updates for USGS-R#36

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: sensorQC
 Type: Package
 Title: sensorQC
-Version: 0.3.2
-Date: 2015-10-21
-Author: Jordan S Read, Brad Garner, Brian Pellerin
+Version: 0.3.3
+Date: 2015-10-22
+Author: Jordan S Read, Brad Garner, Brian Pellerin, Luke Loken
 Maintainer: Jordan S Read <jread@usgs.gov>
 Description: tools for QAQCing water quality sensor data.
 License: file LICENSE

NAMESPACE

@@ -2,6 +2,8 @@
 
 S3method("[",sensor)
 S3method(calc_flags,sensor)
+S3method(clean,numeric)
+S3method(clean,sensor)
 S3method(flag,numeric)
 S3method(flag,sensor)
 S3method(flags,sensor)
@@ -14,6 +16,7 @@ S3method(times,sensor)
 S3method(values,sensor)
 S3method(window,sensor)
 export(MAD)
+export(clean)
 export(flag)
 export(flag.data.frame)
 export(persist)

R/clean.R

@@ -0,0 +1,50 @@
+#' clean a sensor or a flagged sensor
+#' 
+#' clean a sensor or a flagged sensor
+#' 
+#' @param x sensor object
+#' @param which flags to replace
+#' @param \dots additional flags to use (passed to flag(x,...))
+#' @param replace replacement value for flagged indices. 
+#' NULL removes the flagged row
+#' @rdname clean
+#' 
+#' @examples 
+#' data = c(999999, 1,2,3,4,2,3,4)
+#' sensor = flag(data, 'x > 9999')
+#' clean(sensor)
+#' clean(data, 'x > 9999', 'persist(x) > 10', 'MAD(x) > 3', replace=NA)
+#' @export
+clean = function(x, which, ..., replace){
+  UseMethod('clean')
+}
+
+#' @export
+clean.numeric <- function(x, which = 'all', ..., replace=NULL){
+  x = sensor(x)
+  clean(x, which = which, ..., replace=replace)
+}
+
+#' @export
+clean.sensor <- function(x, which = 'all', ..., replace=NULL){
+
+  if (which == 'all'){
+    if (!is.null(x$flags)){
+      flag.i = sort(unique(unlist(sapply(flags(x), function(x) x$flag.i))))
+      x$flags <- NULL
+    } else {
+      return(x)
+    }
+
+    if (is.null(replace)){
+      x$sensor <- x$sensor[c(-flag.i),]
+      rownames(x$sensor) <- seq_len(nrow(x$sensor))
+    } else {
+      x$sensor$x[flag.i] <- replace
+    }
+    return(x)
+  } else {
+    x <- flag(x, flag.defs=which, ...)
+    clean(x, which = 'all', replace=replace)
+  }
+}

R/plot-sensor.R

@@ -2,14 +2,9 @@
 plot.sensor <- function(x, y=NULL, ...){
   args = expand.grid(...)
   # check that ylab and xlab aren't in ...
-  plot.x = x$sensor$times
-  plot.y = x$sensor$x
-  if (!is.null(flags(x))){
-    flag.i <- sort(unique(unlist(sapply(flags(x), function(x) x$flag.i))))
-    plot.x = plot.x[-flag.i]
-    plot.y = plot.y[-flag.i]
-
-  }
 
-  plot(plot.x, plot.y, ylab='sensor', xlab='DateTime')
+  x <- clean(x, which='all',replace=NULL)
+
+
+  plot(x$sensor$times, x$sensor$x, ylab='sensor', xlab='DateTime')
 }

README.Rmd

@@ -60,6 +60,7 @@ Use sensorQC with a simple vector of numbers:
 flag(c(3,2,4,3,3,4,2,4),'MAD(x) > 3')
 ```
 
+#### plotting data
 plot dataset w/ outliers:  
 ```{r}
 plot(sensor)
@@ -70,3 +71,17 @@ plot dataset w/o outliers:
 flagged = flag(sensor, 'x == 999999', 'persist(x) > 3', 'MAD(x,w) > 3', 'MAD(x) > 3')
 plot(flagged)
 ```
+
+#### cleaning data
+The `clean` function can be used to strip flagged data points from the record or replace them with other values (such as `NA` or -9999)  
+```{r}
+data = c(999999, 1,2,3,4,2,3,4)
+sensor = flag(data, 'x > 9999')
+clean(sensor)
+```
+or flag data and clean data all in one step:  
+```{r}
+clean(data, 'x > 9999', 'persist(x) > 10', 'MAD(x) > 3', replace=NA)
+```
+
+

README.md

@@ -25,7 +25,7 @@ This package is still very much in development, so the API may change at any tim
 
 High-frequency aquatic sensor QAQC procedures. `sensorQC` imports data, and runs various statistical outlier detection techniques as specified by the user.
 
-### `sensorQC` Functions (as of v0.3.2)
+### `sensorQC` Functions (as of v0.3.3)
 
 | Function | Title                                                  |
 |----------|:-------------------------------------------------------|
@@ -123,6 +123,8 @@ flag(c(3,2,4,3,3,4,2,4),'MAD(x) > 3')
     ## 
     ## MAD(x) > 3 (0 flags)
 
+#### plotting data
+
 plot dataset w/ outliers:
 
 ``` r
@@ -139,3 +141,40 @@ plot(flagged)
 ```
 
 ![](README_files/figure-markdown_github/unnamed-chunk-7-1.png)
+
+#### cleaning data
+
+The `clean` function can be used to strip flagged data points from the record or replace them with other values (such as `NA` or -9999)
+
+``` r
+data = c(999999, 1,2,3,4,2,3,4)
+sensor = flag(data, 'x > 9999')
+clean(sensor)
+```
+
+    ## object of class "sensor"
+    ##   x
+    ## 1 1
+    ## 2 2
+    ## 3 3
+    ## 4 4
+    ## 5 2
+    ## 6 3
+    ## 7 4
+
+or flag data and clean data all in one step:
+
+``` r
+clean(data, 'x > 9999', 'persist(x) > 10', 'MAD(x) > 3', replace=NA)
+```
+
+    ## object of class "sensor"
+    ##    x
+    ## 1 NA
+    ## 2  1
+    ## 3  2
+    ## 4  3
+    ## 5  4
+    ## 6  2
+    ## 7  3
+    ## 8  4

man/clean.Rd

@@ -0,0 +1,28 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/clean.R
+\name{clean}
+\alias{clean}
+\title{clean a sensor or a flagged sensor}
+\usage{
+clean(x, which, ..., replace)
+}
+\arguments{
+\item{x}{sensor object}
+
+\item{which}{flags to replace}
+
+\item{replace}{replacement value for flagged indices.
+NULL removes the flagged row}
+
+\item{\dots}{additional flags to use (passed to flag(x,...))}
+}
+\description{
+clean a sensor or a flagged sensor
+}
+\examples{
+data = c(999999, 1,2,3,4,2,3,4)
+sensor = flag(data, 'x > 9999')
+clean(sensor)
+clean(data, 'x > 9999', 'persist(x) > 10', 'MAD(x) > 3', replace=NA)
+}
+