Merge pull request #204 from ldecicco-USGS/master

Splitting up big function

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: toxEval
 Type: Package
 Title: ToxCast Evaluations
-Version: 0.3.8.9003
+Version: 0.3.8.9004
 Date: 2017-10-04
 Authors@R: c( person("Steven", "Corsi", role = c("aut"),
  email = "srcorsi@usgs.gov"),

R/get_chemical_summary.R

@@ -73,30 +73,55 @@ get_chemical_summary <- function(ACClong, filtered_ep,
 
  graphData <- graph_chem_data(chemicalSummary)
 
- orderClass <- graphData %>%
+ orderClass_df <- orderClass(graphData)
+
+ orderChem_df <- orderChem(graphData, orderClass_df)
+
+ chemicalSummary$chnm <- factor(chemicalSummary$chnm,
+ levels = orderChem_df$chnm) 
+
+ chemicalSummary$Class <- factor(chemicalSummary$Class,
+ levels = rev(levels(orderChem_df$Class)))
+
+ return(chemicalSummary)
+}
+
+#' orderClass
+#' 
+#' @param graphData data frame
+orderClass <- function(graphData){
+
+ chnm <- Class <- maxEAR <- median <- max_med <- ".dplyr"
+
+ orderClass_df <- graphData %>%
  group_by(chnm, Class) %>%
  summarise(median = quantile(maxEAR[maxEAR != 0],0.5)) %>%
  group_by(Class) %>%
  summarise(max_med = max(median, na.rm = TRUE)) %>%
  arrange(desc(max_med))
-
- orderChem <- graphData %>%
+
+ return(orderClass_df)
+}
+
+#' orderChem
+#' 
+#' @param graphData data frame
+#' @param orderClass_df data frame
+orderChem <- function(graphData, orderClass_df){
+
+ chnm <- Class <- maxEAR <- median <- ".dplyr"
+
+ orderChem_df <- graphData %>%
  group_by(chnm,Class) %>%
  summarise(median = quantile(maxEAR[maxEAR != 0],0.5)) %>%
  data.frame() %>%
- mutate(Class = factor(Class, levels = rev(as.character(orderClass$Class))))
-
- orderChem$median[is.na(orderChem$median)] <- 0
+ mutate(Class = factor(Class, levels = rev(as.character(orderClass_df$Class))))
 
- orderChem <- arrange(orderChem, Class, median)
-
- chemicalSummary$chnm <- factor(chemicalSummary$chnm,
- levels = orderChem$chnm) 
+ orderChem_df$median[is.na(orderChem_df$median)] <- 0
 
- chemicalSummary$Class <- factor(chemicalSummary$Class,
- levels = rev(levels(orderChem$Class)))
+ orderChem_df <- arrange(orderChem_df, Class, median)
 
- return(chemicalSummary)
+ return(orderChem_df)
 }
 
 #' remove_flags