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Recent Releases of OBI

OBI - v4.2.3

Changed

  • Rename organization of repo to nmi-agro

Consumption - Agriculture and Nutrition - R
Published by SvenVw 4 months ago

OBI - v4.2.2

What's Changed

Consumption - Agriculture and Nutrition - R
Published by BrentWHR 4 months ago

OBI - Version 4.2.1

Added

  • Adds GitHub action to check the package on R-hub

Fixed

  • Fixes external link at obic_water_functions

Consumption - Agriculture and Nutrition - R
Published by SvenVw 5 months ago

OBI - Version 4.2.0

What's Changed

Added

  • Function ind_gw_target() to modify I_H_GWR (renamed to I_E_GWR) with a correction factor based on
    soiltype and groundwaterclass akin to the groundwaterrecharge score from BBWPC.

Changed

  • Argument useClassicOBI is added to obi_field(), obi_field_dt(), and obi_farm().
    This argument defaults to TRUE, when TRUE, only agronomic indicators are calculated
    and aggregated. When FALSE, water-related indicators (groundwater recharge,
    pesticide leaching, and nitrogen use efficiency in relation to groundwater
    and surface water) are included in the environmental score and subsequently in
    the total score.
  • When useClassicOBI = FALSE, indicators for water quality and quantity (
    I_E_GW_NLEA, I_E_SW_NLEA, I_E_PEST, and I_E_GWR) are included in the
    calculation of S_E_OBI_A.
  • B_DRAIN no longer has a default value and must be supplied when useClassicOBI = FALSE
  • M_GREEN is set to TRUE for potato and maize on sandy soils by add_management(). This
    means that M_GREEN is overwritten for such cultivations when using one of the wrapper
    functions.
  • renamed I_H_NGW to I_E_GW_NLEA
  • renamed I_H_NSW to I_E_SW_NLEA
  • renamed I_H_PEST to I_E_PEST
  • renamed I_H_GWR to I_E_GWR
  • renamed I_E_NGW to I_E_GW_NRET, I_E_NGW is still part of the obic_field() and
    obic_farm() outputs but its use is deprecated, switch over to I_E_GW_NRET
  • renamed I_E_NSW to I_E_SW_NRET, I_E_NSW is still part of the obic_field() and
    obic_farm() outputs but its use is deprecated, switch over to I_E_SW_NRET
  • calc_psp() no longer changes makkink factors for specific months in a rotation.
    Instead, makkink factors are adjusted within a single year. For example, if in 2015
    potato is grown followed by a green manure and grassland in 2016, the makkink factors
    in 2015 for months 1,2 3, 10, 11, and 12 are set to 0.6 (even tough the green manure
    partially grows in 2016). One can now indicate in which months a green manure is
    grown, default is from 10 up to and including 3. Lastly, the makkink factor for green
    manure is only set to 0.6, and only when this is higher than the non-green manure
    factor. The makkink factor for month 10 used to be 0.74
  • Introduced argument B_AREA_DROUGHT for obic_field() and as possible column in
    obic_field_dt() and obic_farm(). This argument is passed on to ind_gw_recharge()
    which is only called when useClassicOBI == FALSE. When B_AREA_DROUGHT is missing
    but required, it is assigned a value in by obic_field() based on B_SOILTYPE_AGR
    and B_AER_CBS whilst raising a warning.

Fixed

  • B_FERT_NORM_FR and B_DRAIN can now be supplied when using obic_field_dt() or
    obic_farm(). The value is set to 1 when not supplied.

