.Rhistory

# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
library(ContDataQC)
?Export.StreamThermal
#~~~~~~~~~~~~~~~~~~~~~~
# Example 2, ContDataQC Summary Stats Data
#~~~~~~~~~~~~~~~~~~~~~~
# 2.1. Load ContDataQC file that has been processed with SummaryStats
myFile <- "DATA_test2_Aw_20130101_20141231.csv"
myData <- read.csv(file.path(path.package("ContDataQC"),"extdata",myFile), stringsAsFactors=FALSE)
# Subset
Col.Keep <- c("SiteID", "Date", "Water.Temp.C")
sitedata <- myData[,Col.Keep]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sitedata <- Export.StreamThermal(myData)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' # 2.2. Run StreamThermal
require(StreamThermal)
#~~~~~
# StreamThermal
(ST.freq <- T_frequency(sitedata))
(ST.mag  <- T_magnitude(sitedata))
(ST.roc  <- T_rateofchange(sitedata))
(ST.tim  <- T_timing(sitedata))
(ST.var  <- T_variability(sitedata))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Save Results to Excel (each group on its own worksheet)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
library(XLConnect)
# Descriptions
#
Desc.freq <- "Frequency metrics indicate numbers of days in months or seasons
that key events exceed user-defined temperatures. "
#
Desc.mag <- "Magnitude metrics characterize monthly and seasonal averages and
the maximum and minimum from daily temperatures as well as 3-, 7-, 14-, 21-,
and 30-day moving averages for mean and maximum daily temperatures."
#
Desc.roc <- "Rate of change metrics include monthly and seasonal rate of
change, which indicates the difference in magnitude of maximum and minimum
temperatures divided by number of days between these events."
#
Desc.tim <- "Timing metrics indicate Julian days of key events including
mean, maximum, and minimum temperatures; they also indicate Julian days of
mean, maximum, and minimum values over moving windows of specified size."
#
Desc.var <- "Variability metrics summarize monthly and seasonal range in
daily mean temperatures as well as monthly coefficient of variation of daily
mean, maximum, and minimum temperatures. Variability metrics also include
moving averages for daily ranges and moving variability in extreme
temperatures, calculated from differences in average high and low
temperatures over various time periods"
#
Group.Desc <- c(Desc.freq, Desc.mag, Desc.roc, Desc.tim, Desc.var)
df.Groups <- as.data.frame(cbind(c("freq","mag","roc","tim","var"),Group.Desc))
#
SiteID <- sitedata[1,1]
myDate <- format(Sys.Date(),"%Y%m%d")
myTime <- format(Sys.time(),"%H%M%S")
Notes.User <- Sys.getenv("USERNAME")
# Notes section (add min/max dates)
Notes.Names <- c("Dataset (SiteID)", "Analysis.Date (YYYYMMDD)"
, "Analysis.Time (HHMMSS)", "Analysis.User")
Notes.Data <- c(SiteID, myDate, myTime, Notes.User)
df.Notes <- as.data.frame(cbind(Notes.Names, Notes.Data))
Notes.Summary <- summary(sitedata)
# Open/Create file
## New File Name
myFile.XLSX <- paste("StreamThermal", SiteID, myDate, myTime, "xlsx", sep=".")
## Copy over template with Metric Definitions
file.copy(file.path(path.package("ContDataQC"),"extdata","StreamThermal_MetricList.xlsx")
, myFile.XLSX)
## load workbook, create if not existing
wb <- loadWorkbook(myFile.XLSX, create = TRUE)
# create sheets
createSheet(wb, name = "NOTES")
createSheet(wb, name = "freq")
createSheet(wb, name = "mag")
createSheet(wb, name = "roc")
createSheet(wb, name = "tim")
createSheet(wb, name = "var")
# write to worksheet
writeWorksheet(wb, df.Notes, sheet = "NOTES", startRow=1)
writeWorksheet(wb, df.Groups, sheet="NOTES", startRow=10)
writeWorksheet(wb, Notes.Summary, sheet = "NOTES", startRow=20)
writeWorksheet(wb, ST.freq, sheet = "freq")
writeWorksheet(wb, ST.mag, sheet = "mag")
writeWorksheet(wb, ST.roc, sheet = "roc")
writeWorksheet(wb, ST.tim, sheet = "tim")
