From c2c89ebe8189b2ca6991ba0bb20a98be26e2c6b1 Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 16:36:42 +0100
Subject: [PATCH 01/10] set version to 2.2.1

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b261a93..2f85b23 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BBWPC
 Type: Package
 Title: Calculator for BedrijfsBodemWaterPlan (BBWP)
-Version: 2.1.1
+Version: 2.2.1
 Authors@R: c(
     person("Gerard", "Ros", email = "gerard.ros@nmi-agro.nl", role = c("aut","cre")),
     person("Sven", "Verweij", email = "sven.verweij@nmi-agro.nl", role = c("aut")),

From af4fb8326fc22bf3e314186cf46acf28c45860c6 Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 16:58:07 +0100
Subject: [PATCH 02/10] add penalty argument to wf

---
 R/bbwp_helpers.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/R/bbwp_helpers.R b/R/bbwp_helpers.R
index 16e86bf..ac1f48a 100644
--- a/R/bbwp_helpers.R
+++ b/R/bbwp_helpers.R
@@ -33,18 +33,22 @@ cdf_rank <- function(smean,ssd,svalue){
 #' 
 #' @param x The risk or score value to be weighted
 #' @param type Use the weighing function for indicators or score
+#' @param penalty (boolean) the option to apply a penalty for high risk BBWP field indicators
 #' 
 #' @export
-wf <- function(x, type = "indicators") {
+wf <- function(x, type = "indicators", penalty = TRUE) {
   
-  if (type == "indicators") {
+  if (type == "indicators" & penalty == TRUE) {
     
     y <- 1 / (1 - x + 0.2)
     
-  } else if (type == "score") {
+  } else if (type == "score" & penalty == TRUE) {
     
     y <- 1 / (x * 0.01 + 0.2)
     
+  } else if(penalty == FALSE){
+    
+    y = 1
   }
   
   return(y)

From 5b7b7ba2f5ed8ecb5f0834f5512ac935923b03a1 Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 16:58:18 +0100
Subject: [PATCH 03/10] add penalty argument to field_indicators

---
 R/bbwp_field_indicators.R | 53 ++++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 23 deletions(-)

diff --git a/R/bbwp_field_indicators.R b/R/bbwp_field_indicators.R
index 5223531..2d7a64f 100644
--- a/R/bbwp_field_indicators.R
+++ b/R/bbwp_field_indicators.R
@@ -30,6 +30,7 @@
 #' @param D_WUE_WWRI (numeric) The relative score of soil wetness stress for improved efficiency of water
 #' @param D_WUE_WDRI (numeric) The relative score of drought stress for improved efficiency of water
 #' @param D_WUE_WHC (numeric) The relative score of drought stress for improved efficiency of water
+#' @param penalty (boolean) the option to apply a penalty for high risk BBWP field indicators
 #' 
 #' @import data.table
 #' @import OBIC
@@ -40,7 +41,7 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
                                   D_NSW_SCR,D_NSW_GWT,D_NSW_RO,D_NSW_SLOPE, D_NSW_WS,D_NSW_NLV,
                                   D_PSW_SCR,D_PSW_GWT,D_PSW_RO,D_PSW_SLOPE,D_PSW_WS,D_PSW_PCC,D_PSW_PSG,D_PSW_PRET,
                                   D_NUE_WRI,D_NUE_PBI,D_NUE_WDRI,D_NUE_NLV,
-                                  D_WUE_WWRI,D_WUE_WDRI,D_WUE_WHC){
+                                  D_WUE_WWRI,D_WUE_WDRI,D_WUE_WHC, penalty = TRUE){
   
   # add visual bindings
   D_RISK_NGW = D_RISK_NSW = D_RISK_PSW = D_RISK_NUE = D_RISK_WB = id = NULL
@@ -93,30 +94,31 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
   
   
   # integrate all relative field risk indicators into one for indictor for N loss to groundwater
-  dt[, D_RISK_NGW := (wf(D_NGW_SCR) * D_NGW_SCR + 
-                  3 * wf(D_NGW_LEA) * D_NGW_LEA + 
-                  2 * wf(D_NGW_NLV) * D_NGW_NLV) /
-       (wf(D_NGW_SCR) + 3 * wf(D_NGW_LEA) + 2 * wf(D_NGW_NLV))]
+  dt[, D_RISK_NGW := (wf(D_NGW_SCR,penalty) * D_NGW_SCR + 
+                  3 * wf(D_NGW_LEA,penalty) * D_NGW_LEA + 
+                  2 * wf(D_NGW_NLV,penalty) * D_NGW_NLV) /
+       (wf(D_NGW_SCR,penalty) + 3 * wf(D_NGW_LEA,penalty) + 2 * wf(D_NGW_NLV,penalty))]
   
   # integrate all relative field risk indicators into one for indictor for N loss to surface water
-  dt[, D_RISK_NSW := (wf(D_NSW_SCR) * D_NSW_SCR + 
-                      wf(D_NSW_GWT) * D_NSW_GWT + 
-                      wf(D_NSW_SLOPE) * D_NSW_SLOPE +
-                      wf(D_NSW_RO) * D_NSW_RO + 
-                      wf(D_NSW_WS) * D_NSW_WS + 
-                  3 * wf(D_NSW_NLV) * D_NSW_NLV ) /
-       (wf(D_NSW_SCR) + wf(D_NSW_GWT) + wf(D_NSW_SLOPE) + wf(D_NSW_RO) + wf(D_NSW_WS) + 3 * wf(D_NSW_NLV))]
+  dt[, D_RISK_NSW := (wf(D_NSW_SCR,penalty) * D_NSW_SCR + 
+                      wf(D_NSW_GWT,penalty) * D_NSW_GWT + 
+                      wf(D_NSW_SLOPE,penalty) * D_NSW_SLOPE +
+                      wf(D_NSW_RO,penalty) * D_NSW_RO + 
+                      wf(D_NSW_WS,penalty) * D_NSW_WS + 
+                  3 * wf(D_NSW_NLV,penalty) * D_NSW_NLV ) /
+       (wf(D_NSW_SCR,penalty) + wf(D_NSW_GWT,penalty) + wf(D_NSW_SLOPE,penalty) + wf(D_NSW_RO,penalty) + wf(D_NSW_WS,penalty) + 3 * wf(D_NSW_NLV,penalty))]
   
