Merge pull request #158 from AgroCares/fix-spelling

Release/v2.0.1

.Rbuildignore

@@ -7,3 +7,4 @@
 ^DEV$
 ^\.github$
 ^codecov\.yml$
+^LICENSE

.gitignore

@@ -2,6 +2,8 @@
 .Rhistory
 .RData
 .Ruserdata
+.Renviron
+.Rproj
 inst/doc
 doc
 Meta

DESCRIPTION

@@ -1,24 +1,25 @@
 Package: OBIC
 Type: Package
-Title: Calculate the Open Bodem Index (OBI) score to evaluate the soil quality of agricultural fields
-Version: 2.0.0
+Title: Calculate the Open Bodem Index (OBI) Score
+Version: 2.0.1
 Authors@R: c(
     person("Sven", "Verweij", email = "[email protected]", role = c("aut","cre")),
     person("Gerard", "Ros", email = "[email protected]", role = "aut"),
+    person("Yuki", "Fujita", email = "[email protected]", role = "aut"),
+    person("Brent", "Riechelman", email = '[email protected]', role = "aut"),
     person("Job", "de Pater", email = "[email protected]", role = "ctb"),
-    person("Yuki", "Fujita", email = "[email protected]", role = "ctb"),
-    person("Brent", "Riechelman", email = '[email protected]', role = "ctb"),
     person("Nutriënten Managment Instituut", email = "[email protected]", role = "cph"))
 Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
     The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. 
-    By providing results of a soil analysis and management info the OBIC package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
-    More information about the Open Bodem Index can be found at https://www.openbodemindex.nl/.
+    By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
+    More information about the Open Bodem Index can be found at <https://www.openbodemindex.nl/>.
 Depends:
     R (>= 3.5.0)
 Imports: 
     checkmate,
     data.table
-License: GPL-3 | file LICENSE
+License: 
+    GPL-3
 URL: https://github.com/AgroCares/Open-Bodem-Index-Calculator
 BugReports: https://github.com/AgroCares/Open-Bodem-Index-Calculator/issues
 Encoding: UTF-8

DEV/scripts/ppr_maatregel.R

@@ -39,14 +39,21 @@
     cols <- colnames(m.obic)[grepl('melk',colnames(m.obic))]
     m.obic[,(cols) := lapply(.SD,function(x) fifelse(is.na(x),0,x)),.SDcols = cols]
 
+    # overwrite name
+    setnames(m.obic, "Bodemfunctie / indicator",'m_soilfunction')
+
     # check if there is missing data for any indicator
-    load('dev/column_description_obic.RData')
+    column_description.obic <- readRDS('dev/data/column_description_obic.rds')
     cols <- column_description.obic[grepl('^I_C_|^I_P_|^I_B_',column),column]
 
     # make temporary data.table with for each unknown indicator a zero impact measure
     cols <- cols[!cols %in% unique(m.obic$OBICvariable)]
     ind.miss <- CJ(maatregel_nr = 1:max(m.obic$maatregel_nr), OBICvariable = cols)
-    ind.add  <- merge(unique(m.obic[,c(1:3,5:6)]),ind.miss,by='maatregel_nr')
+    ind.miss <- merge(ind.miss,
+                      column_description.obic[,.(OBICvariable = column,m_soilfunction = description_nl)],
+                      by = 'OBICvariable')
+    ind.add  <- merge(ind.miss,unique(m.obic[,.(maatregel_nr,omschrijving,Prio_M,Order)]),
+                      by='maatregel_nr')
 
     # add missing columns with value 0, and a tresshold value of 0.5
     cols <- colnames(m.obic)[grepl('melk|groente|akker|boom|klei|veen|zand|loss|Ef',colnames(m.obic))]
@@ -93,38 +100,31 @@
     # setkey
     setkey(m.obic,indicator,m_sector,m_soiltype)
 