writeWorksheet(wb, ST.var, sheet = "var")
# save workbook
saveWorkbook(wb, myFile.XLSX)
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
library(ContDataQC)
?Export.StreamThermal
# generate Vignette
library(ContDataQC)
library(devtools)
devtools::build_vignettes()
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
# generate Vignette
library(ContDataQC)
library(devtools)
devtools::build_vignettes()
library(ContDataQC)
?Export.IHA
# 1.B. Use saved data
myFile <- "01187300_Gage_20150101_20161231.csv"
myCol.DateTime <- "Date.Time"
myCol.Discharge <- "Discharge.ft3.s"
getwd()
# 1.A. Use ContDataQC and Save (~1min for download)
myData.Operation    <- "GetGageData" #Selection.Operation[1]
myData.SiteID       <- "01187300" # Hubbard River near West Hartland, CT
myData.Type         <- "Gage"
myData.DateRange.Start  <- "2015-01-01"
myData.DateRange.End    <- "2016-12-31"
myDir.import <- getwd()
myDir.export <- getwd()
ContDataQC(myData.Operation, myData.SiteID, myData.Type
, myData.DateRange.Start, myData.DateRange.End
, myDir.import, myDir.export)
?Export.StreamThermal
head(myData.IHA)
myData.IHA <- Export.IHA(myFile
, fun.myCol.DateTime = myCol.DateTime
, fun.myCol.Parameter = myCol.Discharge
)
head(myData.IHA)
?Export.IHA
# User info
SiteID <- myData.SiteID
Notes.User <- "Erik.Leppo@tetratech.com"
#~~~~~
SiteID
?ContDataQC
# 1.  Get Gage Data
#
# 1.A. Use ContDataQC and Save (~1min for download)
myData.Operation    <- "GetGageData" #Selection.Operation[1]
myData.SiteID       <- "01187300" # Hubbard River near West Hartland, CT
myData.Type         <- "Gage"
myData.DateRange.Start  <- "2015-01-01"
myData.DateRange.End    <- "2016-12-31"
myDir.import <- getwd()
myDir.export <- getwd()
ContDataQC(myData.Operation, myData.SiteID, myData.Type
, myData.DateRange.Start, myData.DateRange.End
, myDir.import, myDir.export)
#
# 1.B. Use saved data
myFile <- "01187300_Gage_20150101_20161231.csv"
myCol.DateTime <- "Date.Time"
myCol.Discharge <- "Discharge.ft3.s"
#
# 2. Prep Data
myData.IHA <- Export.IHA(myFile
, fun.myCol.DateTime = myCol.DateTime
, fun.myCol.Parameter = myCol.Discharge
)
# User info
SiteID <- myData.SiteID
Notes.User <- Sys.getenv("USERNAME")
#~~~~~
# Library (load)
require(IHA)
require(XLConnect)
# IHA
myYr <- "calendar" # "water" or "calendar"
# IHA Metrics
## IHA parameters group 1; Magnitude of monthly water conditions
Analysis.Group.1 <- group1(myData.IHA, year=myYr)
## IHA parameters group 2: Magnitude of monthly water condition and include 12 parameters
Analysis.Group.2 <- group2(myData.IHA, year=myYr)
Analysis.Group.3 <- group3(myData.IHA, year=myYr)
## IHA parameters group 4; Frequency and duration of high and low pulses
# defaults to 25th and 75th percentiles
Analysis.Group.4 <- group4(myData.IHA, year=myYr)
## IHA parameters group 5; Rate and frequency of water condition changes
Analysis.Group.5 <- group5(myData.IHA, year=myYr)
#~~~~~
# Save Results to Excel (each group on its own worksheet)
Group.Desc <- c("Magnitude of monthly water conditions"
,"Magnitude of monthly water condition and include 12 parameters"
,"Timing of annual extreme water conditions"
,"Frequency and duration of high and low pulses"
,"Rate and frequency of water condition changes")
df.Groups <- as.data.frame(cbind(paste0("Group",1:5),Group.Desc))
#
myDate <- format(Sys.Date(),"%Y%m%d")
myTime <- format(Sys.time(),"%H%M%S")
# Notes section (add min/max dates)
Notes.Names <- c("Dataset (SiteID)","IHA.Year","Analysis.Date (YYYYMMDD)","Analysis.Time (HHMMSS)","Analysis.User")
Notes.Data <- c(SiteID, myYr, myDate, myTime, Notes.User)
df.Notes <- as.data.frame(cbind(Notes.Names,Notes.Data))
Notes.Summary <- summary(myData.IHA)
# Open/Create file
myFile.XLSX <- paste("IHA", SiteID, myYr, myDate, myTime, "xlsx", sep=".")
