Merge pull request #76 from ldecicco-USGS/master

Dependency work

DESCRIPTION

@@ -18,21 +18,21 @@ Depends:
     R (>= 3.0)
 Imports:
     dplyr,
-    tidyr
-Suggests:
-    rmarkdown,
-    knitr,
-    testthat,
-    pander,
+    tidyr,
     DT,
     leaflet,
-    formattable,
     ggplot2,
     gridExtra,
     grid,
     shiny,
     data.table,
     RColorBrewer
+Suggests:
+    rmarkdown,
+    testthat,
+    pander,
+    formattable,
+    knitr
 VignetteBuilder: knitr
 BuildVignettes: true
 LazyLoad: yes

NAMESPACE

@@ -8,9 +8,36 @@ export(chemSummBasic)
 export(endPointInfo)
 export(endPointSumm)
 export(endPointToxCreate)
+export(explore_endpoints)
 export(siteSumm)
 export(totalSamples)
-import(dplyr)
-importFrom(tidyr,gather)
-importFrom(tidyr,gather_)
-importFrom(tidyr,separate)
+import(DT)
+import(RColorBrewer)
+import(data.table)
+import(ggplot2)
+import(grid)
+import(gridExtra)
+import(tidyr)
+importFrom(dplyr,arrange)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,filter_)
+importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_)
+importFrom(dplyr,rename)
+importFrom(dplyr,rename_)
+importFrom(dplyr,right_join)
+importFrom(dplyr,select)
+importFrom(dplyr,select_)
+importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
+importFrom(leaflet,addCircles)
+importFrom(leaflet,addLegend)
+importFrom(leaflet,clearControls)
+importFrom(leaflet,clearShapes)
+importFrom(leaflet,leaflet)
+importFrom(shiny,runApp)

R/chemSumm.R

@@ -8,7 +8,6 @@
 #' @param classCol column name of chemical class
 #' @param siteCol column name of site
 #' @param dateCol column name of date
-#' @import dplyr
 #' @export
 #' @examples
 #' wData <- wData
@@ -73,10 +72,7 @@ chemSumm <- function(chemicalSummary,EAR.key="EAR",chnmCol="chnm",
 #' @param code_pCode character name of code column in pCodeInfo
 #' @param casrn_ep character name of class column in endPoint
 #' @return chemicalSummary data frame
-#' @import dplyr
-#' @importFrom tidyr gather_
-#' @importFrom tidyr gather
-#' @importFrom tidyr separate
+#' @import tidyr 
 #' @export
 #' @examples
 #' wData <- wData
@@ -114,7 +110,6 @@ chemSummBasic <- function(wData, pCodeInfoDF,endPoint,
 #' @param units_pCode character name of units column in pCodeInfo
 #' @param mlWt_pCode character name of molecular weight column in pCodeInfo
 #' @return endPoint data frame
-#' @import dplyr
 #' @export
 #' @examples
 #' pCodeInfo <- pCodeInfo

R/endPointSumm.R

@@ -8,15 +8,16 @@
 #' @param endPointInfo dataframe
 #' @param endPointInfo.Key column name of endpoint
 #' @param EAR.key column name in chemicalSummary of EAR
-#' @import dplyr
 #' @export
 #' @examples
+#' \dontrun{
 #' wData <- wData
 #' pCodeInfo <- pCodeInfo
 #' endPoint <- endPointToxCreate(pCodeInfo)
 #' chemicalSummary <- chemSummBasic(wData,pCodeInfo,endPoint)
 #' endPointInfo <- endPointInfo
 #' epSumm <- endPointSumm(chemicalSummary, endPointInfo=endPointInfo)
+#' }
 endPointSumm <- function(chemicalSummary, chemicalSummary.Key="endPoint",chemicalSummary.site="site",
                          endPointInfo, endPointInfo.Key = "assay_component_endpoint_name",
                          EAR.key="EAR"){