OBIC 4.1.0 2025-08-04

Added

  • BRP crop codes for 2025: 7137, 7138, 7135, 7134

Consumption - Agriculture and Nutrition - R
Published by BrentWHR 6 months ago

OBI - Version 4.0.0

What's Changed

BREAKING CHANGES

Changed

  • the format of groundwater class values (B_GWL_CLASS) that are accepted by OBIC
    functions and recorded in OBIC tables. Acceptable input values for B_GWL_CLASS are now:
    "I", "Ia", "Ic", "II", "IIa", "IIb", "IIc", "III", "IIIa", "IIIb", "IV",
    "IVc", "IVu", "sV", "sVb", "V", "Va", "Vad", "Vao", "Vb", "Vbd", "Vbo", "VI",
    "VId", "VII", "VIId", "VIII", "VIIId", "VIIIo", "VIIo", "VIo".
  • OBIC no longer supports B_GWL_CLASS value "-". For fields with groundwater class "-", the user is advised to use expert judgment on
    what the most suitable groundwater class is. Fields with "-" are typically found
    in locations with very variable or very deep groundwater levels such as flood plains
    or hills.
  • In the table nleach_table, column B_GT is renamed B_GWL_CLASS for consistency.
    The values in this column have also been modified to no longer have the prefix "Gt"
    to align with the rest of the package.
  • In the table waterstress.obic, column gt is renamed B_GWL_CLASS for consistency.
    The values in this column have also been modified to no longer have the prefix "Gt"
    to align with the rest of the package.

Added

  • The table waterstress.obic now supports more groundwaterclasses. Classes such as
    IIIb are now included in waterstress.obic$B_GWL_CLASS. The new classes with
    prefixes and suffixes have the same values as rows with the same roman numeral.
    So, with the same cropname and soilunit, III and IIIb have the same values for
    the different stresses.
  • additional B_GWL_CLASS values to nleach_table ("Ia", "Ic", "IIa", "IIc", "IIIa",
    "IVu", "IVc", "Va", "Vao", "Vad", "Vbo", "Vbd", "sV", "sVb", "VIo", "VId", "VIIo", "VIId", "VIIIo", "VIIId")

Removed

  • function format_gwt(). OBIC now supports groundwater classes with prefixes and suffixes.
    For fields with groundwater class "-", the user is advised to use expert judgment on
    what the most suitable groundwater class is. Fields with "-" are typically found
    in locations with very variable or very deep groundwater levels such as flood plains
    or hills.

Consumption - Agriculture and Nutrition - R
Published by BrentWHR 11 months ago

OBI - Version 3.0.3

OBIC 3.0.3 2024-08-12

Added

  • Adds the new cultivations from 2024 [PL-33]

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 2 years ago

OBI - Version 3.0.2

Fixed

  • Fixes error in validation of B_LU_BRP by enabling calculations with brp codes of 2023 [OBI-28]
  • Fixes classification of grasland met/zonder herinzaai in crops.obic

Changed

  • B_LU_WATERSTRESS_OBIC of 265 (grasland blijvend), 331, and 3718 from 'grasland met herinzaai' to 'grasland zonder herinzaai' in crops.obic

Removed

  • Removes urls to bodemconsult.nl due to invalid SSL certificate, which is not accepted by CRAN

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 2 years ago

OBI - Version 2.0.4

Fixed

  • Fixes calculation of field capacity at calc_waterretention

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 3 years ago

OBI - Version 2.0.3

Fixed

Fixes plotting of regime curve in workability vignette #149

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 3 years ago

OBI - Version 2.0.1

Changed

  • The function ind_sulpher is renamed to ind_sulfur in documentation

Added

  • all functions are extended with examples and return

Changed

  • standardize output variables of pedotransfer parameters Wosten

Fixed

  • Fixes many spelling errors in the documentation
  • Set title in decription to title case
  • Fix links to external websites
  • Fix duplicated indicator in recom.obic (in dev/ppr_maatregel.r), issue #164
  • Fix setorder after merge in calc_n_effieciency
  • Fix setorder after merge in calc_som_balance

Removed

  • Removes /docs as the documentation website is now automatically generated by GitHub Actions

Deprecated

  • The function ind_sulpher is deprecated due to renaming

Consumption - Agriculture and Nutrition - R
Published by SvenVw about 4 years ago

OBI - Version 2.0.2 paper edition

Special version to freeze the code used for the paper: An Open Soil health assessment framework facilitating sustainable soil management