   # integrate all relative field risk indicators into one for indictor for P loss to surface water
-  dt[, D_RISK_PSW := (2 * wf(D_PSW_SCR) * D_PSW_SCR + 
-                          wf(D_PSW_GWT) * D_PSW_GWT + 
-                      2 * wf(D_PSW_RO) * D_PSW_RO + 
+  dt[, D_RISK_PSW := (2 * wf(D_PSW_SCR,penalty) * D_PSW_SCR + 
+                          wf(D_PSW_GWT,penalty) * D_PSW_GWT + 
+                      2 * wf(D_PSW_RO,penalty) * D_PSW_RO + 
                           wf(D_PSW_SLOPE) * D_PSW_SLOPE +
-                      2 * wf(D_PSW_WS) * D_PSW_WS + 
-                          wf(D_PSW_PCC) * D_PSW_PCC + 
-                          wf(D_PSW_PSG) * D_PSW_PSG + 
-                          wf(D_PSW_PRET) * D_PSW_PRET) /
-       (2 * wf(D_PSW_SCR) + wf(D_PSW_GWT) + 2 * wf(D_PSW_RO) + wf(D_PSW_SLOPE) + 2 * wf(D_PSW_WS) + wf(D_PSW_PCC) + wf(D_PSW_PSG) + wf(D_PSW_PRET))]
+                      2 * wf(D_PSW_WS,penalty) * D_PSW_WS + 
+                          wf(D_PSW_PCC,penalty) * D_PSW_PCC + 
+                          wf(D_PSW_PSG,penalty) * D_PSW_PSG + 
+                          wf(D_PSW_PRET,penalty) * D_PSW_PRET) /
+       (2 * wf(D_PSW_SCR,penalty) + wf(D_PSW_GWT,penalty) + 2 * wf(D_PSW_RO,penalty) + wf(D_PSW_SLOPE,penalty) + 
+          2 * wf(D_PSW_WS,penalty) + wf(D_PSW_PCC,penalty) + wf(D_PSW_PSG,penalty) + wf(D_PSW_PRET,penalty))]
   
   # minimize risks when there are no ditches around (wet surrounding fraction < 0.2)
   dt[D_NSW_WS <= 0.2 & D_PSW_SLOPE < 1,D_RISK_PSW := 0.1]
@@ -125,11 +127,16 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
   dt[D_NSW_WS <= 0.1 & D_PSW_SLOPE < 1,D_RISK_NSW := 0.01]
   
   # integrate all relative field risk indicators into one for indictor for N and P efficiency of inputs
-  dt[, D_RISK_NUE := (wf(D_NUE_WRI) * D_NUE_WRI + 2 * wf(D_NUE_PBI) * D_NUE_PBI + wf(D_NUE_NLV) * D_NUE_NLV + wf(D_NUE_WDRI) * D_NUE_WDRI) /
-       (wf(D_NUE_WRI) + 2 * wf(D_NUE_PBI) + wf(D_NUE_NLV) + wf(D_NUE_WDRI))]
+  dt[, D_RISK_NUE := (wf(D_NUE_WRI,penalty) * D_NUE_WRI + 
+                        2 * wf(D_NUE_PBI,penalty) * D_NUE_PBI + 
+                        wf(D_NUE_NLV,penalty) * D_NUE_NLV + 
+                        wf(D_NUE_WDRI,penalty) * D_NUE_WDRI) /
+       (wf(D_NUE_WRI,penalty) + 2 * wf(D_NUE_PBI,penalty) + wf(D_NUE_NLV,penalty) + wf(D_NUE_WDRI,penalty))]
   
   # integrate all relative field risk indicators into one for indictor for water retention and efficiency
-  dt[, D_RISK_WB := (wf(D_WUE_WWRI) * D_WUE_WWRI + wf(D_WUE_WDRI) * D_WUE_WDRI + 2 * wf(D_WUE_WHC) * D_WUE_WHC) / (wf(D_WUE_WWRI) + wf(D_WUE_WDRI) + 2 * wf(D_WUE_WHC))]
+  dt[, D_RISK_WB := (wf(D_WUE_WWRI,penalty) * D_WUE_WWRI + 
+                       wf(D_WUE_WDRI,penalty) * D_WUE_WDRI + 
+                       2 * wf(D_WUE_WHC,penalty) * D_WUE_WHC) / (wf(D_WUE_WWRI,penalty) + wf(D_WUE_WDRI,penalty) + 2 * wf(D_WUE_WHC,penalty))]
   
   # normalise these indicators ???
   

From 1d51a5419e2a9b1e11ede0b0f9ceb5ac61e964f3 Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 16:58:42 +0100
Subject: [PATCH 04/10] add penalty argument to field_scores

---
 R/bbwp_field_scores.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/bbwp_field_scores.R b/R/bbwp_field_scores.R
index d3c682e..86f6fb8 100644
--- a/R/bbwp_field_scores.R
+++ b/R/bbwp_field_scores.R
@@ -23,7 +23,7 @@
 #' @param B_CT_NSW_MAX (numeric) the max critical target for N reduction loss (kg N / ha)
 #' @param measures (data.table) the measures planned / done per fields
 #' @param sector (string) a vector with the farm type given the agricultural sector (options: 'dairy', 'arable', 'tree_nursery', 'bulbs')
-#' 
+#' @param penalty (boolean) the option to apply a penalty for high risk BBWP field indicators 
 #'   
 #' @import data.table
 #'
@@ -32,7 +32,7 @@
 bbwp_field_scores <- function(B_SOILTYPE_AGR, B_GWL_CLASS, A_P_SG, B_SLOPE_DEGREE, B_LU_BBWP,B_AER_CBS,
                               M_DRAIN, D_SA_W, D_RISK_NGW, D_RISK_NSW, D_RISK_PSW, D_RISK_NUE, D_RISK_WB,
                               B_GWP, B_AREA_DROUGHT, B_CT_PSW, B_CT_NSW, 
-                              B_CT_PSW_MAX = 0.5, B_CT_NSW_MAX = 5.0, measures, sector){
+                              B_CT_PSW_MAX = 0.5, B_CT_NSW_MAX = 5.0, measures, sector,penalty = TRUE){
   
   # add visual bindings
   cfngw = cfwb = cfnsw = cfpsw = cfnue = NULL
@@ -182,13 +182,13 @@ bbwp_field_scores <- function(B_SOILTYPE_AGR, B_GWL_CLASS, A_P_SG, B_SLOPE_DEGRE
   dt[,S_BBWP_NUE := 100 * D_OPI_NUE]
   dt[,S_BBWP_WB := 100 * D_OPI_WB]
   
