Package: OBIC 4.3.0

Sven Verweij

OBIC: Calculate the Open Bodem Index (OBI) Score

The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices. The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI. More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.

Authors:Sven Verweij [aut, cre], Gerard Ros [aut], Yuki Fujita [aut], Wilbrand Hendrik Riechelman [aut], Kees van den Dool [aut], Job de Pater [ctb], Nutriënten Managment Instituut [cph]

OBIC_4.3.0.tar.gz
OBIC_4.3.0.tar.gz(r-4.7-any)OBIC_4.3.0.tar.gz(r-4.6-any)
OBIC_4.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OBIC/json (API)

# Install 'OBIC' in R:
install.packages('OBIC', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nmi-agro/open-bodem-index-calculator/issues

Datasets:
  • binnenveld - Example dataset for use in OBIC package
  • bouwsteen_tb - Table with water retention properties of 'bouwstenen'
  • 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
  • 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
  • recom.obic - Applicability range of measures, including literature based estimates, of effects on soil indicators
  • recom.obic_bkp - Effects of measures 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

On CRAN:

Conda:

4.38 score 1 stars 24 scripts 345 downloads 82 exports 3 dependencies

Last updated from:e63d685712. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK202
source / vignettesOK259
linux-release-x86_64OK185
wasm-releaseOK125

Exports:add_managementcalc_aggregatestabilitycalc_bcscalc_bulk_densitycalc_ceccalc_copper_availabilitycalc_cropclasscalc_crumbleabilitycalc_grass_agecalc_magnesium_availabilitycalc_makkinkcalc_man_esscalc_managementcalc_n_efficiencycalc_nleachcalc_nlvcalc_organic_carboncalc_permeabilitycalc_pesticide_leachingcalc_ph_deltacalc_phosphate_availabilitycalc_pmncalc_potassium_availabilitycalc_pspcalc_root_depthcalc_rotation_fractioncalc_sbal_arablecalc_sealing_riskcalc_slvcalc_sombalancecalc_waterretentioncalc_waterstressindexcalc_winderodibilitycalc_workabilitycalc_zinc_availabilitycf_ind_importanceevaluate_logisticevaluate_parabolicformat_aerformat_soilcompactionind_aggregatestabilityind_bcsind_cecind_compactionind_copperind_crumbleabilityind_gw_rechargeind_gw_targetind_magnesiumind_man_essind_managementind_n_efficiencyind_nematodesind_nematodes_listind_nitrogenind_nretentionind_permeabilityind_pesticide_leachingind_phind_phosphate_availabilityind_pmnind_potassiumind_pspind_resistanceind_sealingind_sulfurind_sulpherind_waterretentionind_waterstressindexind_winderodibilityind_workabilityind_zincobic_evalmeasureobic_farmobic_fieldobic_field_dtobic_recommendationsobic_recommendations_bkppF_curvepFpara_classpFpara_ptf_Wosten1999pFpara_ptf_Wosten2001

Dependencies:backportscheckmatedata.table

Note on OBI score aggregation
Introduction | Aggregation | Pre-processing | Aggregation within category | Aggregation over years | Aggregation to single OBI score | Brief recap | Comparison with other aggregation methods | Data description | Correction factors | Effects of different aggregation method on OBIC total score | Effects of aggregating categories on OBIC total score | Alternative aggregation methods on Binnenveld fields | Aggregation in other soil quality assessment frameworks | References
Rendered fromobic_score_aggregation.Rmdusingknitr::rmarkdown

