From b6cbb6fd1e2a9364458e3a689f85ffa97071eae0 Mon Sep 17 00:00:00 2001
From: Jordan S Read <jread@usgs.gov>
Date: Thu, 10 Jul 2014 10:13:10 -0500
Subject: [PATCH] adding doc and optional args

---
 R/clean.data.R    | 34 +++++++++++++++++++++++++++++++---
 man/clean.data.Rd | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 3 deletions(-)
 create mode 100644 man/clean.data.Rd

diff --git a/R/clean.data.R b/R/clean.data.R
index b1de709..ff21812 100644
--- a/R/clean.data.R
+++ b/R/clean.data.R
@@ -1,5 +1,22 @@
+#'@title cleans sensor data with user-specified routines
+#'@description 
+#'cleans sensor data according to details within the user-specified config (*yml) file  \cr
+#'
+#'@param deploy a string for the *.yml file name
+#'@param folder a string which specifies the folder of the *.yml file
+#'@param plot.diagnostic a boolean for creating a diagnostic plot
+#'@param write.file a boolean for creating a timeseries file output
+#'@return An optional plot and optional file output handle
+#'@keywords methods
+#'@author
+#'Jordan S. Read
+#'@examples 
+#'\dontrun{
+#'clean.data(deploy='pellerin',folder='/[User]/Desktop/Science Projects/sensorQC/',plot.diagnostic=FALSE)
+#'clean.data(deploy='pellerin',folder='/[User]/Desktop/Science Projects/sensorQC/',plot.diagnostic=TRUE,write.file=TRUE)
+#'}
 #'@export
-clean.data <- function(deploy='pellerin',folder='../examples/'){
+clean.data <- function(deploy='pellerin',folder='../examples/',plot.diagnostic=TRUE, write.file= FALSE){
   #is an example wrapper for sensorQC calls 
   
   #
@@ -23,8 +40,19 @@ clean.data <- function(deploy='pellerin',folder='../examples/'){
   old.inst.flags <- build_flags(data.in=windowed.data,sqc=simple.sqc$outlier_removal,verbose=F)
   old.sensor <- block_stats(windowed.data=windowed.data,old.inst.flags)
   
-  plot_summary(inst.data=windowed.data,inst.flags,block.data=sensor.stats,block.flags,
-               compare.data=old.sensor,sqc=cnfg)
+  if (plot.diagnostic){
+    plot_summary(inst.data=windowed.data,inst.flags,block.data=sensor.stats,block.flags,
+                 compare.data=old.sensor,sqc=cnfg)
+  }
+  
+  if (write.file){
+    output = paste0(folder,deploy,"_sqc_out.tsv")
+    flat.block <- flatten_flags(block.flags)
+    write.out <- sensor.stats[!flat.block, ]
+    write.table(write.out,file=output,col.names=TRUE, quote=FALSE, row.names=FALSE, sep="\t")
+  }
+  
+  
 
   
 
diff --git a/man/clean.data.Rd b/man/clean.data.Rd
new file mode 100644
index 0000000..3655fbd
--- /dev/null
+++ b/man/clean.data.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
+\name{clean.data}
+\alias{clean.data}
+\title{cleans sensor data with user-specified routines}
+\usage{
+clean.data(deploy = "pellerin", folder = "../examples/",
+  plot.diagnostic = TRUE, write.file = FALSE)
+}
+\arguments{
+\item{deploy}{a string for the *.yml file name}
+
+\item{folder}{a string which specifies the folder of the *.yml file}
+
+\item{plot.diagnostic}{a boolean for creating a diagnostic plot}
+
+\item{write.file}{a boolean for creating a timeseries file output}
+}
+\value{
+An optional plot and optional file output handle
+}
+\description{
+cleans sensor data according to details within the user-specified config (*yml) file  \cr
+}
+\examples{
+\dontrun{
+clean.data(deploy='pellerin',folder='/[User]/Desktop/Science Projects/sensorQC/',plot.diagnostic=FALSE)
+clean.data(deploy='pellerin',folder='/[User]/Desktop/Science Projects/sensorQC/',plot.diagnostic=TRUE,write.file=TRUE)
+}
+}
+\author{
+Jordan S. Read
+}
+\keyword{methods}
+