-  dt[,S_BBWP_TOT := (S_BBWP_NGW * wf(S_BBWP_NGW, type="score") + 
-                      S_BBWP_NSW * wf(S_BBWP_NSW, type="score") + 
-                      S_BBWP_PSW * wf(S_BBWP_PSW, type="score") + 
-                      S_BBWP_NUE * wf(S_BBWP_NUE, type="score") + 
-                      S_BBWP_WB * wf(S_BBWP_WB, type="score")) /
-       (wf(S_BBWP_NGW, type="score") + wf(S_BBWP_NSW, type="score") +  wf(S_BBWP_PSW, type="score") +  
-          wf(S_BBWP_NUE, type="score") +  wf(S_BBWP_WB, type="score"))]
+  dt[,S_BBWP_TOT := (S_BBWP_NGW * wf(S_BBWP_NGW, type="score",penalty) + 
+                      S_BBWP_NSW * wf(S_BBWP_NSW, type="score",penalty) + 
+                      S_BBWP_PSW * wf(S_BBWP_PSW, type="score",penalty) + 
+                      S_BBWP_NUE * wf(S_BBWP_NUE, type="score",penalty) + 
+                      S_BBWP_WB * wf(S_BBWP_WB, type="score",penalty)) /
+       (wf(S_BBWP_NGW, type="score",penalty) + wf(S_BBWP_NSW, type="score",penalty) +  wf(S_BBWP_PSW, type="score",penalty) +  
+          wf(S_BBWP_NUE, type="score",penalty) +  wf(S_BBWP_WB, type="score",penalty))]
   
   # order the fields
   setorder(dt, id)

From 6b8447f85b74cf65324d7d0d1354a8663b1fde6c Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 16:59:12 +0100
Subject: [PATCH 05/10] add penalty argument to main

---
 R/bbwp_main.R | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/R/bbwp_main.R b/R/bbwp_main.R
index 906e80c..eab14a0 100644
--- a/R/bbwp_main.R
+++ b/R/bbwp_main.R
@@ -37,7 +37,8 @@
 #' @param measures (data.table) the measures planned / done per fields
 #' @param sector (string) a vector with the farm type given the agricultural sector (options: options: 'dairy', 'arable', 'tree_nursery', 'bulbs')
 #' @param output (string) a vector specifying the output type of the function. Options: scores, measures 
-#' 
+#' @param penalty (boolean) the option to apply a penalty for high risk BBWP field indicators
+#'  
 #' @details 
 #' B_SLOPE_DEGREE should be used, for backwards compatibility B_SLOPE can still be used. At least one of the must be used, when both are supplied, B_SLOPE is ignored.
 #' LSW is by default a data.table with LSW properties, being calculated from bbwp_lsw_properties. Note that all B_LSW_IDs should be preset in the LSW data.table.
@@ -52,7 +53,7 @@ bbwp <- function(B_SOILTYPE_AGR, B_LU_BBWP,B_GWL_CLASS, B_SC_WENR, B_HELP_WENR,B
                  B_GWP, B_AREA_DROUGHT, B_CT_PSW, B_CT_NSW,B_CT_PSW_MAX = 0.5, B_CT_NSW_MAX = 5.0, 
                  D_SA_W, D_RO_R, B_AREA, 
                  M_DRAIN, B_LSW_ID, LSW = NULL,
-                 measures, sector,output = 'scores'){
+                 measures, sector,output = 'scores',penalty=TRUE){
   
   # add visual binding
   field_id = code = value_min = value_max = NULL
@@ -158,7 +159,8 @@ bbwp <- function(B_SOILTYPE_AGR, B_LU_BBWP,B_GWL_CLASS, B_SC_WENR, B_HELP_WENR,B
                                   D_NUE_NLV = dt$npe_nlv,
                                   D_WUE_WWRI = dt$wue_wwri,
                                   D_WUE_WDRI = dt$wue_wdri,
-                                  D_WUE_WHC = dt$wue_whc
+                                  D_WUE_WHC = dt$wue_whc,
+                                  penalty = penalty
                                 )
   
   # Calculate BBWP field scores
@@ -187,7 +189,8 @@ bbwp <- function(B_SOILTYPE_AGR, B_LU_BBWP,B_GWL_CLASS, B_SC_WENR, B_HELP_WENR,B
                                     B_CT_PSW_MAX = B_CT_PSW_MAX, 
                                     B_CT_NSW_MAX = B_CT_NSW_MAX,
                                     measures = measures,
-                                    sector = sector
+                                    sector = sector,
+                                    penalty = penalty
                                   )
   
   # Calculate the BBWP farm score

From 20e8ea4134f112148fcff437dde03511e4d96dac Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 16:59:19 +0100
Subject: [PATCH 06/10] update news

---
 NEWS.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index a69af59..f2b0987 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# BBWPC v2.2.1 2023-12-28
+## Added
+* possibility to falisfy the weighing fraction for evaluation of risks in `wf` function, default set to TRUE, #BBWP-67
+* argument `penalty` added to the functions `bbwp_field_indicators`, `bbwp_field_scores` and `bbwp_main`
+
 # BBWPC v2.1.1 2023-12-27
 ## Added
 * function `bbwp_format_sc_wenr` to ensure that B_SC_WENR is an integer conform format Van den Akker (2006), #BBWP-66

From 1ff6f3ce2ce4c81e66650a3423ae2c93e44ae284 Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 17:08:33 +0100
Subject: [PATCH 07/10] fix errors after check and update documentation

---
 NEWS.md                      |  2 +-
 R/bbwp_field_indicators.R    | 59 ++++++++++++++++++------------------
 R/bbwp_field_scores.R        | 12 ++++----
 man/bbwp.Rd                  |  5 ++-
 man/bbwp_field_indicators.Rd |  5 ++-
 man/bbwp_field_scores.Rd     |  5 ++-
 man/wf.Rd                    |  4 ++-
 7 files changed, 52 insertions(+), 40 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index f2b0987..11bcfd7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,7 @@
 # BBWPC v2.2.1 2023-12-28
 ## Added
 * possibility to falisfy the weighing fraction for evaluation of risks in `wf` function, default set to TRUE, #BBWP-67
-* argument `penalty` added to the functions `bbwp_field_indicators`, `bbwp_field_scores` and `bbwp_main`
+* argument `penalty` added to the functions `bbwp_field_indicators`, `bbwp_field_scores` and `bbwp_main`, #BBWP-67
 
