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leppottleppott
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v2.0.5.9012
ggplot in QC report, issue #83, issue #84 update file import to na.strings to inclue "NA" not just "".
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‎.Rhistory

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‎DESCRIPTION

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Package: ContDataQC
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Title: Quality Control (QC) of Continous Monitoring Data
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Version: 2.0.5.9011
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Version: 2.0.5.9012
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Authors@R: c(
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person("Erik W.", "Leppo", email="[email protected]",role=c("aut","cre")),
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person("Ann","Roseberry Lincoln", role="ctb"),
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Imports:
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dataRetrieval,
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doBy,
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ggplot2,
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knitr,
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rmarkdown,
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shiny,
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survival,
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zoo
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Suggests:
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ggplot2,
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IHA,
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installr,
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rLakeAnalyzer,

‎NEWS

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<!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
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#> Last Update: 2019-02-19 13:24:28
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#> Last Update: 2019-02-21 10:13:18
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# Planned Updates
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# Version History
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## v2.0.5.9012
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2019-02-21
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- Update plots in QC Report to ggplot. Issues \#83 and 84.
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- Import files fix, na.strings=
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- Use c(“”,“NA”) not just “”.
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## v2.0.5.9011
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2019-02-19

‎NEWS.rmd

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# Version History
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## v2.0.5.9012
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2019-02-21
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* Update plots in QC Report to ggplot. Issues #83 and 84.
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* Import files fix, na.strings=
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+ Use c("","NA") not just "".
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## v2.0.5.9011
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2019-02-19
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‎R/fun.PeriodStats.R

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@@ -228,7 +228,7 @@ PeriodStats <- function(fun.myDate
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#
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}##IF.file.END
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# 2.2. Load File
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df.load <- read.csv(file.path(fun.myDir.import, fun.myFile),as.is=TRUE,na.strings="")
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df.load <- read.csv(file.path(fun.myDir.import, fun.myFile),as.is=TRUE,na.strings=c("","NA"))
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# 2.3. Error Checking, data field names
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param.len <- length(fun.myParam.Name)
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myNames2Match <- c(fun.myParam.Name, fun.myDateTime.Name)

‎R/fun.QC.File.R

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@@ -244,8 +244,8 @@ fun.QC.File <- function(fun.myFile
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#data.import=read.table(strFile,header=F,varSep)
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#varSep = "\t" (use read.delim instead of read.table)
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# as.is = T so dates come in as text rather than factor
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#data.import <- read.delim(strFile,as.is=TRUE,na.strings="")
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings="")
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#data.import <- read.delim(strFile,as.is=TRUE,na.strings=c("","NA"))
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings=c("","NA"))
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#
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# QC required fields: SiteID & (DateTime | (Date & Time))
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fun.QC.ReqFlds(names(data.import),file.path(myDir.data.import,strFile))
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#************************
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#data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings="")
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#data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings=c("","NA"))
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#
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# B.4.0. Columns
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# B.4.1. Check for DataFields (may have already been done)

‎R/fun.QC.R

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, fun.myReport.Dir
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, fun.CreateReport=TRUE) {##FUN.fun.QC.START
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#
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boo_DEBUG <- "FALSE"
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# A. Data Prep ####
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# Convert Data Type to proper case
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fun.myData.Type <- paste(toupper(substring(fun.myData.Type,1,1)),tolower(substring(fun.myData.Type,2,nchar(fun.myData.Type))),sep="")
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#varSep = "\t" (use read.delim instead of read.table)
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# as.is = T so dates come in as text rather than factor
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#data.import <- read.delim(strFile,as.is=TRUE,na.strings="")
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# data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings="")
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings="")
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# data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings=c("","NA"))
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings=c("","NA"))
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#
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# QC required fields: SiteID & (DateTime | (Date & Time))
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fun.QC.ReqFlds(names(data.import),paste(myDir.data.import,strFile,sep="/"))
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#************************
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#data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings="")
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#data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings=c("","NA"))
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#
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# B.4.0. Columns
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# B.4.1. Check for DataFields (may have already been done)
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# insert QC Report so runs without user intervention
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# DEBUG, REPORT ####
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if(boo_DEBUG==TRUE){##IF~boo_DEBUG~START
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fun.myData.SiteID <- strFile.SiteID
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fun.myData.Type <- strFile.DataType
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fun.myData.DateRange.Start <- fun.myData.DateRange.Start
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fun.myData.DateRange.End <- fun.myData.DateRange.End
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fun.myDir.BASE <- fun.myDir.BASE
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fun.myDir.SUB.import <- fun.myDir.SUB.export
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fun.myDir.SUB.export <- fun.myDir.SUB.export
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fun.myFile.Prefix <- strFile.Out.Prefix
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}##IF~boo_DEBUG~END
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# run with same import and export directory
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###
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# B.10.3. Report ####
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) }##IF.CreateReport.END
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# QC
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# ##
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# fun.myData.SiteID <- strFile.SiteID
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# fun.myData.Type <- strFile.DataType
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# fun.myData.DateRange.Start <- fun.myData.DateRange.Start
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# fun.myData.DateRange.End <- fun.myData.DateRange.End
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# fun.myDir.BASE <- fun.myDir.BASE
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# fun.myDir.SUB.import <- fun.myDir.SUB.export
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# fun.myDir.SUB.export <- fun.myDir.SUB.export
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# fun.myFile.Prefix <- strFile.Out.Prefix
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# B.11. Clean up
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# B.11.1. Inform user of progress and update LOG

‎R/fun.Report.File.R

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}
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#import the file
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings="")
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings=c("","NA"))
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# pick 'report' based on prefix

‎R/fun.Report.R

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}##IF.file.END
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#import the file
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#data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings="")
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings="")
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#data.import <- read.csv(paste(myDir.data.import,strFile,sep="/"),as.is=TRUE,na.strings=c("","NA"))
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings=c("","NA"))
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# pick 'report' based on prefix

‎R/fun.Stats.File.R

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#import the file
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings="")
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data.import <- read.csv(file.path(myDir.data.import,strFile),as.is=TRUE,na.strings=c("","NA"))
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#
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# QC required fields: SiteID & (DateTime | (Date & Time))
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#fun.QC.ReqFlds(names(data.import),paste(myDir.data.import,strFile,sep="/"))

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