Initial work for making "Chemical" a mandatory column in the chemical…

… tab.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: toxEval
 Type: Package
 Title: Exploring Biological Relevance of Environmental Chemistry Observations
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(person("Laura", "DeCicco", 
                      role = c("aut","cre"),
                      email = "ldecicco@usgs.gov",

NEWS

@@ -1,3 +1,8 @@
+toxEval 1.3.1
+===========
+* Made "Chemical" a required column in the Chemical tab. Now all plot names will key off that column instead of the names listed in tox_chemicals.
+*
+
 toxEval 1.3.0
 ===========
 * Switched to version 3.5 of the ToxCast database

R/create_toxEval.R

@@ -82,10 +82,10 @@ create_toxEval <- function(excel_file_path, ...) {
     names(chem_info) <- names(chem_info) %>%
       allowed_names(c("casrn", "casn", "CASRN", "CASN"), "CAS")
 
-    if ("CAS" %in% names(chem_info)) {
+    if (all(c("CAS", "Chemical") %in% names(chem_info))){
       chem_info$CAS <- as.character(chem_info$CAS)
     } else {
-      message("Chemical tab missing CAS column")
+      message("Chemical tab missing CAS or Chemical column")
     }
   }
 

R/get_chemical_summary.R

@@ -83,30 +83,29 @@ get_chemical_summary <- function(tox_list, ACC = NULL, filtered_ep = "All",
 
   if (is.null(ACC)) {
     ACC <- tox_list[["benchmarks"]]
+    ACC <- dplyr::select(ACC, CAS, endPoint, ACC_value, groupCol)
   } else {
-    ACC <- dplyr::select(ACC, CAS, chnm, endPoint, ACC_value)
+    ACC <- dplyr::select(ACC, CAS, endPoint, ACC_value)
   }
-
+
+
+
   if (is.character(chem_data$Value)) {
     chem_data$Value <- as.numeric(chem_data$Value)
   }
 
   chemical_summary <- full_join(ACC,
-    dplyr::select(
-      chem_data,
-      CAS, SiteID, Value, `Sample Date`
-    ),
-    by = "CAS"
-  ) %>%
-    filter(
+    dplyr::select(chem_data,
+                   CAS, SiteID, Value, `Sample Date`),
+            by = "CAS") %>%
+    dplyr::filter(
       !is.na(ACC_value),
-      !is.na(Value)
-    ) %>%
-    mutate(EAR = Value / ACC_value) %>%
-    rename(
-      site = SiteID,
-      date = `Sample Date`
-    )
+      !is.na(Value)) %>%
+    dplyr::mutate(EAR = Value / ACC_value) %>%
+    dplyr::rename(site = SiteID,
+                  date = `Sample Date`) %>%
+    dplyr::left_join(dplyr::select(chem_info, CAS, chnm = Chemical),
+                     by = "CAS")
 
   if (all(filtered_ep != "All")) {
     chemical_summary <- chemical_summary %>%

R/side_by_side.R

@@ -149,7 +149,7 @@ get_concentration_summary <- function(tox_list,
                                       chem_data = NULL,
                                       chem_site = NULL,
                                       chem_info = NULL,
-                                      tox_names = TRUE) {
+                                      tox_names = FALSE) {
   # Getting rid of NSE warnings:
   chnm <- endPoint <- ACC_value <- Substance_Name <- Value <- `Sample Date` <- SiteID <- ".dplyr"
   EAR <- `Short Name` <- Substance_CASRN <- CAS <- Chemical <- Class <- site <- casrn <- groupCol <- ".dplyr"
@@ -189,42 +189,11 @@ get_concentration_summary <- function(tox_list,
       endPoint = "Concentration"
     ) %>%
     left_join(select(chem_site,
-      site = SiteID,
-      shortName = `Short Name`
-    ),
-    by = "site"
-    ) %>%
-    left_join(select(chem_info, CAS, Class), by = "CAS")
-
-  if (tox_names) {
-    tox_names_key <- tox_chemicals %>%
-      select(CAS = Substance_CASRN, chnm = Substance_Name) %>%
-      filter(CAS %in% chem_info$CAS)
-
-    chemical_summary <- chemical_summary %>%
-      left_join(tox_names_key, by = "CAS")
-
-    if (any(is.na(chemical_summary$chnm))) {
-      if ("Chemical" %in% names(chem_info)) {
-        chemical_summary <- chemical_summary %>%
-          left_join(select(chem_info, CAS, Chemical), by = "CAS")
-      } else {
-        chemical_summary$Chemical <- as.character(as.numeric(factor(chemical_summary$CAS)))
-      }
-
-      chemical_summary$chnm[is.na(chemical_summary$chnm)] <- chemical_summary$Chemical[is.na(chemical_summary$chnm)]
-
-      chemical_summary <- select(chemical_summary, -Chemical)
-    }
-  } else {
-    if ("Chemical" %in% names(chem_info)) {
-      chemical_summary <- chemical_summary %>%
-        left_join(select(chem_info, CAS, chnm = Chemical), by = "CAS")
-    } else {
-      message("Add a Chemical column to the Chemicals tab to get custom chemical names")
-      chemical_summary$chnm <- as.character(as.numeric(factor(chemical_summary$CAS)))
-    }
-  }
+                     site = SiteID,
+                     shortName = `Short Name`),
+      by = "site") %>%
+    left_join(select(chem_info, CAS, Class, chnm = Chemical),
+              by = "CAS")
 
   graphData <- graph_chem_data(chemical_summary)