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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
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.