NEWS.md

OBIC 3.0.3 2024-08-12s

Added

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

OBIC 3.0.2 2024-02-09

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 2023-11-24

Fixed

• Fixes calculation of N surplus used for I_H_NGW and I_H_NSW

OBIC 3.0.0 2023-10-16

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 2022-03-26

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