Revise dumpsite and trash scores with updated RSA point spreadsheet

Updated spreadsheet is in the previous commit

Author: shannarucker

R/trash.R

@@ -23,13 +23,13 @@ assess_trash <- function(df_reach, reach_prefix_from_table, reach_prefix_from_la
                   id = dplyr::all_of(paste0(reach_prefix_from_table, ".featureGlobalID_key")),
                   date = dplyr::all_of(paste0(reach_prefix_from_table, ".assessment_time")),
                   trash_extent = dplyr::all_of(paste0(reach_prefix_from_table, ".trash_extent"))) %>%
-    dplyr::filter(date >= start_date & date <= end_date) %>%
-    dplyr::group_by(id) %>%
-    dplyr::slice_max(date, n=1, with_ties = FALSE) %>% # Remove duplicate reaches. Keep most recent reach assessment. If same date/time and ID, maintain only one record
-    dplyr::ungroup() %>%
     dplyr::left_join(trash_score, by = "trash_extent") %>%
     dplyr::left_join(location_name, by = "location_name") %>%
-    dplyr::filter(!is.na(trash_extent))   # Remove data records with no trash extent entry
+    dplyr::filter(!is.na(trash_extent)) %>%    # Remove data records with no trash extent entry
+    dplyr::arrange(score) %>% # Arrange assessments by score so When removing duplicates, if there are duplicate reaches with the same time, choose the lowest score to be more conservative
+    dplyr::group_by(id) %>%
+    dplyr::slice_max(date, n=1, with_ties = FALSE) %>% # Remove duplicate reaches. Keep most recent reach assessment. If same date/time and ID, maintain only one record
+    dplyr::ungroup()
 