 # BBWPC v2.1.1 2023-12-27
 ## Added
diff --git a/R/bbwp_field_indicators.R b/R/bbwp_field_indicators.R
index 2d7a64f..401dc3b 100644
--- a/R/bbwp_field_indicators.R
+++ b/R/bbwp_field_indicators.R
@@ -94,31 +94,32 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
   
   
   # integrate all relative field risk indicators into one for indictor for N loss to groundwater
-  dt[, D_RISK_NGW := (wf(D_NGW_SCR,penalty) * D_NGW_SCR + 
-                  3 * wf(D_NGW_LEA,penalty) * D_NGW_LEA + 
-                  2 * wf(D_NGW_NLV,penalty) * D_NGW_NLV) /
-       (wf(D_NGW_SCR,penalty) + 3 * wf(D_NGW_LEA,penalty) + 2 * wf(D_NGW_NLV,penalty))]
+  dt[, D_RISK_NGW := (wf(D_NGW_SCR,penalty = penalty) * D_NGW_SCR + 
+                  3 * wf(D_NGW_LEA,penalty = penalty) * D_NGW_LEA + 
+                  2 * wf(D_NGW_NLV,penalty = penalty) * D_NGW_NLV) /
+       (wf(D_NGW_SCR,penalty = penalty) + 3 * wf(D_NGW_LEA,penalty = penalty) + 2 * wf(D_NGW_NLV,penalty = penalty))]
   
   # integrate all relative field risk indicators into one for indictor for N loss to surface water
-  dt[, D_RISK_NSW := (wf(D_NSW_SCR,penalty) * D_NSW_SCR + 
-                      wf(D_NSW_GWT,penalty) * D_NSW_GWT + 
-                      wf(D_NSW_SLOPE,penalty) * D_NSW_SLOPE +
-                      wf(D_NSW_RO,penalty) * D_NSW_RO + 
-                      wf(D_NSW_WS,penalty) * D_NSW_WS + 
-                  3 * wf(D_NSW_NLV,penalty) * D_NSW_NLV ) /
-       (wf(D_NSW_SCR,penalty) + wf(D_NSW_GWT,penalty) + wf(D_NSW_SLOPE,penalty) + wf(D_NSW_RO,penalty) + wf(D_NSW_WS,penalty) + 3 * wf(D_NSW_NLV,penalty))]
+  dt[, D_RISK_NSW := (wf(D_NSW_SCR,penalty = penalty) * D_NSW_SCR + 
+                      wf(D_NSW_GWT,penalty = penalty) * D_NSW_GWT + 
+                      wf(D_NSW_SLOPE,penalty = penalty) * D_NSW_SLOPE +
+                      wf(D_NSW_RO,penalty = penalty) * D_NSW_RO + 
+                      wf(D_NSW_WS,penalty = penalty) * D_NSW_WS + 
+                  3 * wf(D_NSW_NLV,penalty = penalty) * D_NSW_NLV ) /
+       (wf(D_NSW_SCR,penalty = penalty) + wf(D_NSW_GWT,penalty = penalty) + wf(D_NSW_SLOPE,penalty = penalty) + 
+          wf(D_NSW_RO,penalty = penalty) + wf(D_NSW_WS,penalty = penalty) + 3 * wf(D_NSW_NLV,penalty = penalty))]
   
   # integrate all relative field risk indicators into one for indictor for P loss to surface water
-  dt[, D_RISK_PSW := (2 * wf(D_PSW_SCR,penalty) * D_PSW_SCR + 
-                          wf(D_PSW_GWT,penalty) * D_PSW_GWT + 
-                      2 * wf(D_PSW_RO,penalty) * D_PSW_RO + 
-                          wf(D_PSW_SLOPE) * D_PSW_SLOPE +
-                      2 * wf(D_PSW_WS,penalty) * D_PSW_WS + 
-                          wf(D_PSW_PCC,penalty) * D_PSW_PCC + 
-                          wf(D_PSW_PSG,penalty) * D_PSW_PSG + 
-                          wf(D_PSW_PRET,penalty) * D_PSW_PRET) /
-       (2 * wf(D_PSW_SCR,penalty) + wf(D_PSW_GWT,penalty) + 2 * wf(D_PSW_RO,penalty) + wf(D_PSW_SLOPE,penalty) + 
-          2 * wf(D_PSW_WS,penalty) + wf(D_PSW_PCC,penalty) + wf(D_PSW_PSG,penalty) + wf(D_PSW_PRET,penalty))]
+  dt[, D_RISK_PSW := (2 * wf(D_PSW_SCR,penalty = penalty) * D_PSW_SCR + 
+                          wf(D_PSW_GWT,penalty = penalty) * D_PSW_GWT + 
+                      2 * wf(D_PSW_RO,penalty = penalty) * D_PSW_RO + 
+                          wf(D_PSW_SLOPE, penalty = penalty) * D_PSW_SLOPE +
+                      2 * wf(D_PSW_WS,penalty = penalty) * D_PSW_WS + 
+                          wf(D_PSW_PCC,penalty = penalty) * D_PSW_PCC + 
+                          wf(D_PSW_PSG,penalty = penalty) * D_PSW_PSG + 
+                          wf(D_PSW_PRET,penalty = penalty) * D_PSW_PRET) /
+       (2 * wf(D_PSW_SCR,penalty = penalty) + wf(D_PSW_GWT,penalty = penalty) + 2 * wf(D_PSW_RO,penalty = penalty) + wf(D_PSW_SLOPE,penalty = penalty) + 
+          2 * wf(D_PSW_WS,penalty = penalty) + wf(D_PSW_PCC,penalty = penalty) + wf(D_PSW_PSG,penalty = penalty) + wf(D_PSW_PRET,penalty = penalty))]
   
   # minimize risks when there are no ditches around (wet surrounding fraction < 0.2)
   dt[D_NSW_WS <= 0.2 & D_PSW_SLOPE < 1,D_RISK_PSW := 0.1]
@@ -127,16 +128,16 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
   dt[D_NSW_WS <= 0.1 & D_PSW_SLOPE < 1,D_RISK_NSW := 0.01]
   
