Merge pull request #2 from jread-usgs/master

v0.1.0 release changes

NAMESPACE

@@ -3,6 +3,7 @@
 export(MAD)
 export(block_stats)
 export(build_flags)
+export(clean.data)
 export(error_code)
 export(get.outliers)
 export(load.sensor)

R/build.flags.R

@@ -61,9 +61,9 @@ flatten_flags <- function(flag.bool){
   return(data.flags)
 }
 
-#'compresses boolean flags into int matrix padded with NAs
-#'flags are compressed because it is assumed that they don't happen incredibly frequently
-#'example: flag.bool <- matrix(nrow=3,ncol=4,data=c(F,F,F,F,F,F,T,T,F,F,F,F))
+# compresses boolean flags into int matrix padded with NAs
+# flags are compressed because it is assumed that they don't happen incredibly frequently
+# example: flag.bool <- matrix(nrow=3,ncol=4,data=c(F,F,F,F,F,F,T,T,F,F,F,F))
 compress_flags <- function(flag.bool){
   # find longest j dimension of T
   num.row <- max(colSums(flag.bool))

R/clean.data.R

@@ -1,8 +1,26 @@
-clean.data <- function(deploy='pellerin'){
+#'@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/',plot.diagnostic=TRUE, write.file= FALSE){
   #is an example wrapper for sensorQC calls 
 
   #
-  cnfg <- load.sqc(deploy.name=deploy,folder='../examples/')
+  cnfg <- load.sqc(deploy.name=deploy,folder=folder)
 
   sensor.file <- paste(cnfg$data_source[[1]]$folder_name,cnfg$data_source[[1]]$file_name,sep='')
 
@@ -22,11 +40,20 @@ clean.data <- function(deploy='pellerin'){
   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")
+  }
+
+
 
 
 
 }
-
-
-#

R/load.sensor.R

@@ -37,7 +37,7 @@ read.wide_burst <- function(filename,date.type){
 
   fileLines <- readLines(c)
   close(c)
-  cat('num lines:');cat(length(fileLines));cat('\n')
+  cat('number of observations:');cat(length(fileLines)*30);cat('\n')
   sens.vec <- vector(mode="numeric",length=length(fileLines)*60)
   date.vec <- rep(as.POSIXct('1900-01-01'),length(fileLines)*60)
 

R/plot_summary.R

@@ -9,9 +9,6 @@ plot_summary <- function(inst.data,inst.flags,block.data,block.flags,compare.dat
 
   xlm = c(min(inst.data[, 1]), max(inst.data[, 1]))
   ylm = c(0,1.1*max(block.data[, 2]))
-  plot(inst.data[, 1],rep(NA,nrow(inst.data)),ylim=ylm,
-       ylab="SUNA nitrate concentration (micromoles)",
-       xlab="",xlim=xlm)
 
   layout(panels)
   par(mai=c(0,1.5,.1, .5),omi=c(0,0,0,0))
@@ -32,7 +29,7 @@ plot_summary <- function(inst.data,inst.flags,block.data,block.flags,compare.dat
     points(inst.data[use.i,1],rep(i-.5,length(use.i)),pch=15,cex=2.5,
           col=rgb(0, 0, 0, .2, maxColorValue = 1))
     abline(h = i)
-    nme <- cnfg$outlier_removal[[i]]$alias
+    nme <- sqc$outlier_removal[[i]]$alias
     ynames <- c(ynames,nme)
   }
   ix = i
@@ -42,7 +39,7 @@ plot_summary <- function(inst.data,inst.flags,block.data,block.flags,compare.dat
     points(block.data[flags,1],rep(ix-.5,sum(flags)),pch=15,cex=2.5,
            col=rgb(1, 0, 0, .4, maxColorValue = 1))
     abline(h = ix)
-    nme <- cnfg$block_stats[[k]]$alias
+    nme <- sqc$block_stats[[k]]$alias
     ynames <- c(ynames,nme)
   }
 

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}
+