Last update: 2026-01-30
Started: 2022-04-05

The Open Soil Index
nocite: |@Rinot2019, @Bunemann2018, @R-base, @R-data.table, @R-ggplot2, @R-OBIC, @R-patchwork | 1. introduction | Background | The Open Soil Index Framework | 2. The Open Soil Index Calculator (OBIC) | Data: Binnenveld | Running OBIC for a single field | The Soil Functions in the OBIC | General supporting soil properties | Estimate bulk density | Estimate other general properties | Calculate series of chemical soil functions | Nitrogen supplying capacity | Phosphorus Availability Index | Potassium supply | Sulfur supply | Magnesium supply | Copper supply | Zinc supply | Soil Acidity | Soil Cation Buffering | Calculate series of physical soil functions | Water Stress due to drought or wetness | Sealing Soil Surface and Wind Erodibility | Aggregate Stability and Crumbleability | Subsoil compaction | Visual Soil Assessment | Water retention in topsoil | Calculate series of biological soil functions | Potentially mineralizable nitrogen | Disease resistance | Earthworm density | Calculate series of environmental soil functions | N retention preventing N leaching | N retention preventing N runoff | Evaluate Soil Management | Measures | Crop rotation and SOM balance | Recommendations | Integrating Soil Functions into OBIC scores | Evaluating soil functions | Crop and soil dependent applicability of functions | Aggregated indicators per category | Integrating over time | Holistic OBI score | Some examples of outputs | References
Rendered fromobic_introduction.Rmdusingknitr::rmarkdown

Last update: 2026-01-30
Started: 2022-04-05

Description of the OBI-water functions
nocite: |@Groenendijk2016, @Tiktak2006, @CommissieDeskundigenMeststoffenwet2017, @Wosten2001, @Geurts2021, @TNO1988 | Intorduction | Ground water recharge | Precipitation surplus and unsaturated permeability | Nitrogen use efficiency | Pesticide leaching | References
Rendered fromobic_water_functions.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2023-10-19

Workability illustration
OBI-workability | B_GWL_ZCRIT | References
Rendered fromobic_workability.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2022-04-05

Description of the columns for OBIC
Rendered fromdescription-of-the-columns.Rmdusingknitr::rmarkdown