   # integrate all relative field risk indicators into one for indictor for N and P efficiency of inputs
-  dt[, D_RISK_NUE := (wf(D_NUE_WRI,penalty) * D_NUE_WRI + 
-                        2 * wf(D_NUE_PBI,penalty) * D_NUE_PBI + 
-                        wf(D_NUE_NLV,penalty) * D_NUE_NLV + 
-                        wf(D_NUE_WDRI,penalty) * D_NUE_WDRI) /
-       (wf(D_NUE_WRI,penalty) + 2 * wf(D_NUE_PBI,penalty) + wf(D_NUE_NLV,penalty) + wf(D_NUE_WDRI,penalty))]
+  dt[, D_RISK_NUE := (wf(D_NUE_WRI,penalty = penalty) * D_NUE_WRI + 
+                        2 * wf(D_NUE_PBI,penalty = penalty) * D_NUE_PBI + 
+                        wf(D_NUE_NLV,penalty = penalty) * D_NUE_NLV + 
+                        wf(D_NUE_WDRI,penalty = penalty) * D_NUE_WDRI) /
+       (wf(D_NUE_WRI,penalty = penalty) + 2 * wf(D_NUE_PBI,penalty = penalty) + wf(D_NUE_NLV,penalty = penalty) + wf(D_NUE_WDRI,penalty = penalty))]
   
   # integrate all relative field risk indicators into one for indictor for water retention and efficiency
-  dt[, D_RISK_WB := (wf(D_WUE_WWRI,penalty) * D_WUE_WWRI + 
-                       wf(D_WUE_WDRI,penalty) * D_WUE_WDRI + 
-                       2 * wf(D_WUE_WHC,penalty) * D_WUE_WHC) / (wf(D_WUE_WWRI,penalty) + wf(D_WUE_WDRI,penalty) + 2 * wf(D_WUE_WHC,penalty))]
+  dt[, D_RISK_WB := (wf(D_WUE_WWRI,penalty = penalty) * D_WUE_WWRI + 
+                       wf(D_WUE_WDRI,penalty = penalty) * D_WUE_WDRI + 
+                       2 * wf(D_WUE_WHC,penalty = penalty) * D_WUE_WHC) / (wf(D_WUE_WWRI,penalty = penalty) + wf(D_WUE_WDRI,penalty = penalty) + 2 * wf(D_WUE_WHC,penalty = penalty))]
   
   # normalise these indicators ???
   
diff --git a/R/bbwp_field_scores.R b/R/bbwp_field_scores.R
index 86f6fb8..2844141 100644
--- a/R/bbwp_field_scores.R
+++ b/R/bbwp_field_scores.R
@@ -182,13 +182,13 @@ bbwp_field_scores <- function(B_SOILTYPE_AGR, B_GWL_CLASS, A_P_SG, B_SLOPE_DEGRE
   dt[,S_BBWP_NUE := 100 * D_OPI_NUE]
   dt[,S_BBWP_WB := 100 * D_OPI_WB]
   
-  dt[,S_BBWP_TOT := (S_BBWP_NGW * wf(S_BBWP_NGW, type="score",penalty) + 
-                      S_BBWP_NSW * wf(S_BBWP_NSW, type="score",penalty) + 
-                      S_BBWP_PSW * wf(S_BBWP_PSW, type="score",penalty) + 
-                      S_BBWP_NUE * wf(S_BBWP_NUE, type="score",penalty) + 
+  dt[,S_BBWP_TOT := (S_BBWP_NGW * wf(S_BBWP_NGW, type="score",penalty = penalty) + 
+                      S_BBWP_NSW * wf(S_BBWP_NSW, type="score",penalty = penalty) + 
+                      S_BBWP_PSW * wf(S_BBWP_PSW, type="score",penalty = penalty) + 
+                      S_BBWP_NUE * wf(S_BBWP_NUE, type="score",penalty = penalty) + 
                       S_BBWP_WB * wf(S_BBWP_WB, type="score",penalty)) /
-       (wf(S_BBWP_NGW, type="score",penalty) + wf(S_BBWP_NSW, type="score",penalty) +  wf(S_BBWP_PSW, type="score",penalty) +  
-          wf(S_BBWP_NUE, type="score",penalty) +  wf(S_BBWP_WB, type="score",penalty))]
+       (wf(S_BBWP_NGW, type="score",penalty = penalty) + wf(S_BBWP_NSW, type="score",penalty = penalty) +  wf(S_BBWP_PSW, type="score",penalty = penalty) +  
+          wf(S_BBWP_NUE, type="score",penalty = penalty) +  wf(S_BBWP_WB, type="score",penalty = penalty))]
   
   # order the fields
   setorder(dt, id)
diff --git a/man/bbwp.Rd b/man/bbwp.Rd
index eb8964a..d56723e 100644
--- a/man/bbwp.Rd
+++ b/man/bbwp.Rd
@@ -38,7 +38,8 @@ bbwp(
   LSW = NULL,
   measures,
   sector,
-  output = "scores"
+  output = "scores",
+  penalty = TRUE
 )
 }
 \arguments{
@@ -109,6 +110,8 @@ bbwp(
 \item{sector}{(string) a vector with the farm type given the agricultural sector (options: options: 'dairy', 'arable', 'tree_nursery', 'bulbs')}
 
 \item{output}{(string) a vector specifying the output type of the function. Options: scores, measures}
+
+\item{penalty}{(boolean) the option to apply a penalty for high risk BBWP field indicators}
 }
 \description{
 Estimate the potential to contribute to agronomic and environmental challenges in a region for a farm and assess the impact of farm measures taken.
diff --git a/man/bbwp_field_indicators.Rd b/man/bbwp_field_indicators.Rd
index 8167bd9..fbc04c2 100644
--- a/man/bbwp_field_indicators.Rd
+++ b/man/bbwp_field_indicators.Rd
@@ -28,7 +28,8 @@ bbwp_field_indicators(
   D_NUE_NLV,
   D_WUE_WWRI,
   D_WUE_WDRI,
-  D_WUE_WHC
+  D_WUE_WHC,
+  penalty = TRUE
 )
 }
 \arguments{
@@ -79,6 +80,8 @@ bbwp_field_indicators(
 \item{D_WUE_WDRI}{(numeric) The relative score of drought stress for improved efficiency of water}
 
 \item{D_WUE_WHC}{(numeric) The relative score of drought stress for improved efficiency of water}
+
+\item{penalty}{(boolean) the option to apply a penalty for high risk BBWP field indicators}
 }
 \description{
 These include indicators: 
diff --git a/man/bbwp_field_scores.Rd b/man/bbwp_field_scores.Rd
index 1bbc227..04afdcb 100644
--- a/man/bbwp_field_scores.Rd
+++ b/man/bbwp_field_scores.Rd
@@ -25,7 +25,8 @@ bbwp_field_scores(
   B_CT_PSW_MAX = 0.5,
   B_CT_NSW_MAX = 5,
   measures,
-  sector
+  sector,
+  penalty = TRUE
 )
 }
 \arguments{
@@ -70,6 +71,8 @@ bbwp_field_scores(
 \item{measures}{(data.table) the measures planned / done per fields}
 