 
   df_score <- df_summary %>%

data/StreamPoints_20231002_INT.xlsx

@@ -1,26 +1,26 @@
-"","sci_subshed","Dumpsites","Effective Impervious Area","Temperature, water","pH","Dissolved oxygen (DO)","Escherichia coli","Turbidity","Conductivity","Nitrogen","Phosphorus, Total (as P)","Connectivity","Fish","Habitat","Macroinvertebrates"
-"1","Broad Branch",7,2,10,9.49484604605374,10,3.96201632162848,10,1.39551171022171,2.53189561427939,10,10,2,4,6
-"2","Fort Davis Tributary",1,2,10,10,10,4.56378937695466,3.40381314529514,1.28521704525446,0.950005376536892,1.78543632558786,1,1,5,5
-"3","Fort Dupont Tributary",2,8,10,10,8.19644566724721,4.39637929649141,3.667361623274,2.99612324159937,0.749069894299005,10,1,3,4,6
-"4","Fort Stanton Tributary",4,1,9.49458887028815,10,10,3.49306972579195,8.24161710963122,2.14961627380251,0.950005376536892,10,1,1,3,7
-"5","Normanstone Creek",4,1,10,8.9888961180284,10,4.46891175504634,10,1.49230558316491,2.58568816872641,10,10,3,3,6
-"6","Oxon Run",8,1,9.49482509665549,10,10,4.08034192298863,7.26446748330366,2.73668115439965,0.677223449104501,0.963293817107756,10,4,4,4
-"7","Pinehurst Branch",7,6,10,9.45561327204199,10,6.86529198320573,10,1.64381726305677,2.53189561427939,10,10,2,4,5
-"8","Rock Creek",7,1,9.03991429859265,9.63931584712039,10,4.75298766520739,8.85351874858907,3.01758638876789,2.35646823207748,10,10,5,4,5
-"9","Watts Branch",5,1,9.32024027311975,9.03799489304956,9.94283156569335,3.52383649640539,8.10990235278729,2.71307679688268,0.80598894736693,4.92721388547487,10,4,3,6
-"10","Battery Kemble Creek",10,6,10,10,10,7.17122657287291,10,1.32946707229891,1.1722461961956,10,10,3,4,7
-"11","Dalecarlia Tributary",10,4,9.49281310022025,9.49429215204554,10,2.26543812278347,7.88130147148155,1.57723215112077,1.64140564675688,1.50035060003774,1,2,3,6
-"12","Dumbarton Oaks",10,4,10,10,10,8.54782802837774,10,1.70833294620897,1.32807710704536,2.8679579947462,10,3,5,7
-"13","Foundry Branch",10,2,10,10,10,5.43588122762784,4.44089503244838,2.9615349603606,2.05698424129608,10,1,1,4,NA
-"14","Fort Chaplin Tributary",10,2,10,10,9.44055926057385,3.66863632512962,8.77121712686461,2.01955422326341,1.09628813677057,10,1,1,4,3
-"15","Fenwick Branch",10,3,9.49476657878656,10,10,6.8791964501452,10,1.75285115573104,2.32427732195356,10,10,2,3,6
-"16","Hickey Run",10,9,9.32570696570447,10,9.31006357105735,1.71733915151806,7.52739827502453,1.92353016456839,0.749069894299005,2.7927191991411,10,6,2,4
-"17","Klingle Valley Run",10,2,10,10,10,6.5392010054142,10,2.16336911176854,1.52948677601239,10,10,2,3,6
-"18","Luzon Branch",10,1,10,10,10,2.74149789121648,5.16856938057974,1.68139016788936,2.13654818496565,2.91985046082419,10,2,3,6
-"19","Reservation 630",10,3,9.49484222518253,10,10,4.89875662885154,6.54810880322023,1.95694969141548,2.32427732195356,10,10,4,7,7
-"20","Nash Run",10,3,8.97058038494947,9.49162145959481,10,2.85130675778872,8.98648127446675,3.13741218623777,1.09628813677057,10,10,6,5,4
-"21","Pope Branch",10,3,10,10,10,6.70307871860358,4.63848137391428,2.04750999680075,0.950005376536892,10,1,4,6,8
-"22","Portal Branch",10,3,10,8.98692894850945,10,4.24400479220216,6.90674993457207,1.02448007263146,2.74453544775747,10,10,1,3,6
-"23","Piney Branch",10,1,10,10,10,6.24485935433058,10,1.37920467622303,2.43350524767764,10,10,3,2,4
-"24","Soapstone Creek",10,1,10,8.98764540312439,10,6.80566463860387,10,1.91408087817814,2.53189561427939,2.88434296861746,10,2,3,6
-"25","Texas Avenue Tributary",10,3,10,10,10,3.54658539291944,7.3375495518317,1.74050116850977,0.837784090876652,10,1,1,5,3
+"","sci_subshed","Trash","Dumpsites","Effective Impervious Area","Temperature, water","pH","Dissolved oxygen (DO)","Escherichia coli","Turbidity","Conductivity","Nitrogen","Phosphorus, Total (as P)","Connectivity","Fish","Habitat","Macroinvertebrates"
+"1","Battery Kemble Creek",8.375,10,6,10,10,10,7.17122657287291,10,1.32946707229891,1.1722461961956,10,10,3,4,7
+"2","Broad Branch",8.64516129032258,7,2,10,9.49484604605374,10,3.96201632162848,10,1.39551171022171,2.53189561427939,10,10,2,4,6
+"3","Dalecarlia Tributary",9.25,10,4,9.49281310022025,9.49429215204554,10,2.26543812278347,7.88130147148155,1.57723215112077,1.64140564675688,1.50035060003774,1,2,3,6
+"4","Dumbarton Oaks",7.75,10,4,10,10,10,8.54782802837774,10,1.70833294620897,1.32807710704536,2.8679579947462,10,3,5,7
+"5","Fenwick Branch",7.42857142857143,10,3,9.49476657878656,10,10,6.8791964501452,10,1.75285115573104,2.32427732195356,10,10,2,3,6
+"6","Fort Chaplin Tributary",2.5,10,2,10,10,9.44055926057385,3.66863632512962,8.77121712686461,2.01955422326341,1.09628813677057,10,1,1,4,3
+"7","Fort Davis Tributary",7.27272727272727,1,2,10,10,10,4.56378937695466,3.40381314529514,1.28521704525446,0.950005376536892,1.78543632558786,1,1,5,5
+"8","Fort Dupont Tributary",7.51063829787234,2,8,10,10,8.19644566724721,4.39637929649141,3.667361623274,2.99612324159937,0.749069894299005,10,1,3,4,6
+"9","Fort Stanton Tributary",6.57142857142857,4,1,9.49458887028815,10,10,3.49306972579195,8.24161710963122,2.14961627380251,0.950005376536892,10,1,1,3,7
+"10","Foundry Branch",8.91803278688525,10,2,10,10,10,5.43588122762784,4.44089503244838,2.9615349603606,2.05698424129608,10,1,1,4,NA
+"11","Hickey Run",8.03846153846154,10,9,9.32570696570447,10,9.31006357105735,1.71733915151806,7.52739827502453,1.92353016456839,0.749069894299005,2.7927191991411,10,6,2,4
+"12","Klingle Valley Run",7.4,10,2,10,10,10,6.5392010054142,10,2.16336911176854,1.52948677601239,10,10,2,3,6
+"13","Luzon Branch",5.2,10,1,10,10,10,2.74149789121648,5.16856938057974,1.68139016788936,2.13654818496565,2.91985046082419,10,2,3,6
+"14","Nash Run",7.6,10,3,8.97058038494947,9.49162145959481,10,2.85130675778872,8.98648127446675,3.13741218623777,1.09628813677057,10,10,6,5,4
+"15","Normanstone Creek",7.35294117647059,4,1,10,8.9888961180284,10,4.46891175504634,10,1.49230558316491,2.58568816872641,10,10,3,3,6
+"16","Oxon Run",5.8,8,1,9.49482509665549,10,10,4.08034192298863,7.26446748330366,2.73668115439965,0.677223449104501,0.963293817107756,10,4,4,4
+"17","Pinehurst Branch",8.57142857142857,7,6,10,9.45561327204199,10,6.86529198320573,10,1.64381726305677,2.53189561427939,10,10,2,4,5
+"18","Piney Branch",8,10,1,10,10,10,6.24485935433058,10,1.37920467622303,2.43350524767764,10,10,3,2,4
+"19","Pope Branch",8,10,3,10,10,10,6.70307871860358,4.63848137391428,2.04750999680075,0.950005376536892,10,1,4,6,8
+"20","Portal Branch",7,10,3,10,8.98692894850945,10,4.24400479220216,6.90674993457207,1.02448007263146,2.74453544775747,10,10,1,3,6
+"21","Reservation 630",9.34782608695652,10,3,9.49484222518253,10,10,4.89875662885154,6.54810880322023,1.95694969141548,2.32427732195356,10,10,4,7,7
+"22","Rock Creek",8.19158878504673,7,1,9.03991429859265,9.63931584712039,10,4.75298766520739,8.85351874858907,3.01758638876789,2.35646823207748,10,10,5,4,5
+"23","Soapstone Creek",8.3,10,1,10,8.98764540312439,10,6.80566463860387,10,1.91408087817814,2.53189561427939,2.88434296861746,10,2,3,6
+"24","Texas Avenue Tributary",7,10,3,10,10,10,3.54658539291944,7.3375495518317,1.74050116850977,0.837784090876652,10,1,1,5,3
+"25","Watts Branch",3.71428571428571,5,1,9.32024027311975,9.03799489304956,9.94283156569335,3.52383649640539,8.10990235278729,2.71307679688268,0.80598894736693,4.92721388547487,10,4,3,6

