Merge pull request #164 from ldecicco-USGS/master

instruction updates

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: toxEval
 Type: Package
 Title: ToxCast Evaluations
-Version: 0.2.0
-Date: 2016-02-10
+Version: 0.2.1
+Date: 2016-10-05
 Authors@R: c( person("Steven", "Corsi", role = c("aut"),
     email = "srcorsi@usgs.gov"),
     person("Laura", "DeCicco", role = c("aut","cre"),

R/chemSumm.R

@@ -87,14 +87,16 @@ chemSummBasic <- function(wData, pCodeInfoDF,endPoint,
                      casrn_pCode="casrn",class_pCode="class",code_pCode="parameter_cd",
                      casrn_ep="casn"){
 
+  endPoint <- select(endPoint, -Units, -mlWt, -conversion) 
+
   chemicalSummary <- wData %>%
     gather_("pCode", "measuredValue", gather_cols=names(wData)[!(names(wData) %in% c(date,station))]) %>%
     rename_("date"=date) %>%
     filter(!is.na(measuredValue)) %>%
     separate(pCode, into=c("colHeader","pCode"), "_") %>% #totally not generalized
     left_join(pCodeInfoDF[c(code_pCode,casrn_pCode,class_pCode)], by=c("pCode"=code_pCode))  %>%
+    select(-colHeader, -pCode) %>%
     right_join(endPoint, by=c(casrn=casrn_ep)) %>%
-    select(-mlWt, -conversion, -Units, -pCode, -colHeader) %>%
     gather(endPoint, endPointValue, -class, -site, -measuredValue, -chnm, -date, -casrn)  %>% 
     filter(!is.na(endPointValue)) %>%
     mutate(EAR=measuredValue/endPointValue) %>%

README.md

@@ -2,6 +2,64 @@
 
 Initial code for studying ToxCast data in relation to measured concentrations.
 
+## Installation of R and RStudio
+
+This section should only need to be done once per computer.
+
+The following link walks you through an installation of R and RStudio:
+
+[Installation Instructions](https://owi.usgs.gov/R/training-curriculum/intro-curriculum/Before/)
+
+If you follow those instructions exactly, you should have the USGS R repository (GRAN) added to your R profile. If that step doesn't ring a bell, paste the following into your R console:
+
+```r
+rprofile_path = file.path(Sys.getenv("HOME"), ".Rprofile")
+write('\noptions(repos=c(getOption(\'repos\'),
+    CRAN=\'https://cloud.r-project.org\',
+    USGS=\'https://owi.usgs.gov/R\'))\n',
+      rprofile_path, 
+      append =  TRUE)
+
+cat('Your Rprofile has been updated to include GRAN.
+    Please restart R for changes to take effect.')
+```
+
+*RESTART RSTUDIO!*
+
+Useful links:
+
+* [Download R Windows](https://cran.r-project.org/bin/windows/base/)
+* [Download R Mac](https://cran.r-project.org/bin/macosx/)
+* [Download RStudio](https://www.rstudio.com/products/rstudio/download/)
+
+
+## Installation of toxEval
+
+This section should also only have to be done once. It assumes the USGS R repository (GRAN) was added to your R profile as described above.
+
+```r
+install.packages("toxEval")
+```
+
+Regularly, it is a good idea to update *ALL* your packages in R. If using RStudio, this is quite easy, there's an Update button in the "Packages" tab. This checks CRAN and GRAN for updates. It is a good idea to click this update regularly.
+
+![update](images/update.png)
+
+## Run toxEval
+
+To run the toxEval app:
+
+1. Open RStudio
+2. In the Console (lower-left window of RStudio) paste the following:
+
+```r
+library(toxEval)
+explore_endpoints()
+
+```
+
+## At-your-own-risk, highly developmental, probably buggy code installation instructions
+
 To pull the upstream changes in from github in RStudio. In the Git tab, choose the More dropdown, and choose Shell. In that window, enter:
 
 ```

inst/shiny/server.R

@@ -111,7 +111,11 @@ shinyServer(function(input, output,session) {
       choices =  c("All",duluthSites$shortName)
     } else if(input$data == "NPS"){
       npsSites <- readRDS(file.path(pathToApp,"npsSite.rds"))
-      choices =  c("All",npsSites$shortName)  
+      choices =  c("All",npsSites$shortName) 
+
+    } else if(input$data == "App State"){
+      leviSites <- readRDS(file.path(pathToApp,"leviSites.rds"))
+      choices = c("All",leviSites$shortName)
     } else {
       choices =  c("All","2016 GLRI SP sites",summaryFile$site)
     }