Creates a date frame (and file export) from Continuous Data in the format used by the StreamThermal package.
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
)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).
Column name for SiteID. Default = SiteID (as defined in config.R)
Column name for SiteID. Default = Date (as defined in config.R)
Column name for SiteID. Default = Water.Temp.C (as defined in config.R)
Returns a data frame formatted for use with the R library StreamThermal (SiteID, Date, MaxT, MinT, MeanT). Statistics are calculated in the function.
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")
#~~~~~~~~~~~~~~~~~~~~~~
# 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)
#> Loading required package: StreamThermal
#~~~~~
# StreamThermal
(ST.freq <- T_frequency(sitedata))
#> SiteInfo FmaxcT1 FmaxcT2 FmaxcT3 FmaxcT4 FmaxcT5 FmaxcT6 FmaxcT7 FmaxcT8
#> 1 01382310 0 0 0 0 17 29 31 30
#> FmaxcT9 FmaxcT10 FmaxcT11 FmaxcT12 FmincT1 FmincT2 FmincT3 FmincT4 FmincT5
#> 1 30 12 0 0 0 0 0 0 7
#> FmincT6 FmincT7 FmincT8 FmincT9 FmincT10 FmincT11 FmincT12 FmeancT1 FmeancT2
#> 1 24 31 28 25 3 0 0 0 0
#> FmeancT3 FmeancT4 FmeancT5 FmeancT6 FmeancT7 FmeancT8 FmeancT9 FmeancT10
#> 1 0 0 10 26 31 28 26 7
#> FmeancT11 FmeancT12 FmaxcTsp FmincTsp FmeancTsp FmaxcTsu FmincTsu FmeancTsu
#> 1 0 0 17 7 10 90 83 85
#> FmaxcTfa FmincTfa FmeancTfa FmaxcTwi FmincTwi FmeancTwi
#> 1 42 28 33 0 0 0
(ST.mag <- T_magnitude(sitedata))
#> SiteInfo ADmax1 ADmax2 ADmax3 ADmax4 ADmax5 ADmax6 ADmax7 ADmax8
#> 1 01382310 1.825806 1.775 4.864516 9.88 17.20645 21.47333 24.09677 22.68387
#> ADmax9 ADmax10 ADmax11 ADmax12 ADmin1 ADmin2 ADmin3 ADmin4
#> 1 20.03 15.01613 9.793333 6.2 0.9419355 0.5214286 2.764516 7.513333
#> ADmin5 ADmin6 ADmin7 ADmin8 ADmin9 ADmin10 ADmin11 ADmin12
#> 1 14.65806 18.62 20.36452 19.96774 18.46333 13.23548 8.106667 4.825806
#> ADmean1 ADmean2 ADmean3 ADmean4 ADmean5 ADmean6 ADmean7 ADmean8
#> 1 1.322581 1.107143 3.654839 8.566667 15.89355 20 22.01613 21.32903
#> ADmean9 ADmean10 ADmean11 ADmean12 MaxDmeanSp MinDmeanSp AvgDmeanSp
#> 1 19.27667 14.16774 8.916667 5.535484 22.4 1.6 9.380435
#> MaxDmeanSu MinDmeanSu AvgDmeanSu MaxDmeanFa MinDmeanFa AvgDmeanFa MaxDmeanWi
#> 1 25 13.8 21.12717 21.5 7.2 14.12088 8.6
#> MinDmeanWi AvgDmeanWi Max30MovingAMeanT Max30MovingAMaxT Max21MovingAMeanT
#> 1 0.1 2.706667 22.16667 24.32333 22.40476
#> Max21MovingAMaxT Max14MovingAMeanT Max14MovingAMaxT Max7MovingAMeanT
#> 1 24.59048 22.67857 24.73571 23.21429
#> Max7MovingAMaxT Max3MovingAMeanT Max3MovingAMaxT