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 4 years ago

OBI - Version 2.0.0

Added

  • Add ppr_bouwplan_tables.R in dev/scripts
  • Add merge_nema_tables.R in dev/scripts
  • Add ppr_crops_crumbleability.R in dev/scripts
  • Add arguments B_GWL_GHG, B_GWL_GLG and B_Z_TWO to obic_field and obic_field_dt
  • Activate calc_workability
  • Add calc_makkink to add makkink factors to crop table
  • Add calc_psp to estimate precipitation surplus
  • Add ind_nematodes and ind_nematodes_list to estimate the index for nematode risks
  • Add ind_gw_recharge to estimate the groundwater recharge index
  • Add calc_n_efficiency and ind_n_efficiency to estimate N efficiency
  • Add calc_pesticide_leaching and ind_pesticide_leaching to evaluate retention of pesticides in topsoil
  • Add check to ppr_weight_obic to check if all indicators in weight.obic occur in column_descriptions_obic
  • Add vignette obic_workability, describing how workability is calculated and affected by its input variables
  • Add vignette obic_introduction as a short tutorial describing the OBIC principles
  • Add vignette obic_score_aggregation to illustrate the aggregation principles used
  • Add table weather.obic with monthly mean precipitation, temperature and evaporation
  • Add table crops.makkink with mean Makkink factors per crop type
  • Add table nema.crop.rot.obic added with crop sensitivity for nematodes
  • Add table nema.obic with treshold values per species
  • Add GitHub Action to run R-CMD-Check for changes on master and development
  • Add coverage of unit tests

Changed

  • Update documentation for workability
  • Update weight.obic for workability
  • Update column_descriptions_obic.Rdata
  • Update documentation for nematodes
  • Update calc_workability
  • Rename B_Z_TWO to B_GWL_ZCRIT
  • Improve function description of ind_workability
  • Increase required days post GLG for maize on sand or loess to match October 1
  • Increase required days post GLG for maize on other soils to match October 20
  • season.obic can now be merged on both landuse and soiltype
  • Update binnenveld with BodemSchat data (via OBIC-helpers)
  • obic_field can be used for multiple fields with field-ID

Removed

  • Removes A_COM_FR and A_CACO3_IF from input as they were not used #145

Fixed

  • Error in grass_age: age was incorrectly estimated for multiple fields
  • Removed negative values from season.obic
  • Ensured total_days >= req_days_pre_glg + req_days_post_glg in season.obic
  • Root depth was incorrectly assigned for maize and nature
  • Fix the format of NEWS.md so that it is shown on the package website
  • Remove the prefixes and suffixed of B_GWL_CLASS

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 4 years ago

OBI - Version 1.0.4

Added

  • Check on column names in obic_field_dt
  • tests on obic_field_dt

Fixed

  • Fixed check on required column names in obic_field_dt

Consumption - Agriculture and Nutrition - R
Published by gerardhros over 4 years ago

OBI - Versie 1.0.3

Version 1.0.3 2021-09-16

Added

  • Adds unit test for obic_field

Removed

  • Removes A_COM_FR and A_CACO3_IF from input as they were not used #145

Fixed

  • Fixes ascii signs issues

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 4 years ago

OBI - Versie 1.0.2

Version 1.0.2 2021-05-20

Added

  • ind_man_ess.R and tests are added for update aggregated management scores, issue #131

Changed

  • obic_field() makes use of ind_man_ess

Consumption - Agriculture and Nutrition - R
Published by gerardhros about 5 years ago

OBI - Version 1.0.1

Added

  • management.obic table added to link management measures to ecosystem services
  • calc_man_ess.R and tests are added to estimate grouped impact of management on ecosystem servcices, issue #125

Changed

  • I_M_* and I_*_BCS indicators for management measures and BCS are removed, issue #126
  • values -999 are replaced by NA
  • column_descriptons_obic.Rdata is updated
  • weight.obic is updated

Consumption - Agriculture and Nutrition - R
Published by SvenVw about 5 years ago

OBI - Version 1.0.0

Added

  • column crops_season to crops.obic
  • column scientific_names to crops.obic
  • preparation crops.obic in dev
  • function format_gwt to reformat input for groundwater table
  • function format_soilcompaction to reformat input for subsoil compaction
  • season.obic added as data.table
  • new function and tests for workability indicator
  • nema.obic added as data.table
  • new function and tests for nematode indicator
  • preparation nema.obic in dev
  • preparation season.obic in dev
  • obic_field is added to run obic score for one field
  • ppr_column_description plus column_descriptons_obic.Rdata
  • ppr_maatregel plus recom_obic.Rdata
  • ppr_weights plus weights.obic
  • I_P_DS and I_P_WS added (drought and wetness stress separately)
  • add_management added to estimate default values for measures when not given
  • set of eight I_M_XX indicators for measures are added
  • set of nine I_X_BCS indicators are added (optional)
  • new M_codes added: M_LIME, M_NONINVTILL, M_SSPM, M_SOLIDMANURE,M_STRAWRESIDUE, M_MECHWEEDS, M_PESTICIDES_DST, issue #107
  • obic_field_dt to run obic_field() for a data.table input

