Merge pull request #33 from jread-usgs/master

updates for v0.3.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: sensorQC
 Type: Package
 Title: sensorQC
-Version: 0.3.0
-Date: 2014-08-26
+Version: 0.3.1
+Date: 2015-10-20
 Author: Jordan S Read, Brad Garner, Brian Pellerin
 Maintainer: Jordan S Read <[email protected]>
 Description: tools for QAQCing water quality sensor data.

R/01-on_load.R

@@ -0,0 +1,3 @@
+.onAttach <- function(libname, pkgname) {
+  packageStartupMessage("This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information. Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.")
+}

R/custom-functions.R

@@ -16,7 +16,7 @@ MAD.values <- function(vals, b = 1.4826){
 
 MAD.windowed <- function(vals, windows){
   stopifnot(length(vals) == length(windows))
-
+  . <- '_dplyr_var'
   mad <- group_by_(data.frame(x=vals,w=windows), 'w') %>% mutate_(mad='sensorQC:::MAD.values(x)') %>% .$mad
   return(mad)
 }
@@ -25,7 +25,7 @@ MAD.windowed <- function(vals, windows){
 #'@aliases MAD
 #'@aliases median.absolute.deviation
 #'@param x values
-#'@param windows vector of equal length to x specifying windows
+#'@param w vector of equal length to x specifying windows
 #'@return a vector of MAD normalized values relative to an undefined rejection criteria (usually 2.5 or 3).
 #'@keywords MAD
 #'@importFrom dplyr group_by_ mutate_ %>%
@@ -41,6 +41,11 @@ MAD <- function(x, w){
 
 }
 
+#' function for checking persistent values
+#' 
+#' repeated values of a vector
+#' @param x a numeric vector
+#' @return a vector that provides a count of persistance
 #' @export
 persist <- function(x){
   tmp <- rle(x)

R/flag.R

@@ -25,9 +25,11 @@ flag <- function(x, flag.defs, ...){
   UseMethod('flag')
 }
 
+
 #' @export
-flag.data.frame <- function(x, flag.defs, ...){
-  UseMethod('flag',sensor(x, flag.defs, ...))
+flag.data.frame = function(x, flag.defs, ...){
+  x = sensor(x)
+  UseMethod('flag', x)
 }
 
 #' @export

R/read.R

@@ -2,10 +2,11 @@
 #' 
 #' read from file and create sensor or qconfig object
 #' 
+#' @param file filename
+#' @param \dots additional arguments passed to file read methods
+#' @param format format for file
+#' @param date.format data format of file
 #' @rdname read
-#' @aliases 
-#' read
-#' read.default
 #' 
 #' @examples 
 #' qconfig = read(system.file('extdata','pedro.yml', package = 'sensorQC'))
@@ -47,13 +48,13 @@ read.config <- function(file, ...){
 
   return(as.qconfig(sqc))
 }
-#' @aliases 
-#' read
-#' read.default
-#' @examples 
-#' file <- system.file('extdata', 'test_data.txt', package = 'sensorQC') 
-#' data_out <- read(file, format="wide_burst", date.format="%m/%d/%Y %H:%M")
+
+#' read default method 
+#' 
+#' read in sensor data
+#' 
 #' @rdname read
+#' 
 #' @export
 read.default <- function(file, format, date.format, ...){
 

R/sensor-class.R

@@ -1,3 +1,10 @@
+#' create a sensor object
+#' 
+#' sensor data
+#' 
+#' @param x a data.frame or sensor object
+#' @param flag.defs definitions for flags. Functions that can be evaluated to T/F
+#' @param \dots additional flag.defs
 #' @export
 sensor <- function(x, flag.defs, ...){
   UseMethod('sensor')

R/window.R

@@ -3,6 +3,7 @@
 #' @description 
 #' Breaks up time series data into window chunks.  \cr
 #' @param x a data.frame of time series data
+#' @param \dots not used
 #' @param type numeric, in seconds, specifying the window time width. or 
 #' "auto" to automatically window data
 #' @return a list of time series data and indices for breaks
@@ -13,7 +14,7 @@
 #' @author
 #' Jordan S. Read
 #' @export
-window.sensor<- function(x,  type){
+window.sensor<- function(x, ..., type){
 
   # breaks up data into time-windowed chunks
   # returns a list of breaks

man/MAD.Rd

@@ -9,7 +9,7 @@ MAD(x, w)
 \arguments{
 \item{x}{values}
 
-\item{windows}{vector of equal length to x specifying windows}
+\item{w}{vector of equal length to x specifying windows}
 }
 \value{
 a vector of MAD normalized values relative to an undefined rejection criteria (usually 2.5 or 3).

man/persist.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/custom-functions.R
+\name{persist}
+\alias{persist}
+\title{function for checking persistent values}
+\usage{
+persist(x)
+}
+\arguments{
+\item{x}{a numeric vector}
+}
+\value{
+a vector that provides a count of persistance
+}
+\description{
+repeated values of a vector
+}
+

man/read.Rd

@@ -9,12 +9,21 @@ read(file, ...)
 
 read.default(file, format, date.format, ...)
 }
+\arguments{
+\item{file}{filename}
+
+\item{format}{format for file}
+
+\item{date.format}{data format of file}
+
+\item{\dots}{additional arguments passed to file read methods}
+}
 \description{
 read from file and create sensor or qconfig object
+
+read in sensor data
 }
 \examples{
 qconfig = read(system.file('extdata','pedro.yml', package = 'sensorQC'))
-file <- system.file('extdata', 'test_data.txt', package = 'sensorQC')
-data_out <- read(file, format="wide_burst", date.format="\%m/\%d/\%Y \%H:\%M")
 }
 

man/sensor.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/sensor-class.R
+\name{sensor}
+\alias{sensor}
+\title{create a sensor object}
+\usage{
+sensor(x, flag.defs, ...)
+}
+\arguments{
+\item{x}{a data.frame or sensor object}
+
+\item{flag.defs}{definitions for flags. Functions that can be evaluated to T/F}
+
+\item{\dots}{additional flag.defs}
+}
+\description{
+sensor data
+}
+

man/window.Rd

@@ -5,13 +5,15 @@
 \alias{window.sensor}
 \title{window sensorQC data}
 \usage{
-\method{window}{sensor}(x, type)
+\method{window}{sensor}(x, ..., type)
 }
 \arguments{
 \item{x}{a data.frame of time series data}
 
 \item{type}{numeric, in seconds, specifying the window time width. or
 "auto" to automatically window data}
+
+\item{\dots}{not used}
 }
 \value{
 a list of time series data and indices for breaks