New arguments were added to CALAND() so that C density and C accumulation input statistics could be specified separately and in any combination (i.e. mean, + standard deviation, - standard deviation, min, max, standard error). This allows for individual sensitivity analyses of C density and C accumulation (as well as any other combination of statistics for each). Additionally, a routine was setup that determines the combination of statistics and applies it to a unique output filename.

8. A new routine tracks the land categories that are depleted of soil c in the eco c density section (i.e. have negative soil C density and area greater than 0). The data associated with these cases is saved as a .csv at the end of annual loop, which includes land_cat_ID, year, ownership, land type, total area and neg c density associated with it. The filename also includes the value of total negative C cleared across all years (sum of neg c dens * tot area).

9. (issue #13) The implementation of afforestation was changed from an annual change relative to the initial (2010) area, to a direct prescribed annual area change. This is the same as the addition of annual restoration area in meadows and marshes.