Changed

  • calculation PBI updated for grassland
  • PBI input is flexible for both grassland and arable
  • calculation SLV updated
  • update element_names for A_P_CC, A_P_AL in phosphate_availability.R
  • update element_names for A_S_RT, A_SOM_LOI, B_AER_CBS, B_SOILTYPE_AGR in sulpher.R
  • update element_names for B_GWL_CLASS in wateravailability.R
  • update element_names for B_GWL_CLASS and B_AER_CBS in nretention.R
  • correct weighing for S_C_A
  • all element names are updated to english ones
  • weighing for score calculated is changed into a more generic approach
  • structure for running obi is changed into one function
  • weights.obic is extended and used to distinguish for relevant/non-relevant indicators
  • grass_age function is updated: count actual years
  • BCS is optional input, and when given it overwrite risk indicators compaction / aggregate stability
  • M codes for no advice, issue #62
  • directory dev is updated and cleaned, issue #104
  • lower and upper limits for soil properties updated
  • allow unknown B_HELP_WENR in checkmate water_availability, issue 65
  • very low Mg indicator values for maize are changed, plus tests updated
  • very low Mg indicator values for grassland on clay and peat, issue 84
  • evaluation and calculation for Cu are updated

Fixed

  • setorder in winderodibility

Consumption - Agriculture and Nutrition - R
Published by SvenVw about 5 years ago

OBI - Version 0.11.1

Version 0.11.1 2020-09-02

Changed

  • The water holding capacity is now between 0 and 1 (as theta should be) and uses new evaluation function #67
  • Lower range of D_NLV is set to -30
  • Upper range of D_MG is set to 1000
  • Range of D_P_DU is set between 0 and 1

Fixed

  • Fixed the use of B_LG_CBS at sulphur
  • ID can now also be character and does not have to be numeric #66

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 5 years ago

OBI - Version 0.11.0

Added

  • Adds two other pedotransfer functions (PTFs) to calculate water retention parameters #53

Changed

  • Optimal pH values of grassland are now the middle value of the class good #55
  • pF of field capacity is changed from 2.2 to 2.0 #53
  • Bulk density in the default PTF is now aggregated into 1 continous function #53
  • Parameters of evaluation for PAW are adjusted #53
  • Parameters for the evaluation of sealing are adjusted #57
  • Changes the formula to calculate nitrogen leaching and run-off #58
  • Parameters for the evaluation of nretention are adjusted #58
  • Paramaters and funs for CEC are updated and split for soil fertility and aggregate stability #59
  • Parameters for the evaluation of Cu availability are adjusted #59
  • potassium index is multiplied so that the evaluation is equal for grass and maize #60

Fixed

  • Improved the function for crumbleability to match the factsheet #54 #56
  • Fix error in calc_potassium_availability #59

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 6 years ago

OBI - Version 0.10.0

Version 0.10.0 2019-12-13

Added

  • Adds the evaluation of measures #37
  • Adds giving recommendations based on the OBI score #37
  • A relative score per reference group is added #31
  • Adds the leaching of nitrogen to surface water and groundwater #17
  • Adds a table with the description of the columns and a vignette about it #46
  • Adds scoring for environmental performance #31

Changed

  • Update of crumbeability groups in crops.obic
  • Maximum value of A_MN_CC is increased from 30000 to 250000
  • The code for evaluating in ind_crumbeability is simplified
  • M_M10 user input changed in D_CP_RUST input, plus comments added #29
  • new table with weighing factors included 'weight.obic' #32
  • weighing factors updated in obic_indicators.R #32
  • Improved the zinc indicator function #39
  • The evaluation function for sulphur on maize and grass is updated #40
  • The management function is improved, especially for maize #38
  • The maximum score of ind_management is adjusted #38
  • The parameter values for sulphur on arable land is adjusted #41
  • The optimal pH for grassland depends now on organic matter content and presence of clover #42
  • The score aggragation is now 60% average of last 4 years and 40% of older years #31
  • The maximum value for D_CR is limited to 10 #47
  • The parameters for the evaluation for I_C_K is set to the same as grassland #51
  • The evaluation for I_C_N is now split into grassland and arable land #50
  • Set lifecyle status to maturing
  • The evaluation of I_C_MG is adjusted according to factsheet

