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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
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
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
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They may not be fully stable and should be used with caution. We make no claims about them.
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