-# update april 2021
-
-  # I_P_MS is splitted into droughtstress and wetness stress separately
-  m1.copy <- m.obic[indicator=='I_P_MS'][,indicator := 'I_P_DS']
-  m2.copy <- m.obic[indicator=='I_P_MS'][,indicator := 'I_P_WS']
-
-  # add to m.obic
-  m.obic <- rbind(m.obic[!indicator=='I_P_MS'],m1.copy,m2.copy)
-
-
-
-# update september 2021
-
-  # add workability, assuming similar impacts on workability as on wetness stress
-  m2.copy <- m.obic[indicator=='I_P_WS'][,indicator := 'I_P_WO']
-
-  # add to m.obic
-  m.obic <- rbind(m.obic,m2.copy)
-
-  # setkey
-  setkey(m.obic,indicator,m_sector,m_soiltype)
-
-# update august 2021
-
-  # I_P_WO is added to with dummy values to prevent error
-  m1.copy <- m.obic[indicator=='I_P_DS'][,indicator := 'I_P_WO'][,c('m_effect','m_applicability') := 0]
+# update march 2022
+
+    # there where three OBIC indicators added, now with default "no impact
+    # these include: I_B_NEM, I_P_DS, I_P_WS and I_P_WO
+
+    # drought stress and wetness stress: all measures for original moisture stress are applicable
+    # and moisture stress can be deleted
+    m1.copy <- m.obic[indicator=='I_P_MS'][,indicator := 'I_P_DS']
+    m2.copy <- m.obic[indicator=='I_P_MS'][,indicator := 'I_P_WS']
+
+    # add to m.obic
+    m.obic <- m.obic[!indicator %in% c('I_P_DS','I_P_WS','I_P_MS')]
+    m.obic <- rbind(m.obic,m1.copy,m2.copy)
+
+    # add workability, assuming similar impacts on workability as on wetness stress
+    m1.copy <- m.obic[indicator=='I_P_WS'][,indicator := 'I_P_WO']
+    m.obic <- rbind(m.obic[!indicator == 'I_P_WO'],m1.copy)
 
-  # add to m.obic
-  m.obic <- rbind(m.obic,m1.copy)
+    # setkey
+    setkey(m.obic,indicator,m_sector,m_soiltype)
 
-  # setkey
-  setkey(m.obic,indicator,m_sector,m_soiltype)
+    # test
+    if(length(m.obic[,.N,by=.(indicator)][,unique(N)]) != 1){
+      print("warning, there are differences in the number of indicators. that should not be possible. please check")
+    }
 
   # rename to recom.obic
   recom.obic <- m.obic

NAMESPACE

@@ -62,6 +62,7 @@ export(ind_pmn)
 export(ind_potassium)
 export(ind_resistance)
 export(ind_sealing)
+export(ind_sulfur)
 export(ind_sulpher)
 export(ind_waterretention)
 export(ind_waterstressindex)

NEWS.md

@@ -1,3 +1,27 @@
+# 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
@@ -18,7 +42,7 @@
 * 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 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
 
@@ -80,7 +104,7 @@
 ## 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
+* column_descriptions_obic.Rdata is updated
 * weight.obic is updated
 
 
@@ -98,7 +122,7 @@
 * 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_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)
@@ -113,11 +137,11 @@
 * 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 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
+* 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
@@ -143,7 +167,7 @@
 * Range of `D_P_DU` is set between 0 and 1
 
 ## Fixed
-* Fixed the use of `B_LG_CBS` at sulphur
+* Fixed the use of `B_LG_CBS` at sulfur
 * `ID` can now also be character and does not have to be numeric #66
 
 
@@ -154,17 +178,17 @@
 ## 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
+* 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
-* Paramaters and funs for CEC are updated and split for soil fertility and aggregate stability #59
+* 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 factsheet #54 #56
+* 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
@@ -184,30 +208,30 @@
 * 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 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 sulphur on arable land is adjusted #41
+* 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 aggragation is now 60% average of last 4 years and 40% of older years #31
+* 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 lifecyle status to `maturing`
-* The evaluation of `I_C_MG` is adjusted according to factsheet
+* 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 droughtstress, wetnessstress and waterstress values for GtI in `waterstress.obic`
+* 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 uppper limit for `D_BCS` is increased from 40 to 50
+* 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 sulphur for arable fields #26
+* Changed evaluation of sulfur for arable fields #26
 
 ## Fixed
 * Fixed typo if mais in `ind_managment`
@@ -222,7 +246,7 @@
 ## Added
 * Adds index and evaluation of the BodemConditieScore
 * Adds potassium to main functions
-* Adds a random recommondation to the output
+* Adds a random recommendation to the output
 
 ## Changed
 * The upper limit for `A_MN_CC` is increased from 20000 to 30000
@@ -231,12 +255,12 @@
 ## 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`
+* 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 paramaters
+* 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)
@@ -264,7 +288,7 @@
 
