Merge pull request #331 from USEPA/replicates_kh

Pair Replicates Function
USEPA · Jan 22, 2024 · 7e0aaeb · 7e0aaeb
2 parents 96bdcb7 + f9b5333
commit 7e0aaeb
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Showing 12 changed files with 474 additions and 206 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -48,6 +48,7 @@ export(TADA_InsertBreaks)
 export(TADA_JoinWQPProfiles)
 export(TADA_OrderCols)
 export(TADA_OverviewMap)
+export(TADA_PairReplicates)
 export(TADA_RandomTestingData)
 export(TADA_ReadWQPWebServices)
 export(TADA_RetainRequired)

diff --git a/R/DataDiscoveryRetrieval.R b/R/DataDiscoveryRetrieval.R
@@ -702,10 +702,11 @@ TADA_JoinWQPProfiles <- function(FullPhysChem = "null",
     if (nrow(Sites.df) > 0) {
       join1 <- FullPhysChem.df %>%
         # join stations to results
-        dplyr::left_join(Sites.df, 
-                         by = "MonitoringLocationIdentifier", 
-                         multiple = "all",
-                         relationship = "many-to-many") %>%
+        dplyr::left_join(Sites.df,
+          by = "MonitoringLocationIdentifier",
+          multiple = "all",
+          relationship = "many-to-many"
+        ) %>%
         # remove ".x" suffix from column names
         dplyr::rename_at(dplyr::vars(dplyr::ends_with(".x")), ~ stringr::str_replace(., "\\..$", "")) %>%
         # remove columns with ".y" suffix

diff --git a/R/Figures.R b/R/Figures.R
@@ -399,22 +399,24 @@ TADA_OverviewMap <- function(.data) {
     sumdat <- .data %>%
       dplyr::group_by(MonitoringLocationIdentifier, MonitoringLocationName, TADA.LatitudeMeasure, TADA.LongitudeMeasure) %>%
       dplyr::summarise("Sample_Count" = length(unique(ResultIdentifier)), "Visit_Count" = length(unique(ActivityStartDate)), "Parameter_Count" = length(unique(TADA.CharacteristicName)), "Organization_Count" = length(unique(OrganizationIdentifier)))
-
-    pt_sizes <- round(quantile(sumdat$Sample_Count, probs = c(0.1,0.25, 0.5, 0.75)), 0)
-    pt_labels <- c(paste0("<=",pt_sizes[1]),
-                  paste0(">",pt_sizes[1]),
-                  paste0(">",pt_sizes[2]),
-                  paste0(">",pt_sizes[3]),
-                  paste0(">",pt_sizes[4]))
-
+
+    pt_sizes <- round(quantile(sumdat$Sample_Count, probs = c(0.1, 0.25, 0.5, 0.75)), 0)
+    pt_labels <- c(
+      paste0("<=", pt_sizes[1]),
+      paste0(">", pt_sizes[1]),
+      paste0(">", pt_sizes[2]),
+      paste0(">", pt_sizes[3]),
+      paste0(">", pt_sizes[4])
+    )
+
     sumdat$radius <- 5
-    sumdat$radius <-ifelse(sumdat$Sample_Count > pt_sizes[1], 10, sumdat$radius)
-    sumdat$radius <-ifelse(sumdat$Sample_Count > pt_sizes[2], 15, sumdat$radius)
+    sumdat$radius <- ifelse(sumdat$Sample_Count > pt_sizes[1], 10, sumdat$radius)
+    sumdat$radius <- ifelse(sumdat$Sample_Count > pt_sizes[2], 15, sumdat$radius)
     sumdat$radius <- ifelse(sumdat$Sample_Count > pt_sizes[3], 20, sumdat$radius)
     sumdat$radius <- ifelse(sumdat$Sample_Count > pt_sizes[4], 30, sumdat$radius)
-    
+
     site_size <- data.frame(Sample_n = pt_labels, Point_size = c(5, 10, 15, 20, 30))
-  
+
     site_legend <- subset(site_size, site_size$Point_size %in% unique(sumdat$radius))
 
     pal <- leaflet::colorBin(