Fixed

  • Preprocessing, indicators and scores make use of internal copy of the table now rather than referencing to an object outside the scope of the function
  • Fixed the droughtstress, wetnessstress and waterstress values for GtI in waterstress.obic
  • For grasslands on peat pr clay, the D_MG is now scaled #51
  • Limit D_SLV between -30 and 250

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 6 years ago

OBI - Version 0.9.0

Version 0.9.0 2019-10-22

Changed

  • The uppper limit for D_BCS is increased from 40 to 50
  • Switch on crumbleability
  • For calc_phosphate_availability the category arable is added for the crop categories
  • Changed evaluation of sulphur for arable fields #26

Fixed

  • Fixed typo if mais in ind_managment
  • Fixed test for winderodibility
  • Use the correct correction factor in calc_sealing_risk #19
  • Fix for calculating I_P_CEC #24
  • Fix for calculating difficult values in calc_sombalance #25
  • Fix for calc_sbal_arable where combinations of soil type and region that do not exist in table 6.2 of Handboek Bodem & Bemesting gave a NA #26
  • Fix for calc_bcs where a value of 1 is given instead of 0 for bcs_om #28

Consumption - Agriculture and Nutrition - R
Published by SvenVw over 6 years ago

OBI - Version 0.8.0

Version 0.8.0 2019-08-02

Added

  • Adds index and evaluation of the BodemConditieScore
  • Adds potassium to main functions
  • Adds a random recommondation to the output

Changed

  • The upper limit for A_MN_CC is increased from 20000 to 30000
  • The upper limit for A_CA_CEC is increased from 100 to 400

Fixed

  • The indicator of pH had the wrong direction
  • Removed the minus sign before ind_zinc
  • The function calc_potassium_availability containted a wrong column name for A_PH_CC
  • Some unknown situations at calc_potassium_availability have now the same values as comparable situations. This should be looked at later

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 7 years ago

OBI - Version 0.7.0

Version 0.7.0 2019-08-02

Added

  • Adds index and evaluation of waterretention paramaters
  • Adds index and evaluation of water related yield stress
  • Adds index and evaluation of metals (Zn and Cu)
  • Adds index and evaluation of microbial activity (PMN)
  • Adds index and evaluation of CEC for soil fertility and structure
  • Adds waterstress.obic table with information of HELP-tables

Changed

  • Change crops.obic with crop category related to water stress

Consumption - Agriculture and Nutrition - R
Published by gerardhros almost 7 years ago

OBI - Version 0.6.0

Version 0.6.0 2019-08-01

Added

  • Adds index and evaluation of K-availability

Consumption - Agriculture and Nutrition - R
Published by gerardhros almost 7 years ago

OBI - Version 0.5.0

Version 0.5.0 2019-07-31

Added

  • Adds crop classification (sensitivity to P, K and S supply)
  • Adds soil organic matter balance (simple one)
  • Adds risk for soil compaction (following risk map Van den Akker, 2013)
  • Adds index and evaluation of Mg-availability
  • Adds index and evaluation of S-availability (evaluation function need still to be parameterized)
  • Adds index and evaluation of winderodibility
  • Adds index and evaluation of soil strategic management (following Label Duurzaam Bodembeheer)
  • Adds columns crop_eos and crop_eos_residue in crops.obic

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 7 years ago

OBI - Version 0.4.0

Version 0.4.0 2019-07-26

Added

  • The existing functions for pH, P, N, crumbleability, sealing and resistance are intergrated into obic()

Changed

  • The column name brp is changed to B_LU_BRP

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 7 years ago

OBI - Version 0.3.0

Version 0.3.0 2019-07-24

Added

  • Adds main function that wraps all the functions needed to calculated the OBI score and recommendations
  • Adds documentation website for package using pkgdown #3

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 7 years ago

OBI - Version 0.2.0

Version 0.2.0 2019-07-12

Added

  • Adds evaluation of pH #1
  • Adds evaluation of nitrogen #2

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 7 years ago

OBI - Version 0.1.0

Version 0.1.0 2019-07-08

First version of OBIC

Consumption - Agriculture and Nutrition - R
Published by SvenVw almost 7 years ago