# Calculate the Open Bodem Index (OBI) Score

## Documentation for package ‘OBIC’ version 2.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_management | Estimate default values for management
binnenveld | Example dataset for use in OBIC package
bouwsteen_tb | Table with water retention properties of 'bouwstenen'
calc_aggregatestability | Calculate aggregate stability index based on occupation CEC
calc_bcs | Calculate the BodemConditieScore
calc_bulk_density | Calculate the bulk density
calc_cec | Calculate a soil fertility index based on the CEC
calc_copper_availability | Calculate the availability of the metal Cu
calc_cropclass | Determine classification rules for crops used to prepare crops.obic
calc_crumbleability | Calculate the crumbleability
calc_grass_age | Calculate the average age of the grass
calc_magnesium_availability | Calculate the capacity of soils to supply Magnesium
calc_makkink | Add Makkink correction factors and crop cover to crop rotation table
calc_management | Calculate the 'performance' of sustainable soil management
calc_man_ess | Calculate the 'performance' of sustainable soil management given a required ecosystem service
calc_nleach | Calculate the N leaching
calc_nlv | Calculate the NLV
calc_n_efficiency | Calculate nitrogen use efficiency and leaching based on N surplus
calc_organic_carbon | Calculate amount of organic carbon
calc_pesticide_leaching | Calculate risk of pesticide leaching
calc_phosphate_availability | Calculate the phosphate availability (PBI)
calc_ph_delta | Calculate the difference between pH and optimum
calc_pmn | Calculate the index for the microbial biological activity
calc_potassium_availability | Calculate the K availability
calc_psp | Calculate the precipitation surplus
calc_root_depth | Determine the root depth of the soil for this crop
calc_rotation_fraction | Calculates the fraction in the crop rotation
calc_sbal_arable | Calculate the indicator for delta S-balance arable
calc_sealing_risk | Calculate soil sealing risk
calc_slv | Calculate the SLV
calc_sombalance | Calculate simple organic matter balance
calc_waterretention | Calculate indicators for water retention in topsoil
calc_waterstressindex | Calculate the Water Stress Index
calc_winderodibility | Calculate indicator for wind erodibility
calc_workability | Calculate indicator for workability
calc_zinc_availability | Calculate the availability of the metal Zinc
cf_ind_importance | Helper function to weight and correct the risk and scores
column_description.obic | Column description for the OBIC
crops.makkink | Makkink correction factor table
crops.obic | Linking table between crops and different functions in OBIC
eval.crumbleability | Coefficient table for evaluating crumbleability
evaluate_logistic | Evaluate using the general logistic function
evaluate_parabolic | Evaluate using parabolic function with
format_aer | Convert possible B_AER_CBS values to standardized values
format_gwt | Convert possible B_GWL_CLASS values to standardized values
format_soilcompaction | Convert possible B_SC_WENR values to standardized values
ind_aggregatestability | Calculate the indicator aggregate stability
ind_bcs | Calculate the indicator for BodemConditieScore
ind_cec | Calculate the indicator for soil fertility given the CEC
ind_compaction | Calculate indicator for subsoil compaction
ind_copper | Calculate the indicator for Cu-availability
ind_crumbleability | Calculate the indicator for crumbleability
ind_gw_recharge | Calculate groundwater recharge of a soil
ind_magnesium | Calculate the indicator for Magnesium
ind_management | Calculate the indicator for sustainable management
ind_man_ess | Calculate the indicator for sustainable management given a required ecoystem service
ind_nematodes | Calculate indicator for plant parasitic nematodes
ind_nematodes_list | Calculate indicator for plant parasitic nematodes
ind_nitrogen | Calculate the indicator for NLV
ind_nretention | Calculate the indicator for N retention for groundwater or surface water
ind_n_efficiency | Calculate an indicator value for nitrogen use efficiency and leaching based on N surplus
ind_pesticide_leaching | Calculate an indicator score for pesticide leaching
ind_ph | Calculate the indicator for pH
ind_phosphate_availability | Calculate the indicator for the the phosphate availability
ind_pmn | Calculate the indicator for microbial biological activity
ind_potassium | Calculate the indicator for Potassium Availability
ind_resistance | Calculate indicator for soil resistance
ind_sealing | Calculate the soil sealing indicator
ind_sulfur | Calculate the indicator for SLV
ind_sulpher | Calculate the indicator for SLV (deprecated)
ind_waterretention | Calculate indicator for Water Retention index
ind_waterstressindex | Calculate the Water Stress Index
ind_winderodibility | Calculate indicator for wind erodibility
ind_workability | Calculate indicator for workability
ind_zinc | Calculate the indicator for Zn-availability
management.obic | Relational table linking soil management measures to ecosystem services
nema.crop.rot.obic | Damage and reproduction of soil-borne pathogens and pests on crops
nema.obic | Nematode table
nleach_table | Table with fractions of excess N which runs off to groundwater and surface water
obic_evalmeasure | Evaluate effects of measures
obic_field | Calculate the Open Bodem Index score for one field
obic_field_dt | Calculate the Open Bodem Index score for a data table
obic_recommendations | Recommend measurements for better soil management
pFpara_class | Parameter estimation based on class of Staringreeks (Tabel 3, Wosten 2001)
pFpara_ptf_Wosten1999 | Estimate water retention curve parameters based on Wosten 1999
pFpara_ptf_Wosten2001 | Estimate water retention curve parameters based on Wosten 2001
pF_curve | Water retention curve
recom.obic | Applicability range of measures, including literature based estimates, of effects on soil indicators
season.obic | Desired growing season period for maximum yield
soils.obic | Linking table between soils and different functions in OBIC
tbl.ph.delta | Table with optimal pH for different crop plans
waterstress.obic | Linking table between crops, soils, groundwater tables and water induced stresses in OBIC
weather.obic | Weather table
weight.obic | Weight of indicators to calculate integrated scores