R/explore_endpoints.R

@@ -0,0 +1,22 @@
+#' Explore endpoint groupings
+#' 
+#' Open an interactive app
+#' 
+#' @param browse use browser for map rendering
+#' @export
+#' @importFrom shiny runApp
+#' @importFrom leaflet leaflet
+#' @importFrom leaflet addLegend
+#' @importFrom leaflet addCircles
+#' @importFrom leaflet clearControls
+#' @importFrom leaflet clearShapes
+#' @import tidyr
+#' @import DT
+#' @import ggplot2
+#' @import data.table
+#' @import RColorBrewer
+#' @import grid
+#' @import gridExtra 
+explore_endpoints <- function(browse=TRUE){
+  runApp(system.file('shiny', package='toxEval'), launch.browser = browse)
+}

R/siteSumm.R

@@ -4,9 +4,9 @@
 #'
 #' @param chemicalSummary data frame returned from \code{chemSummBasic}
 #' @param newSiteKey named vector 
-#' @import  dplyr
 #' @export
 #' @examples
+#' \dontrun{
 #' wData <- wData
 #' pCodeInfo <- pCodeInfo
 #' packagePath <- system.file("extdata", package="toxEval")
@@ -16,6 +16,7 @@
 #' endPoint <- endPointToxCreate(pCodeInfo)
 #' chemicalSummary <- chemSummBasic(wData,pCodeInfo,endPoint)
 #' siteSummary <- siteSumm(chemicalSummary,newSiteKey)
+#' }
 siteSumm <- function(chemicalSummary,newSiteKey){
 
   siteSummary <- chemicalSummary %>%

R/totalSamples.R

@@ -5,7 +5,6 @@
 #' @param chemicalSummary data frame returned from \code{chemSummBasic}
 #' @param chemicalSummary.Key character column name for grouping by (default = "endPoint")
 #' @param chemicalSummary.site character column name for group by site
-#' @import dplyr
 #' @export
 #' @examples
 #' wData <- wData

R/toxEval.R

@@ -21,6 +21,23 @@
 #'
 #' @name toxEval-package
 #' @docType package
+#' @importFrom dplyr filter
+#' @importFrom dplyr rename
+#' @importFrom dplyr group_by
+#' @importFrom dplyr summarize
+#' @importFrom dplyr summarise
+#' @importFrom dplyr select
+#' @importFrom dplyr arrange
+#' @importFrom dplyr distinct
+#' @importFrom dplyr left_join
+#' @importFrom dplyr right_join
+#' @importFrom dplyr desc
+#' @importFrom dplyr filter_
+#' @importFrom dplyr rename_
+#' @importFrom dplyr mutate
+#' @importFrom dplyr group_by_
+#' @importFrom dplyr select_
+#' @importFrom dplyr mutate_
 #' @author Steven Corsi \email{srcorsi@@usgs.gov}, Laura De Cicco \email{ldecicco@@usgs.gov}
 #' @keywords ToxCast
 NULL

inst/doc/SummaryToxCast.R

@@ -10,6 +10,7 @@ library(leaflet)
 library(formattable)
 library(ggplot2)
 library(gridExtra)
+library(data.table)
 
 pCodeInfo <- pCodeInfo
 wData <- wData
@@ -119,7 +120,10 @@ chemicalSummary_passive <- passiveData %>%
   select(-mlWt, -conversion, -casrn,  -Units) %>%
   gather(endPoint, endPointValue, -class, -site, -measuredValue, -chnm) %>%
   filter(!is.na(endPointValue)) %>%
-  mutate(EAR=measuredValue/endPointValue) 
+  mutate(EAR=measuredValue/endPointValue) %>%
+  mutate(hits = as.numeric(EAR > 0.1),
+         endPoint=as.character(endPoint)) %>%
+  filter(!is.na(EAR))
 
