Adjust date range. Used most recent start year that allows for all WQ parameters to be assessed.

Turbidity is the limiting parameter. The most recent year turbidity results are available for the the stations of interest and in units of NTU is 2017. -- Updated code to include a warning when parameters are missing from the processed dataframe.

Author: shannarucker

R/process.R

@@ -40,7 +40,7 @@ format_wq <- function(df){
                                                    TRUE ~ result_format)) %>%
     dplyr::mutate(location_format = gsub("\\s+", "", Location)) %>% # Remove all spaces from location_id
     dplyr::mutate(date_format = as.Date(Date, format = "%d %b %Y"),
-                  result_format = as.numeric(result_format)) # Results in warning that NAs introduced by coercion - this is intended result)
+                  result_format = suppressWarnings(as.numeric(result_format))) # Results in warning that NAs introduced by coercion - this is intended result)
 
 
   return(df)
@@ -90,6 +90,15 @@ process_wq <- function(df, start_date, end_date){
       qualifier = qualifier_format
     )
 
+  # Identify missing parameters
+  missing_params <- dplyr::setdiff(params, unique(df_processed$parameter))
+
+  # Warn the user if any parameters are missing
+  if (length(missing_params) > 0) {
+    warning("The following parameters are missing from the filtered dataset: ",
+            paste(missing_params, collapse = ", "), ". Consider expanding analysis date range.")
+  }
+
 
 
 

output/all_scores.csv

@@ -1,26 +1,26 @@
 "","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
+"1","Battery Kemble Creek",8.375,10,6,10,10,10,6.32062005095886,10,1.29231798230656,1.1722461961956,10,10,3,4,7
+"2","Broad Branch",8.64516129032258,7,2,10,9.11598058121053,10,3.46549967300485,10,1.40786928664922,2.53189561427939,10,10,2,4,6
+"3","Dalecarlia Tributary",9.25,10,4,10,9.11501612829956,10,1.79924220701643,5.39181210894379,1.54095748278918,1.64140564675688,1.50035060003774,1,2,3,6
+"4","Dumbarton Oaks",7.75,10,4,10,10,10,8.69454411312198,10,1.7182364203714,1.32807710704536,2.8679579947462,10,3,5,7
+"5","Fenwick Branch",7.42857142857143,10,3,9.11584178377435,10,10,7.91414335091951,10,1.67080476066,2.32427732195356,10,10,2,3,6
+"6","Fort Chaplin Tributary",2.5,10,2,10,10,10,3.14328341096651,6.7504762638985,2.34331228746609,1.09628813677057,10,1,1,4,3
+"7","Fort Davis Tributary",7.27272727272727,1,2,10,10,10,4.22286031198727,4.18921125717516,1.35529464548602,0.950005376536892,1.78543632558786,1,1,5,5
+"8","Fort Dupont Tributary",7.51063829787234,2,8,10,10,6.96284375057502,3.64726473466637,2.43327471561426,3.40901285108323,0.749069894299005,10,1,3,4,6
+"9","Fort Stanton Tributary",6.57142857142857,4,1,10,10,10,3.29121342861143,10,2.20279397836273,0.950005376536892,10,1,1,3,7
+"10","Foundry Branch",8.91803278688525,10,2,10,10,10,5.66456777163845,3.2907745424067,3.74323286480178,2.05698424129608,10,1,1,4,NA
+"11","Hickey Run",8.03846153846154,10,9,9.41009036527631,10,9.40152724571608,1.4726563880943,8.13425471258536,1.83124163066893,0.749069894299005,2.7927191991411,10,6,2,4
+"12","Klingle Valley Run",7.4,10,2,10,10,10,6.77483210090502,10,2.59915902790879,1.52948677601239,10,10,2,3,6
+"13","Luzon Branch",5.2,10,1,10,10,10,2.78813266445486,2.9961918649383,2.02783283938377,2.13654818496565,2.91985046082419,10,2,3,6
+"14","Nash Run",7.6,10,3,9.11248888034847,10,10,2.71471677210064,10,3.30455432114584,1.09628813677057,10,10,6,5,4
+"15","Normanstone Creek",7.35294117647059,4,1,10,9.1135271129832,10,3.89478721657816,10,1.52837904138215,2.58568816872641,10,10,3,3,6
+"16","Oxon Run",5.8,8,1,10,10,10,4.0747186744388,10,2.27679630352316,0.677223449104501,0.963293817107756,10,4,4,4
+"17","Pinehurst Branch",8.57142857142857,7,6,10,10,10,6.16093987885743,10,1.31319413147893,2.53189561427939,10,10,2,4,5
+"18","Piney Branch",8,10,1,10,10,10,6.0165044795982,10,1.4437683502385,2.43350524767764,10,10,3,2,4
+"19","Pope Branch",8,10,3,10,10,10,6.71945403858055,10,2.05640672559587,0.950005376536892,10,1,4,6,8
+"20","Portal Branch",7,10,3,10,9.10792604923647,10,4.31380455155285,4.85620423789826,1.02900740067405,2.74453544775747,10,10,1,3,6
+"21","Reservation 630",9.34782608695652,10,3,10,10,10,5.10335745387789,4.89901716957291,2.34406341759797,2.32427732195356,10,10,4,7,7
+"22","Rock Creek",8.19158878504673,7,1,8.96387389248844,9.73928966893275,10,4.47912349705504,9.55547144639708,3.31713855234648,2.35646823207748,10,10,5,4,5
+"23","Soapstone Creek",8.3,10,1,10,9.11382163130491,10,6.3737125830251,10,2.22860207640777,2.53189561427939,2.88434296861746,10,2,3,6
+"24","Texas Avenue Tributary",7,10,3,10,10,10,3.32974708185848,6.39509486095813,1.73143114170272,0.837784090876652,10,1,1,5,3
+"25","Watts Branch",3.71428571428571,5,1,9.50858726011676,9.21408928798276,10,3.29401925724737,7.87140978534999,2.76165269687594,0.80598894736693,4.92721388547487,10,4,3,6

workflow.R

@@ -8,15 +8,16 @@ devtools::load_all(".")
 # Input Variables ---------------------------------------------------------
 
 # Excel spreadsheet with Ambient Water Quality Data
-df_wq <- readxl::read_excel("data/ARII_Xtab_AmbWQ_SCI_downloaded_20250102.xlsx")
+df_wq <- readxl::read_excel("data/ARII_Xtab_AmbWQ_SCI_downloaded_20250102.xlsx",
+                            col_types = c("text","text","date","text","text","date", "text","text","text","text"))
 
 # Excel spreadsheet with Rapid Stream Assessment (RSA) reach and point data
 df_reach <- readxl::read_excel("data/StreamReaches_20241105.xlsx")
 df_point <- readxl::read_excel("data/StreamPoints_20241105_INT.xlsx")
 
 # Date ranges used for filtering water quality data
-start_date <- "2015-07-01"
-end_date <- "2020-06-30"
+start_date <- "2017-01-01"
+end_date <- "2024-12-31"
 
 # Field name prefixes for RSA dataset
 # Prefixes change depending on layer and table names pulled from geodatabase