Last update: 2022-04-05
Started: 2022-04-05

Readme and manuals

Help Manual

Help pageTopics
Estimate default values for managementadd_management
Example dataset for use in OBIC packagebinnenveld
Table with water retention properties of 'bouwstenen'bouwsteen_tb
Calculate aggregate stability index based on occupation CECcalc_aggregatestability
Calculate the BodemConditieScorecalc_bcs
Calculate the bulk densitycalc_bulk_density
Calculate a soil fertility index based on the CECcalc_cec
Calculate the availability of the metal Cucalc_copper_availability
Determine classification rules for crops used to prepare crops.obiccalc_cropclass
Calculate the crumbleabilitycalc_crumbleability
Calculate the average age of the grasscalc_grass_age
Calculate the capacity of soils to supply Magnesiumcalc_magnesium_availability
Add Makkink correction factors and crop cover to crop rotation tablecalc_makkink
Calculate the 'performance' of sustainable soil management given a required ecosystem servicecalc_man_ess
Calculate the 'performance' of sustainable soil managementcalc_management
Calculate nitrogen use efficiency and leaching based on N surpluscalc_n_efficiency
Calculate the N leachingcalc_nleach
Calculate the NLVcalc_nlv
Calculate amount of organic carboncalc_organic_carbon
Calculate the permeability of the top soilcalc_permeability
Calculate risk of pesticide leachingcalc_pesticide_leaching
Calculate the difference between pH and optimumcalc_ph_delta
Calculate the phosphate availability (PBI)calc_phosphate_availability
Calculate the index for the microbial biological activitycalc_pmn
Calculate the K availabilitycalc_potassium_availability
Calculate the precipitation surpluscalc_psp
Determine the root depth of the soil for this cropcalc_root_depth
Calculates the fraction in the crop rotationcalc_rotation_fraction
Calculate the indicator for delta S-balance arablecalc_sbal_arable
Calculate soil sealing riskcalc_sealing_risk
Calculate the SLVcalc_slv
Calculate simple organic matter balancecalc_sombalance
Calculate indicators for water retention in topsoilcalc_waterretention
Calculate the Water Stress Indexcalc_waterstressindex
Calculate indicator for wind erodibilitycalc_winderodibility
Calculate indicator for workabilitycalc_workability
Calculate the availability of the metal Zinccalc_zinc_availability
Helper function to weight and correct the risk and scorescf_ind_importance
Column description for the OBICcolumn_description.obic
Makkink correction factor tablecrops.makkink
Linking table between crops and different functions in OBICcrops.obic
Coefficient table for evaluating crumbleabilityeval.crumbleability
Evaluate using the general logistic functionevaluate_logistic
Evaluate using parabolic function withevaluate_parabolic
Convert possible B_AER_CBS values to standardized valuesformat_aer
Convert possible B_SC_WENR values to standardized valuesformat_soilcompaction
Calculate the indicator aggregate stabilityind_aggregatestability
Calculate the indicator for BodemConditieScoreind_bcs
Calculate the indicator for soil fertility given the CECind_cec
Calculate indicator for subsoil compactionind_compaction
Calculate the indicator for Cu-availabilityind_copper
Calculate the indicator for crumbleabilityind_crumbleability
Calculate groundwater recharge of a soilind_gw_recharge
Modify a groundwater recharge indicator with a targetind_gw_target
Calculate the indicator for Magnesiumind_magnesium
Calculate the indicator for sustainable management given a required ecoystem serviceind_man_ess
Calculate the indicator for sustainable managementind_management
Calculate an indicator value for nitrogen use efficiency and leaching based on N surplusind_n_efficiency
Calculate indicator for plant parasitic nematodesind_nematodes
Calculate indicator for plant parasitic nematodesind_nematodes_list
Calculate the indicator for NLVind_nitrogen
Calculate the indicator for N retention for groundwater or surface waterind_nretention
Calculate the indicator score for the permeability of the top soilind_permeability
Calculate an indicator score for pesticide leachingind_pesticide_leaching
Calculate the indicator for pHind_ph
Calculate the indicator for the the phosphate availabilityind_phosphate_availability
Calculate the indicator for microbial biological activityind_pmn
Calculate the indicator for Potassium Availabilityind_potassium
Calculate indicator for precipitation surplusind_psp
Calculate indicator for soil resistanceind_resistance
Calculate the soil sealing indicatorind_sealing
Calculate the indicator for SLVind_sulfur
Calculate the indicator for SLV (deprecated)ind_sulpher
Calculate indicator for Water Retention indexind_waterretention
Calculate the Water Stress Indexind_waterstressindex
Calculate indicator for wind erodibilityind_winderodibility
Calculate indicator for workabilityind_workability
Calculate the indicator for Zn-availabilityind_zinc
Relational table linking soil management measures to ecosystem servicesmanagement.obic
Damage and reproduction of soil-borne pathogens and pests on cropsnema.crop.rot.obic
Nematode tablenema.obic
Table with fractions of excess N which runs off to groundwater and surface waternleach_table
Evaluate effects of measuresobic_evalmeasure
Calculate the Open Bodem Index score for a series of fields belonging to a farmobic_farm
Calculate the Open Bodem Index score for one fieldobic_field
Calculate the Open Bodem Index score for a data tableobic_field_dt
Recommend measurements for better soil managementobic_recommendations
Recommend measurements for better soil managementobic_recommendations_bkp
Water retention curvepF_curve
Parameter estimation based on class of Staringreeks (Tabel 3, Wosten 2001)pFpara_class
Estimate water retention curve parameters based on Wosten 1999pFpara_ptf_Wosten1999
Estimate water retention curve parameters based on Wosten 2001pFpara_ptf_Wosten2001
Applicability range of measures, including literature based estimates, of effects on soil indicatorsrecom.obic
Effects of measures on soil indicatorsrecom.obic_bkp
Desired growing season period for maximum yieldseason.obic
Linking table between soils and different functions in OBICsoils.obic
Table with optimal pH for different crop planstbl.ph.delta
Linking table between crops, soils, groundwater tables and water induced stresses in OBICwaterstress.obic
Weather tableweather.obic
Weight of indicators to calculate integrated scoresweight.obic