Changelog

Source: NEWS.md

OBIC 3.0.3 2024-08-12s2024-09-09

Added

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

OBIC 3.0.2 2024-02-092024-03-05

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

OBIC 3.0.1 2023-11-242023-12-12

Fixed

  • Fixes calculation of N surplus used for I_H_NGW and I_H_NSW

OBIC 3.0.0 2023-10-162023-10-19

Added

  • Add calc_permeability for calculating top soil permeability
  • Add ind_permeability for calculating the index for top soil permeability
  • Add variable leach_to to calc_n_efficiency and ind_n_efficiency to calculate and evaluate leaching to ground water and surface water
  • Add vignette obic_water_functions, describing the functions that evaluates the effect of soil quality on groundwater quality

Changed

  • Updated N use norms for onions
  • Update calc_nleach by soil and land use dependent default n supply, issue #154
  • Update calculations in the functions calc_pesticide_leaching, ind_pesticide_leaching, calc_psp, ind_psp, ind_gw_recharge,calc_n_efficiency and ind_n_efficiency
  • Add soil type and land use dependent NLV estimate in calc_nleach
  • In the input for ind_gw_recharge the variables B_LU_BRP, D_WRI_K, and B_GWL_CLASS are added, and D_WRI_WHC is removed
  • In calc_n_efficiency, D_NLV is removed from the input variables

Fixed

  • Fixes plotting of regime curve in workability vignette #149
  • Extremely high EOS values for some cultivations fixing #162 & #134
  • Updated bibliography of packages in vignettes
  • N use norm for 1935 (maiskolfsilage)
  • N use norms of 1926 and 1927 (agrarisch natuurmengsel and overige akkerbouwgewassen), increased to match “Akkerbouwgewassen, overig” (RVO, 2022)

OBIC 2.2.1 2023-10-16

Added

  • CITATION file and additional author data in the package DESCRIPTION

OBIC 2.2.0 2023-08-29

Added

  • Adds function obic_recommendations_bkp for determining management recommendations to improve soil quality

OBIC 2.1.3 2023-08-29

Fixed

  • Fixes error in formatting of B_AER_CBS for LG01 and LG02 in format_aer [OBI-20]

OBIC 2.1.2 2023-03-28

Fixed

  • Added missing values in nf_ columns in crops.obic

OBIC 2.1.1 2023-03-21

Fixed

  • Update crops.obic for missing b_lu_brp codes

OBIC 2.1.0 2023-03-03

Added

  • add obic_farm to assess soil quality on farm level (plus unit tests), #OBI-8
  • total farm score farm_obi_score as output reflecting the percentage of fields in the highest class for the OBI score, #OBI-8

Changed

  • output handling in obic_field is updated to have more flexibility and avoid undesired calculations

OBIC 2.0.5 2023-02-17

Fixed

  • Fixes to generate clearer error message when incorrect B_LU_BRP is supplied.

OBIC 2.0.4 2023-01-11

Fixed

  • Fixes calculation of field capacity at calc_waterretention

OBIC 2.0.3 2023-01-11

Fixed

  • Fixes plotting of regime curve in workabilty vignette #149

OBIC 2.0.2 2023-01-11

Changed

  • Update the GitHub Actions to the most recent version
  • Update RoxygenNote to v7.2.3

OBIC 2.0.1 2022-03-262022-04-05

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

OBIC 2.0.0 2022-01-11

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 threshold 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

OBIC 1.0.4 2021-09-27

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

OBIC 1.0.3 2021-09-16

Added

  • Adds unit test for obic_field

Fixed

  • Fixes ascii signs issues

OBIC 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

Fixed

  • check B_GWL_CLASS in calc_waterstressindex(), issue #129

OBIC 1.0.1 2021-05-05

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_descriptions_obic.Rdata is updated
  • weight.obic is updated

OBIC 1.0.0 2021-04-28

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_descriptions_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 sulfur.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

OBIC 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 sulfur
  • ID can now also be character and does not have to be numeric #66

OBIC 0.11.0 2020-01-16

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 continuous 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
  • parameters 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 fact sheet #54 #56
  • Fix error in calc_potassium_availability #59

OBIC 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 sulfur 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 sulfur on arable land is adjusted #41
  • The optimal pH for grassland depends now on organic matter content and presence of clover #42
  • The score aggregation 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 lifecycle status to maturing
  • The evaluation of I_C_MG is adjusted according to fact sheet

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 drought stress, wetness stress and water stress 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

OBIC 0.9.0 2019-10-22

Changed

  • The upper 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 sulfur 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

OBIC 0.8.0 2019-08-02

Added

  • Adds index and evaluation of the BodemConditieScore
  • Adds potassium to main functions
  • Adds a random recommendation 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 contained 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

OBIC 0.7.0 2019-08-02

Added

  • Adds index and evaluation of waterretention parameters
  • 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

OBIC 0.6.0 2019-08-01

Added

  • Adds index and evaluation of K-availability

OBIC 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

OBIC 0.4.0 2019-07-26

Added

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

Changed

  • The column name brp is changed to B_LU_BRP

OBIC 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

OBIC 0.2.0 2019-07-12

Added

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

OBIC 0.1.0 2019-07-08

First version of OBIC