 chemicalSummary_passive <- chemicalSummary_passive %>%
   mutate(site=paste0("USGS-",gsub("[^0-9]", "", as.character(site))))%>%
@@ -220,18 +224,18 @@ datatable(chemSum2[,-6], rownames = FALSE,
 
 
 chemSum3 <- chemicalSummary %>%
-  mutate(hits= as.numeric(EAR > 0.1)) %>%
   group_by(chnm,  class, site, endPoint) %>%
   summarize(hits=as.numeric(any(hits > 0)),
             maxEAR=max(EAR)) %>%
   group_by(chnm, class, endPoint) %>%
   summarize(freq=sum(hits)/n_distinct(site),
             nSites=sum(hits),
             maxEAR=max(maxEAR)) %>%
-  mutate(endPoint=as.character(endPoint))%>%
-  left_join(endPointInfo, by=c("endPoint"="assay_component_endpoint_name")) %>% 
+  rename(assay_component_endpoint_name=endPoint) %>%
+  data.table() %>%
+  left_join(data.table(endPointInfo), by="assay_component_endpoint_name") %>% 
   select(chnm, maxEAR, freq, nSites, 
-         endPoint, class, contains("intended_target_")) %>%
+         endPoint=assay_component_endpoint_name, class, contains("intended_target_")) %>%
   rename(type=intended_target_type, type_sub=intended_target_type_sub,
          family=intended_target_family, family_sub=intended_target_family_sub) %>%
   select(-contains("intended_target_"))  %>%
@@ -244,24 +248,9 @@ chemSum3 <- chemicalSummary %>%
     formatRound(c("maxEAR", "freq"), digits = 2)
 
 
-totalSamples_ep <- select(chemicalSummary,site,endPoint) %>%
-  distinct()%>%
-  group_by(endPoint) %>%
-  summarise(totalSites=n())%>%
-  mutate(endPoint=as.character(endPoint))
+endpointSummary <- endPointSumm(chemicalSummary, endPointInfo=endPointInfo)
 
-endpointSummary <- chemicalSummary %>%
-  mutate(hits= as.numeric(EAR > 0.1)) %>%
-  group_by(site, endPoint) %>%
-  summarize(hits=as.numeric(any(hits > 0)),
-            maxEAR=max(EAR)) %>%
-  group_by(endPoint) %>%
-  summarize(nSites=sum(hits),
-            maxEAR=max(maxEAR))  %>%
-  mutate(endPoint=as.character(endPoint))%>%
-  left_join(endPointInfo, by=c("endPoint"="assay_component_endpoint_name")) %>% 
-  left_join(totalSamples_ep, by=c("endPoint")) %>%
-  mutate(freq=nSites/totalSites)%>%
+endpointSummary <- endpointSummary %>%
   select(endPoint, maxEAR, freq, nSites, 
          endPoint, contains("intended_target_")) %>%
   rename(type=intended_target_type, type_sub=intended_target_type_sub,
@@ -394,8 +383,8 @@ datatable(chemSum2_passive_dt, rownames = FALSE,
 
 
 chemSum3_passive <- chemicalSummary_passive %>%
-  group_by(chnm,  class, site, endPoint) %>%
-  summarize(hits= as.numeric(any(EAR > 0.1))) %>% 
+#   group_by(chnm,  class, site, endPoint) %>%
+#   summarize(hits= as.numeric(any(EAR > 0.1))) %>% 
   group_by(chnm, class, endPoint) %>%
   summarize(freq=sum(hits)/n_distinct(site),
             nSites=sum(hits)) 

inst/doc/SummaryToxCast.Rmd

@@ -25,6 +25,7 @@ library(leaflet)
 library(formattable)
 library(ggplot2)
 library(gridExtra)
+library(data.table)
 