 \item{sector}{(string) a vector with the farm type given the agricultural sector (options: 'dairy', 'arable', 'tree_nursery', 'bulbs')}
+
+\item{penalty}{(boolean) the option to apply a penalty for high risk BBWP field indicators}
 }
 \description{
 Estimate the potential to contribute to agronomic and environmental challenges in a region
diff --git a/man/wf.Rd b/man/wf.Rd
index d9be6ea..2292052 100644
--- a/man/wf.Rd
+++ b/man/wf.Rd
@@ -4,12 +4,14 @@
 \alias{wf}
 \title{Helper function to weight and correct the risk and scores}
 \usage{
-wf(x, type = "indicators")
+wf(x, type = "indicators", penalty = TRUE)
 }
 \arguments{
 \item{x}{The risk or score value to be weighted}
 
 \item{type}{Use the weighing function for indicators or score}
+
+\item{penalty}{(boolean) the option to apply a penalty for high risk BBWP field indicators}
 }
 \description{
 Helper function to weight and correct the risk and scores

From 9348a724d474d5fd807ceae4e0967bf1ed7f4446 Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 17:55:36 +0100
Subject: [PATCH 08/10] simplify code field_indicators, and update test-bbwp
 due to small changes

---
 R/bbwp_field_indicators.R  | 153 ++++++++++++++++---------------------
 tests/testthat/test-bbwp.R |  16 ++--
 2 files changed, 75 insertions(+), 94 deletions(-)

diff --git a/R/bbwp_field_indicators.R b/R/bbwp_field_indicators.R
index 401dc3b..e43acba 100644
--- a/R/bbwp_field_indicators.R
+++ b/R/bbwp_field_indicators.R
@@ -45,6 +45,7 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
   
   # add visual bindings
   D_RISK_NGW = D_RISK_NSW = D_RISK_PSW = D_RISK_NUE = D_RISK_WB = id = NULL
+  risk_cor = value = group = risk = mcf = WS = SLOPE = NULL
   
   # check length inputs
   arg.length <- max(
@@ -55,93 +56,73 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
     length(D_WUE_WWRI),length(D_WUE_WDRI),length(D_WUE_WHC)
   )
   