 # OBIC 0.4.0 2019-07-26
 ## Added
-* The existing functions for pH, P, N, crumbleability, sealing and resistance are intergrated into `obic()`
+* 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`

Open-Bodem-Index-Calculator.Rproj

@@ -18,6 +18,3 @@ PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace
 
 QuitChildProcessesOnExit: Yes
-DisableExecuteRprofile: Yes
-
-SpellingDictionary: nl_NL

R/bodemconditiescore.R

@@ -2,7 +2,7 @@
 #' 
 #' This function calculates the BodemConditieScore given input from manual observations made in the field.
 #' The individual parameters are scored in three classes: poor (0), neutral (1) or good (2)
-#' More information on this test can be found \href{http://mijnbodemconditie.nl/}{here}
+#' More information on this test can be found \href{https://mijnbodemconditie.nl/}{here}
 #' 
 #' 
 #' @param B_LU_BRP (numeric) The crop code from the BRP 
@@ -20,13 +20,20 @@
 #' @param A_CC_BCS (integer) The crop cover on the surface (score 0-1-2)
 #' @param type (character) Define output of the function. Options: score (integrated score) and indicator (score per indicator)
 #' 
-#' @references \href{http://mijnbodemconditie.nl/}{mijnbodemconditie.nl}
+#' @references \href{https://mijnbodemconditie.nl/}{mijnbodemconditie.nl}
 #' 
 #' @import data.table
 #' 
+#' @examples
+#' calc_bcs(B_LU_BRP = 265, B_SOILTYPE_AGR = 'dekzand', A_SOM_LOI = 3.5, D_PH_DELTA = 0.4,
+#' A_EW_BCS = 1, A_SC_BCS = 1, A_GS_BCS = 1, A_P_BCS = 1, A_C_BCS = 1, A_RT_BCS =1, A_RD_BCS = 1, 
+#' A_SS_BCS = 1, A_CC_BCS = 1)
+#' 
+#' @return
+#' A visual soil assessment score derived from field observations driven by organic matter content and soil structure properties. Returns a numeric value.
 #' @export
 calc_bcs <- function(B_LU_BRP,B_SOILTYPE_AGR,A_SOM_LOI, D_PH_DELTA,
-                     A_EW_BCS = NA, A_SC_BCS = NA, A_GS_BCS = NA, A_P_BCS = NA, A_C_BCS = NA, A_RT_BCS =NA, A_RD_BCS = NA, 
+                     A_EW_BCS = NA, A_SC_BCS = NA, A_GS_BCS = NA, A_P_BCS = NA, A_C_BCS = NA, A_RT_BCS = NA, A_RD_BCS = NA, 
                      A_SS_BCS = NA, A_CC_BCS = NA,
                      type = 'score'
                      ) {
@@ -153,6 +160,13 @@ calc_bcs <- function(B_LU_BRP,B_SOILTYPE_AGR,A_SOM_LOI, D_PH_DELTA,
 #' 
 #' @param D_BCS (numeric) The value of BCS  calculated by \code{\link{calc_bcs}}
 #' 
+#' @examples 
+#' ind_bcs(D_BCS = 12)
+#' ind_bcs(D_BCS = c(12,18,26,30))
+#' 
+#' @return 
+#' The evaluated score for the Visual Soil Assessment. A numeric value between 0 and 50.
+#' 
 #' @export
 ind_bcs <- function(D_BCS) {
 

R/bulk_density.R

@@ -8,6 +8,14 @@
 #' 
 #' @import data.table
 #' 
+#' @examples
+#' calc_bulk_density(B_SOILTYPE_AGR = 'zeeklei', A_SOM_LOI = 6.5, A_CLAY_MI = 28)
+#' calc_bulk_density(B_SOILTYPE_AGR = 'dekzand', A_SOM_LOI = 3.5)
+#' calc_bulk_density(B_SOILTYPE_AGR = c('dekzand','rivierklei'), A_SOM_LOI = c(3.5,8.5))
+#' 
+#' @return 
+#' The bulk density of an arable soil (kg / m3). A numeric value.
+#' 
 #' @export
 calc_bulk_density <- function(B_SOILTYPE_AGR, A_SOM_LOI, A_CLAY_MI = NULL) {