wb <- loadWorkbook(myFile.XLSX, create = TRUE) # load workbook, create if not existing
# create sheets
createSheet(wb, name = "NOTES")
createSheet(wb, name = "Group1")
createSheet(wb, name = "Group2")
createSheet(wb, name = "Group3")
createSheet(wb, name = "Group4")
createSheet(wb, name = "Group5")
# write to worksheet
writeWorksheet(wb, df.Notes, sheet = "NOTES", startRow=1)
writeWorksheet(wb, Notes.Summary, sheet = "NOTES", startRow=10)
writeWorksheet(wb, df.Groups, sheet="NOTES", startRow=25)
writeWorksheet(wb, Analysis.Group.1, sheet = "Group1")
writeWorksheet(wb, Analysis.Group.2, sheet = "Group2")
writeWorksheet(wb, Analysis.Group.3, sheet = "Group3")
writeWorksheet(wb, Analysis.Group.4, sheet = "Group4")
writeWorksheet(wb, Analysis.Group.5, sheet = "Group5")
# save workbook
saveWorkbook(wb, myFile.XLSX)
# IHA
myYr <- "calendar" # "water" or "calendar"
# IHA Metrics
## IHA parameters group 1; Magnitude of monthly water conditions
Analysis.Group.1 <- group1(myData.IHA, year=myYr)
## IHA parameters group 2: Magnitude of monthly water condition and include 12 parameters
Analysis.Group.2 <- group2(myData.IHA, year=myYr)
Analysis.Group.3 <- group3(myData.IHA, year=myYr)
## IHA parameters group 4; Frequency and duration of high and low pulses
# defaults to 25th and 75th percentiles
Analysis.Group.4 <- group4(myData.IHA, year=myYr)
## IHA parameters group 5; Rate and frequency of water condition changes
Analysis.Group.5 <- group5(myData.IHA, year=myYr)
#~~~~~
# Save Results to Excel (each group on its own worksheet)
Group.Desc <- c("Magnitude of monthly water conditions"
,"Magnitude of monthly water condition and include 12 parameters"
,"Timing of annual extreme water conditions"
,"Frequency and duration of high and low pulses"
,"Rate and frequency of water condition changes")
df.Groups <- as.data.frame(cbind(paste0("Group",1:5),Group.Desc))
#
myDate <- format(Sys.Date(),"%Y%m%d")
myTime <- format(Sys.time(),"%H%M%S")
# Notes section (add min/max dates)
Notes.Names <- c("Dataset (SiteID)","IHA.Year","Analysis.Date (YYYYMMDD)","Analysis.Time (HHMMSS)","Analysis.User")
Notes.Data <- c(SiteID, myYr, myDate, myTime, Notes.User)
df.Notes <- as.data.frame(cbind(Notes.Names,Notes.Data))
Notes.Summary <- summary(myData.IHA)
# Open/Create file
myFile.XLSX <- paste("IHA", SiteID, myYr, myDate, myTime, "xlsx", sep=".")
wb <- loadWorkbook(myFile.XLSX, create = TRUE) # load workbook, create if not existing
# create sheets
createSheet(wb, name = "NOTES")
createSheet(wb, name = "Group1")
createSheet(wb, name = "Group2")
createSheet(wb, name = "Group3")
createSheet(wb, name = "Group4")
createSheet(wb, name = "Group5")
# write to worksheet
writeWorksheet(wb, df.Notes, sheet = "NOTES", startRow=1)
writeWorksheet(wb, Notes.Summary, sheet = "NOTES", startRow=10)
writeWorksheet(wb, df.Groups, sheet="NOTES", startRow=25)
writeWorksheet(wb, Analysis.Group.1, sheet = "Group1")
writeWorksheet(wb, Analysis.Group.2, sheet = "Group2")
writeWorksheet(wb, Analysis.Group.3, sheet = "Group3")
writeWorksheet(wb, Analysis.Group.4, sheet = "Group4")
writeWorksheet(wb, Analysis.Group.5, sheet = "Group5")
# save workbook
saveWorkbook(wb, myFile.XLSX)
# generate Vignette
library(ContDataQC)
library(devtools)
devtools::build_vignettes()
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
library(ContDataQC)
?PeriodStats
df.x <- DATA_period_test2_Aw_20130101_20141231
head(df.x)
View(df.x)
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
library(ContDataQC)
?PeriodStats
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
library(ContDataQC)
?PeriodStats
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
library(ContDataQC)
?PeriodStats
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# generate Vignette
library(ContDataQC)
library(devtools)
devtools::build_vignettes()
# Library Name
myLibrary <- "ContDataQC"
# Load Library
library(devtools)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Create Package
# create(myLibrary)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Document, Install, and Reload Library
## Generate Documentation
setwd(paste0("./",myLibrary))
devtools::document()
## Install New Package (locally)
setwd("..") # return to root directory first
devtools::install(myLibrary)
## Reload library
library(myLibrary,character.only = TRUE)
# change wd back to package
setwd(paste0("./",myLibrary))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~