-  # add checks on input
-  
-  
   # copy input in one data.table
-  dt <- data.table(
-    id = 1:arg.length,
-    D_NGW_SCR = D_NGW_SCR,
-    D_NGW_LEA = D_NGW_LEA,
-    D_NGW_NLV = D_NGW_NLV,
-    D_NSW_SCR = D_NSW_SCR,
-    D_NSW_GWT = D_NSW_GWT,
-    D_NSW_RO = D_NSW_RO,
-    D_NSW_SLOPE = D_NSW_SLOPE,
-    D_NSW_WS = D_NSW_WS,
-    D_NSW_NLV = D_NSW_NLV,
-    D_PSW_SCR = D_PSW_SCR,
-    D_PSW_GWT = D_PSW_GWT,
-    D_PSW_RO = D_PSW_RO,
-    D_PSW_SLOPE = D_PSW_SLOPE,
-    D_PSW_WS = D_PSW_WS,
-    D_PSW_PCC = D_PSW_PCC,
-    D_PSW_PSG = D_PSW_PSG,
-    D_PSW_PRET = D_PSW_PRET,
-    D_NUE_WRI = D_NUE_WRI,
-    D_NUE_PBI = D_NUE_PBI,
-    D_NUE_WDRI = D_NUE_WDRI,
-    D_NUE_NLV = D_NUE_NLV,
-    D_WUE_WWRI = D_WUE_WWRI,
-    D_WUE_WDRI = D_WUE_WDRI,
-    D_WUE_WHC = D_WUE_WHC,
-    D_RISK_NGW = NA_real_,
-    D_RISK_NSW = NA_real_,
-    D_RISK_PSW = NA_real_,
-    D_RISK_NUE = NA_real_,
-    D_RISK_WB = NA_real_
-  )
-  
-  
-  # integrate all relative field risk indicators into one for indictor for N loss to groundwater
-  dt[, D_RISK_NGW := (wf(D_NGW_SCR,penalty = penalty) * D_NGW_SCR + 
-                  3 * wf(D_NGW_LEA,penalty = penalty) * D_NGW_LEA + 
-                  2 * wf(D_NGW_NLV,penalty = penalty) * D_NGW_NLV) /
-       (wf(D_NGW_SCR,penalty = penalty) + 3 * wf(D_NGW_LEA,penalty = penalty) + 2 * wf(D_NGW_NLV,penalty = penalty))]
-  
-  # integrate all relative field risk indicators into one for indictor for N loss to surface water
-  dt[, D_RISK_NSW := (wf(D_NSW_SCR,penalty = penalty) * D_NSW_SCR + 
-                      wf(D_NSW_GWT,penalty = penalty) * D_NSW_GWT + 
-                      wf(D_NSW_SLOPE,penalty = penalty) * D_NSW_SLOPE +
-                      wf(D_NSW_RO,penalty = penalty) * D_NSW_RO + 
-                      wf(D_NSW_WS,penalty = penalty) * D_NSW_WS + 
-                  3 * wf(D_NSW_NLV,penalty = penalty) * D_NSW_NLV ) /
-       (wf(D_NSW_SCR,penalty = penalty) + wf(D_NSW_GWT,penalty = penalty) + wf(D_NSW_SLOPE,penalty = penalty) + 
-          wf(D_NSW_RO,penalty = penalty) + wf(D_NSW_WS,penalty = penalty) + 3 * wf(D_NSW_NLV,penalty = penalty))]
-  
-  # integrate all relative field risk indicators into one for indictor for P loss to surface water
-  dt[, D_RISK_PSW := (2 * wf(D_PSW_SCR,penalty = penalty) * D_PSW_SCR + 
-                          wf(D_PSW_GWT,penalty = penalty) * D_PSW_GWT + 
-                      2 * wf(D_PSW_RO,penalty = penalty) * D_PSW_RO + 
-                          wf(D_PSW_SLOPE, penalty = penalty) * D_PSW_SLOPE +
-                      2 * wf(D_PSW_WS,penalty = penalty) * D_PSW_WS + 
-                          wf(D_PSW_PCC,penalty = penalty) * D_PSW_PCC + 
-                          wf(D_PSW_PSG,penalty = penalty) * D_PSW_PSG + 
-                          wf(D_PSW_PRET,penalty = penalty) * D_PSW_PRET) /
-       (2 * wf(D_PSW_SCR,penalty = penalty) + wf(D_PSW_GWT,penalty = penalty) + 2 * wf(D_PSW_RO,penalty = penalty) + wf(D_PSW_SLOPE,penalty = penalty) + 
-          2 * wf(D_PSW_WS,penalty = penalty) + wf(D_PSW_PCC,penalty = penalty) + wf(D_PSW_PSG,penalty = penalty) + wf(D_PSW_PRET,penalty = penalty))]
-  
-  # minimize risks when there are no ditches around (wet surrounding fraction < 0.2)
-  dt[D_NSW_WS <= 0.2 & D_PSW_SLOPE < 1,D_RISK_PSW := 0.1]
-  dt[D_NSW_WS <= 0.2 & D_PSW_SLOPE < 1,D_RISK_NSW := 0.1]
-  dt[D_NSW_WS <= 0.1 & D_PSW_SLOPE < 1,D_RISK_PSW := 0.01]
-  dt[D_NSW_WS <= 0.1 & D_PSW_SLOPE < 1,D_RISK_NSW := 0.01]
-  
-  # integrate all relative field risk indicators into one for indictor for N and P efficiency of inputs
-  dt[, D_RISK_NUE := (wf(D_NUE_WRI,penalty = penalty) * D_NUE_WRI + 
-                        2 * wf(D_NUE_PBI,penalty = penalty) * D_NUE_PBI + 
-                        wf(D_NUE_NLV,penalty = penalty) * D_NUE_NLV + 
-                        wf(D_NUE_WDRI,penalty = penalty) * D_NUE_WDRI) /
-       (wf(D_NUE_WRI,penalty = penalty) + 2 * wf(D_NUE_PBI,penalty = penalty) + wf(D_NUE_NLV,penalty = penalty) + wf(D_NUE_WDRI,penalty = penalty))]
-  
-  # integrate all relative field risk indicators into one for indictor for water retention and efficiency
-  dt[, D_RISK_WB := (wf(D_WUE_WWRI,penalty = penalty) * D_WUE_WWRI + 
-                       wf(D_WUE_WDRI,penalty = penalty) * D_WUE_WDRI + 
-                       2 * wf(D_WUE_WHC,penalty = penalty) * D_WUE_WHC) / (wf(D_WUE_WWRI,penalty = penalty) + wf(D_WUE_WDRI,penalty = penalty) + 2 * wf(D_WUE_WHC,penalty = penalty))]
-  
-  # normalise these indicators ???
-  
-  setorder(dt, id)
+  dt <- data.table(id = 1:arg.length,
+                   D_NGW_SCR = D_NGW_SCR,
+                   D_NGW_LEA = D_NGW_LEA,
+                   D_NGW_NLV = D_NGW_NLV,
+                   D_NSW_SCR = D_NSW_SCR,
+                   D_NSW_GWT = D_NSW_GWT,
+                   D_NSW_RO = D_NSW_RO,
+                   D_NSW_SLOPE = D_NSW_SLOPE,
+                   D_NSW_WS = D_NSW_WS,
+                   D_NSW_NLV = D_NSW_NLV,
+                   D_PSW_SCR = D_PSW_SCR,
+                   D_PSW_GWT = D_PSW_GWT,
+                   D_PSW_RO = D_PSW_RO,
+                   D_PSW_SLOPE = D_PSW_SLOPE,
+                   D_PSW_WS = D_PSW_WS,
+                   D_PSW_PCC = D_PSW_PCC,
+                   D_PSW_PSG = D_PSW_PSG,
+                   D_PSW_PRET = D_PSW_PRET,
+                   D_NUE_WRI = D_NUE_WRI,
+                   D_NUE_PBI = D_NUE_PBI,
+                   D_NUE_WDRI = D_NUE_WDRI,
+                   D_NUE_NLV = D_NUE_NLV,
+                   D_WUE_WWRI = D_WUE_WWRI,
+                   D_WUE_WDRI = D_WUE_WDRI,
+                   D_WUE_WHC = D_WUE_WHC
+                  )
+  
+  # melt the data.table to simplify corrections
+  dt.melt <- data.table::melt(dt, id.vars = 'id',variable.name = 'risk')
+  
+  # add correction factor based on risk itself
+  dt.melt[,risk_cor := wf(value,type = "indicators",penalty = penalty)]
+  
+  # add groups of risk indicators
+  dt.melt[,group := gsub('_[A-Z]+$','',gsub('D_','',risk))]
+  
+  # add manual weighing factor for risks
+  dt.melt[,mcf := 1]
+  dt.melt[group=='NGW' & grepl('_LEA$',risk), mcf := 2]
+  dt.melt[group=='NGW' & grepl('_NLV$',risk), mcf := 3]
+  dt.melt[group=='NSW' & grepl('_NLV$',risk), mcf := 3]
+  dt.melt[group=='PSW' & grepl('_SCR$|_RO$|_WS$',risk), mcf := 2]
+  dt.melt[group=='NUE' & grepl('_PBI$',risk), mcf := 2]
+  dt.melt[group=='WUE' & grepl('_WHC$',risk), mcf := 2]
+  
+   
+  # minimize risks when there are no ditches around the field (wet surrounding fraction < 0.2)
+  
+    # add criteria properties as column (to use as filter)
+    dt.melt[,WS := value[risk=='D_NSW_WS'],by='id']
+    dt.melt[,SLOPE := value[risk=='D_NSW_SLOPE'],by='id']
+    
+    # ensure that the final risk after aggregation gets the value 0.1 or 0.01
+    dt.melt[WS <= 0.2 & SLOPE < 1 & group %in% c('NSW','PSW'), c('mcf','risk_cor','value') :=  list(1,1000,0.1)]
+    dt.melt[WS <= 0.1 & SLOPE < 1 & group %in% c('NSW','PSW'), c('mcf','risk_cor','value') :=  list(1,1000,0.01)]
+    dt.melt[,c('WS','SLOPE') := NULL]
+  
+  # calculate the mean aggregated risk indicators
+  dt <- dt.melt[,list(risk = sum(risk_cor * value * mcf)/sum(risk_cor * mcf)),by=c('id','group')]
+  dt <- dcast(dt,id~group,value.var='risk')
+  
+  # replace output names
+  setnames(dt,old=c('NGW','NSW','NUE','PSW','WUE'),new = c('D_RISK_NGW','D_RISK_NSW','D_RISK_NUE','D_RISK_PSW','D_RISK_WB'))
+  
+  # sort output based on id
+  setorder(dt,id)
   