#> 1 25.17143 23.96667 26.1
(ST.roc <- T_rateofchange(sitedata))
#> SiteInfo RC1 RC2 RC3 RC4 RC5 RC6 RC7 RC8 RC9
#> 1 01382310 0.108 0.1352941 0.2866667 0.3518519 0.4 1.54 0.96 2.24 0.4357143
#> RC10 RC11 RC12 RCsp RCsu RCfa RCwi
#> 1 0.32 0.4111111 0.2434783 0.2337079 0.5090909 0.1881579 0.02715655
(ST.tim <- T_timing(sitedata))
#> SiteInfo JDmaxMaxT1 JDmaxMaxT2 JDmaxMaxT3 JDmaxMaxT4 JDmaxMaxT5 JDmaxMaxT6
#> 1 01382310 0 48 76 118 150 151
#> JDmaxMaxT7 JDmaxMaxT8 JDmaxMaxT9 JDmaxMaxT10 JDmaxMaxT11 JDmaxMaxT12
#> 1 202 219 246 273 313 339
#> JDminMinT1 JDminMinT2 JDminMinT3 JDminMinT4 JDminMinT5 JDminMinT6 JDminMinT7
#> 1 26 38 61 91 125 156 195
#> JDminMinT8 JDminMinT9 JDminMinT10 JDminMinT11 JDminMinT12 JDmaxMeanT1
#> 1 224 260 301 322 352 1
#> JDmaxMeanT2 JDmaxMeanT3 JDmaxMeanT4 JDmaxMeanT5 JDmaxMeanT6 JDmaxMeanT7
#> 1 48 76 117 150 151 202
#> JDmaxMeanT8 JDmaxMeanT9 JDmaxMeanT10 JDmaxMeanT11 JDmaxMeanT12 JDmaxMaxTSp
#> 1 219 246 273 313 339 150
#> JDminMinTSp JDmaxMeanTSp JDmaxMaxTSu JDminMinTSu JDmaxMeanTSu JDmaxMaxTFa
#> 1 61 150 202 224 202 246
#> JDminMinTFa JDmaxMeanTFa JDmaxMaxTWi JDminMinTWi JDmaxMeanTWi JDM30MAMeanT
#> 1 322 246 339 38 339 198
#> JDM30MAMaxT JDM30MADRT JDM21MAMeanT JDM21MAMaxT JDM21MADRT JDM14MAMeanT
#> 1 198 199 194 194 196 232
#> JDM14MAMaxT JDM14MADRT JDM7MAMeanT JDM7MAMaxT JDM7MADRT JDM3MAMeanT
#> 1 197 195 230 201 196 219.5
#> JDM3MAMaxT JDM3MADRT
#> 1 202 196
(ST.var <- T_variability(sitedata)) # example in package doesn't work
#> Warning: numerical expression has 2 elements: only the first used
#> Warning: longer object length is not a multiple of shorter object length
#> SiteInfo ADrange1 ADrange2 ADrange3 ADrange4 ADrange5 ADrange6 ADrange7
#> 1 01382310 0.883871 1.253571 2.1 2.366667 2.548387 2.853333 3.732258
#> ADrange8 ADrange9 ADrange10 ADrange11 ADrange12 Rmean1 Rmean2 Rmean3 Rmean4
#> 1 2.716129 1.566667 1.780645 1.686667 1.374194 2.7 2.3 4.3 9.5
#> Rmean5 Rmean6 Rmean7 Rmean8 Rmean9 Rmean10 Rmean11 Rmean12 CVDmax1
#> 1 10 7.7 4.8 11.2 6.1 9.6 3.7 5.6 0.003412039
#> CVDmax2 CVDmax3 CVDmax4 CVDmax5 CVDmax6 CVDmax7
#> 1 0.003374441 0.004481093 0.01052133 0.009344021 0.007532948 0.004818057
#> CVDmax8 CVDmax9 CVDmax10 CVDmax11 CVDmax12 CVDmin1
#> 1 0.008345638 0.005903455 0.00829473 0.00336615 0.005113964 0.002115504
#> CVDmin2 CVDmin3 CVDmin4 CVDmin5 CVDmin6 CVDmin7
#> 1 0.002302309 0.003237424 0.009493291 0.009466815 0.008493875 0.004149277
#> CVDmin8 CVDmin9 CVDmin10 CVDmin11 CVDmin12 CVDmean1
