Export.StreamThermal: Export data for StreamThermal package

In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data

Export data for StreamThermal package

Description

Creates a date frame (and file export) from Continuous Data in the format used by the StreamThermal package.

Usage

Export.StreamThermal(
  fun.myDF,
  fun.col.SiteID = ContData.env$myName.SiteID,
  fun.col.Date = ContData.env$myName.Date,
  fun.col.Temp = ContData.env$myName.WaterTemp
)

Arguments

fun.myDF	User data that has been through the QC process of ContDataQC. Required fields are SiteID, Date, Water.Temp.C (or as defined in config.R).
fun.col.SiteID	Column name for SiteID. Default = SiteID (as defined in config.R)
fun.col.Date	Column name for SiteID. Default = Date (as defined in config.R)
fun.col.Temp	Column name for SiteID. Default = Water.Temp.C (as defined in config.R)

Details

Required fields are StationID, Date, dailyMax, dailyMin, and dailyMean The fields are named "siteID", "Date", "MaxT", "MinT", and "MeanT".

The StreamThermal package is available on GitHub. It can be installed with the devtools package:

library(devtools)

install_github("tsangyp/StreamThermal")

Value

Returns a data frame formatted for use with the R library StreamThermal (SiteID, Date, MaxT, MinT, MeanT). Statistics are calculated in the function.

Examples

#~~~~~~~~~~~~~~~~~~~~~~
# Example 1, USGS data
#~~~~~~~~~~~~~~~~~~~~~~
library(dataRetrieval)
# 1.1. Get USGS data
# code from StreamThermal T_frequency example
ExUSGSStreamTemp<-readNWISdv("01382310","00010","2011-01-01","2011-12-31"
                             ,c("00001","00002","00003"))
sitedata<-subset(ExUSGSStreamTemp, select=c("site_no","Date"
                 ,"X_00010_00001","X_00010_00002","X_00010_00003"))
names(sitedata)<-c("siteID","Date","MaxT","MinT","MeanT")
#
# 1.2. Run StreamThermal
# Library (install if needed)
# devtools::install_github("tsangyp/StreamThermal")
# Library (load)
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)) # example in package doesn't work
#
#~~~~~~~~~~~~~~~~~~~~~~
# 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)

leppott/ContDataQC documentation built on Jan. 5, 2025, 10:12 a.m.