   # extract output
   out <- dt[,mget(c('D_RISK_NGW','D_RISK_NSW','D_RISK_PSW','D_RISK_NUE','D_RISK_WB'))]
diff --git a/tests/testthat/test-bbwp.R b/tests/testthat/test-bbwp.R
index 6120f2b..3c13654 100644
--- a/tests/testthat/test-bbwp.R
+++ b/tests/testthat/test-bbwp.R
@@ -115,14 +115,14 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
     test_that("check bbwp", {
       expect_equal(
         object = test$fields$s_bbwp_tot,
-        expected = c(69,45,29),
+        expected = c(68,45,28),
         tolerance = 0.01)
     })
     
     test_that("check bbwp", {
       expect_equal(
         object = as.numeric(unlist(test$farm)),
-        expected = c(58,77,62,66,46,90),
+        expected = c(57,72,62,66,46,90),
         tolerance = 0.01)
     })
 
@@ -227,14 +227,14 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = test$fields$s_bbwp_tot,
-      expected = c(90,45,55),
+      expected = c(89,45,55),
       tolerance = 0.01)
   })
   
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(70,85,63,67,72,92),
+      expected = c(69,82,63,67,72,92),
       tolerance = 0.01)
   })
 
@@ -291,14 +291,14 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = test$fields$s_bbwp_tot,
-      expected = c(69,45,29),
+      expected = c(68,45,28),
       tolerance = 0.01)
   })
   
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(58,77,62,66,46,90),
+      expected = c(57,72,62,66,46,90),
       tolerance = 0.01)
   })
   
@@ -342,7 +342,7 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(24,86,8,6,32,84),
+      expected = c(24,81,8,6,32,84),
       tolerance = 0.01)
   })
   
@@ -430,7 +430,7 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(53,86,49,43,32,84),
+      expected = c(52,81,49,43,32,84),
       tolerance = 0.01)
   })
   

From 005e6babd0117c8cfbc6d38955d2af47469b5a8c Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 18:00:52 +0100
Subject: [PATCH 09/10] update news

---
 NEWS.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 11bcfd7..8c65d88 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,9 @@
 * possibility to falisfy the weighing fraction for evaluation of risks in `wf` function, default set to TRUE, #BBWP-67
 * argument `penalty` added to the functions `bbwp_field_indicators`, `bbwp_field_scores` and `bbwp_main`, #BBWP-67
 
+## Changed
+* function `bbwp_field_indicators` is simplified
+
 # BBWPC v2.1.1 2023-12-27
 ## Added
 * function `bbwp_format_sc_wenr` to ensure that B_SC_WENR is an integer conform format Van den Akker (2006), #BBWP-66

From 9a4269efb280a6982a87a14e9171f2fa7061a01a Mon Sep 17 00:00:00 2001
From: Gerard <gerard.ros@nmi-agro.nl>
Date: Thu, 28 Dec 2023 18:05:01 +0100
Subject: [PATCH 10/10] redo changes in test-bbwp due to small error in
 bbwp_field_indicators. now test remains unchanged

---
 R/bbwp_field_indicators.R  |  4 ++--
 tests/testthat/test-bbwp.R | 17 +++++++++--------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/R/bbwp_field_indicators.R b/R/bbwp_field_indicators.R
index e43acba..202ce59 100644
--- a/R/bbwp_field_indicators.R
+++ b/R/bbwp_field_indicators.R
@@ -95,8 +95,8 @@ bbwp_field_indicators <- function(D_NGW_SCR,D_NGW_LEA,D_NGW_NLV,
   
   # add manual weighing factor for risks
   dt.melt[,mcf := 1]
-  dt.melt[group=='NGW' & grepl('_LEA$',risk), mcf := 2]
-  dt.melt[group=='NGW' & grepl('_NLV$',risk), mcf := 3]
+  dt.melt[group=='NGW' & grepl('_LEA$',risk), mcf := 3]
+  dt.melt[group=='NGW' & grepl('_NLV$',risk), mcf := 2]
   dt.melt[group=='NSW' & grepl('_NLV$',risk), mcf := 3]
   dt.melt[group=='PSW' & grepl('_SCR$|_RO$|_WS$',risk), mcf := 2]
   dt.melt[group=='NUE' & grepl('_PBI$',risk), mcf := 2]
diff --git a/tests/testthat/test-bbwp.R b/tests/testthat/test-bbwp.R
index 3c13654..da02381 100644
--- a/tests/testthat/test-bbwp.R
+++ b/tests/testthat/test-bbwp.R
@@ -115,14 +115,14 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
     test_that("check bbwp", {
       expect_equal(
         object = test$fields$s_bbwp_tot,
-        expected = c(68,45,28),
+        expected = c(69,45,29),
         tolerance = 0.01)
     })
     
     test_that("check bbwp", {
       expect_equal(
         object = as.numeric(unlist(test$farm)),
-        expected = c(57,72,62,66,46,90),
+        expected = c(58,77,62,66,46,90),
         tolerance = 0.01)
     })
 
@@ -227,14 +227,14 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = test$fields$s_bbwp_tot,
-      expected = c(89,45,55),
+      expected = c(90,45,55),
       tolerance = 0.01)
   })
   
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(69,82,63,67,72,92),
+      expected = c(70,85,63,67,72,92),
       tolerance = 0.01)
   })
 
@@ -291,14 +291,14 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = test$fields$s_bbwp_tot,
-      expected = c(68,45,28),
+      expected = c(69,45,29),
       tolerance = 0.01)
   })
   
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(57,72,62,66,46,90),
+      expected = c(58,77,62,66,46,90),
       tolerance = 0.01)
   })
   
@@ -342,7 +342,7 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(24,81,8,6,32,84),
+      expected = c(24,86,8,6,32,84),
       tolerance = 0.01)
   })
   
@@ -430,7 +430,7 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
   test_that("check bbwp", {
     expect_equal(
       object = as.numeric(unlist(test$farm)),
-      expected = c(52,81,49,43,32,84),
+      expected = c(53,86,49,43,32,84),
       tolerance = 0.01)
   })
   
@@ -509,4 +509,5 @@ test <- bbwp(B_SOILTYPE_AGR = c('dekzand', 'loess', 'rivierklei'),
       LSW = NULL
     ))
   })
+  
   
\ No newline at end of file