data/StreamReaches_20231002_INT.xlsx

@@ -14,16 +14,30 @@ knitr::opts_chunk$set(
 )
 ```
 
-# Effective Impervious Area (EIA)
+# Hydrology Index
 
-1.  The Rock Creek mainstem includes both the MS4 and CSS. The Rock Creek watershed also includes additional area beyond the Rock Creek SCI subwatersheds. What area of Rock Creek is used for the SCI analysis?
+##### *Effective Impervious Area (EIA)*
 
-    **The entire Rock Creek watershed is used in the SCI analysis. See the "eia_rock_creek" tab in the lookup spreadsheet for a full list of subsheds included.**
+**The Rock Creek mainstem includes both the MS4 and CSS. The Rock Creek watershed also includes additional area beyond the Rock Creek SCI subwatersheds. What area of Rock Creek is used for the SCI analysis?**
+
+The entire Rock Creek watershed is used in the SCI analysis. See the "eia_rock_creek" tab in the lookup spreadsheet for a full list of subsheds included.
+
+<br>
+
+# Human Health Index
+
+##### *Dumpsites, Trash, E. coli*
+
+**What timeframe is used for the trash and dumpsite analyses?**
+
+Since the analysis uses data from the Rapid Stream Assessments (RSA), the timeframe can vary and is not limited to a set five year period. The most recent data from each assessment point and reach is used.
 
 <br>
 
 # Water Quality Index
 
+##### *Dissolved Oxygen, Turbidity, Conductivity, Temperature, Nitrogen, Phosphorus, pH*
+
 **How are non-detects handled in the dataset?**
 
 The reporting limit is used for non-detect values. For example, results reported as \<0.010, got incorporated in the analysis as 0.010.
@@ -40,6 +54,8 @@ For the nutrient WQ indicatiors (TN and TP), the assess_wq_nutrients() requires
 
 # Aquatic Life Index
 
+##### *Fish, Habitat, Macroinvertebrate, Connection to the Mainstem*
+
 **How are the aquatic life metrics calculated?** 
 
 All four metrics get calculated outside of the R package and get incorporated through lookup tables in data/lookup_tables.xlsx.
@@ -111,7 +127,7 @@ Possible things to try include:
 
 <br>
 
-# Contacts
+# Contact
 
 **Who should I contact if I have questions about the R package?**
 

output/all_scores.csv

@@ -107,7 +107,7 @@ macro <- macroinvertebrate_summary %>% dplyr::select(sci_subshed,
 
 
 # Assess RSA Data
-# trash <- assess_trash(df_reach, reach_prefix_from_table, reach_prefix_from_layer)
+trash <- assess_trash(df_reach, reach_prefix_from_table, reach_prefix_from_layer)
 dumpsite <- assess_dumpsites(df_point, df_reach,
                              reach_prefix_from_table, reach_prefix_from_layer,
                              point_prefix_from_table, point_prefix_from_layer)
@@ -117,9 +117,8 @@ eia <- assess_eia()
 
 # Compile scores
 all_scores <-
-  # trash[["score"]] %>%
-  # dplyr::full_join(dumpsite[["score"]]) %>%
-  dumpsite[["score"]] %>%
+  trash[["score"]] %>%
+  dplyr::full_join(dumpsite[["score"]]) %>%
   dplyr::full_join(eia[["score"]]) %>%
   dplyr::full_join(temp[["score"]]) %>%
   dplyr::full_join(ph[["score"]]) %>%