 pCodeInfo <- pCodeInfo
 wData <- wData
@@ -136,7 +137,10 @@ chemicalSummary_passive <- passiveData %>%
   select(-mlWt, -conversion, -casrn,  -Units) %>%
   gather(endPoint, endPointValue, -class, -site, -measuredValue, -chnm) %>%
   filter(!is.na(endPointValue)) %>%
-  mutate(EAR=measuredValue/endPointValue) 
+  mutate(EAR=measuredValue/endPointValue) %>%
+  mutate(hits = as.numeric(EAR > 0.1),
+         endPoint=as.character(endPoint)) %>%
+  filter(!is.na(EAR))
 
 chemicalSummary_passive <- chemicalSummary_passive %>%
   mutate(site=paste0("USGS-",gsub("[^0-9]", "", as.character(site))))%>%
@@ -294,18 +298,18 @@ This table focuses on the individual endpoint/compound combinations and the prev
 
 
 chemSum3 <- chemicalSummary %>%
-  mutate(hits= as.numeric(EAR > 0.1)) %>%
   group_by(chnm,  class, site, endPoint) %>%
   summarize(hits=as.numeric(any(hits > 0)),
             maxEAR=max(EAR)) %>%
   group_by(chnm, class, endPoint) %>%
   summarize(freq=sum(hits)/n_distinct(site),
             nSites=sum(hits),
             maxEAR=max(maxEAR)) %>%
-  mutate(endPoint=as.character(endPoint))%>%
-  left_join(endPointInfo, by=c("endPoint"="assay_component_endpoint_name")) %>% 
+  rename(assay_component_endpoint_name=endPoint) %>%
+  data.table() %>%
+  left_join(data.table(endPointInfo), by="assay_component_endpoint_name") %>% 
   select(chnm, maxEAR, freq, nSites, 
-         endPoint, class, contains("intended_target_")) %>%
+         endPoint=assay_component_endpoint_name, class, contains("intended_target_")) %>%
   rename(type=intended_target_type, type_sub=intended_target_type_sub,
          family=intended_target_family, family_sub=intended_target_family_sub) %>%
   select(-contains("intended_target_"))  %>%
@@ -318,24 +322,9 @@ chemSum3 <- chemicalSummary %>%
     formatRound(c("maxEAR", "freq"), digits = 2)
   
   
-totalSamples_ep <- select(chemicalSummary,site,endPoint) %>%
-  distinct()%>%
-  group_by(endPoint) %>%
-  summarise(totalSites=n())%>%
-  mutate(endPoint=as.character(endPoint))
+endpointSummary <- endPointSumm(chemicalSummary, endPointInfo=endPointInfo)
   
-endpointSummary <- chemicalSummary %>%
-  mutate(hits= as.numeric(EAR > 0.1)) %>%
-  group_by(site, endPoint) %>%
-  summarize(hits=as.numeric(any(hits > 0)),
-            maxEAR=max(EAR)) %>%
-  group_by(endPoint) %>%
-  summarize(nSites=sum(hits),
-            maxEAR=max(maxEAR))  %>%
-  mutate(endPoint=as.character(endPoint))%>%
-  left_join(endPointInfo, by=c("endPoint"="assay_component_endpoint_name")) %>% 
-  left_join(totalSamples_ep, by=c("endPoint")) %>%
-  mutate(freq=nSites/totalSites)%>%
+endpointSummary <- endpointSummary %>%
   select(endPoint, maxEAR, freq, nSites, 
          endPoint, contains("intended_target_")) %>%
   rename(type=intended_target_type, type_sub=intended_target_type_sub,
@@ -504,8 +493,8 @@ This table focuses on the individual endpoint/compound combinations, and the pre
 
 
 chemSum3_passive <- chemicalSummary_passive %>%
-  group_by(chnm,  class, site, endPoint) %>%
-  summarize(hits= as.numeric(any(EAR > 0.1))) %>% 
+#   group_by(chnm,  class, site, endPoint) %>%
+#   summarize(hits= as.numeric(any(EAR > 0.1))) %>% 
   group_by(chnm, class, endPoint) %>%
   summarize(freq=sum(hits)/n_distinct(site),
             nSites=sum(hits))