#> 1 0.009612627 0.006737451 0.009036975 0.003359177 0.005527881 0.002561632
#> CVDmean2 CVDmean3 CVDmean4 CVDmean5 CVDmean6 CVDmean7
#> 1 0.00252351 0.003427647 0.009716645 0.009179103 0.008198479 0.004453308
#> CVDmean8 CVDmean9 CVDmean10 CVDmean11 CVDmean12 RmaxSp RminSp
#> 1 0.00905868 0.006180587 0.008621446 0.003187786 0.005343299 21.2 19.8
#> RmeanSp RmaxSu RminSu RmeanSu RmaxFa RminFa RmeanFa RmaxWi RminWi RmeanWi
#> 1 20.8 12.6 11.3 11.2 13.8 14.6 14.3 8.6 8.1 8.5
#> Max30MovingADRT DiffExtreme6.30 Max21MovingADRT DiffExtreme5.21
#> 1 3.89 1.95 4.004762 0
#> Max14MovingADRT DiffExtreme4.14 Max7MovingADRT DiffExtreme2.7 Max3MovingADRT
#> 1 4.371429 1.6 4.542857 0.55 5
#> DiffExtreme1.3
#> 1 0
#
#~~~~~~~~~~~~~~~~~~~~~~
# 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))
#> SiteInfo FmaxcT1 FmaxcT2 FmaxcT3 FmaxcT4 FmaxcT5 FmaxcT6 FmaxcT7 FmaxcT8
#> 1 Test2 NaN NaN NaN NaN 17 30 32 31
#> FmaxcT9 FmaxcT10 FmaxcT11 FmaxcT12 FmincT1 FmincT2 FmincT3 FmincT4 FmincT5
#> 1 30 NaN NaN NaN NaN NaN NaN NaN 7
#> FmincT6 FmincT7 FmincT8 FmincT9 FmincT10 FmincT11 FmincT12 FmeancT1 FmeancT2
#> 1 30 32 30 26 NaN NaN NaN NaN NaN
#> FmeancT3 FmeancT4 FmeancT5 FmeancT6 FmeancT7 FmeancT8 FmeancT9 FmeancT10
#> 1 NaN NaN 13 30 32 31 30 NaN
#> FmeancT11 FmeancT12 FmaxcTsp FmincTsp FmeancTsp FmaxcTsu FmincTsu FmeancTsu
#> 1 NaN NaN NaN NaN NaN 93 92 93
#> FmaxcTfa FmincTfa FmeancTfa FmaxcTwi FmincTwi FmeancTwi
#> 1 NaN NaN NaN NaN NaN NaN
(ST.mag <- T_magnitude(sitedata))
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> SiteInfo ADmax1 ADmax2 ADmax3 ADmax4 ADmax5 ADmax6 ADmax7 ADmax8
#> 1 Test2 NaN NaN NaN NaN 16.63206 21.0987 21.19138 21.53984
#> ADmax9 ADmax10 ADmax11 ADmax12 ADmin1 ADmin2 ADmin3 ADmin4 ADmin5
#> 1 20.02567 NaN NaN NaN NaN NaN NaN NaN 14.21474
#> ADmin6 ADmin7 ADmin8 ADmin9 ADmin10 ADmin11 ADmin12 ADmean1 ADmean2
#> 1 18.80953 19.43972 19.36206 17.98767 NaN NaN NaN NaN NaN
#> ADmean3 ADmean4 ADmean5 ADmean6 ADmean7 ADmean8 ADmean9 ADmean10
#> 1 NaN NaN 15.38745 19.89716 20.28798 20.44721 18.84335 NaN
#> ADmean11 ADmean12 MaxDmeanSp MinDmeanSp AvgDmeanSp MaxDmeanSu MinDmeanSu
#> 1 NaN NaN NaN NaN NaN 22.43556 18.06298
#> AvgDmeanSu MaxDmeanFa MinDmeanFa AvgDmeanFa MaxDmeanWi MinDmeanWi AvgDmeanWi
#> 1 20.21498 NaN NaN NaN NaN NaN NaN
#> Max30MovingAMeanT Max30MovingAMaxT Max21MovingAMeanT Max21MovingAMaxT
#> 1 21.11725 22.15333 20.97687 22.03014
#> Max14MovingAMeanT Max14MovingAMaxT Max7MovingAMeanT Max7MovingAMaxT
#> 1 21.23605 22.40393 21.86726 23.198
#> Max3MovingAMeanT Max3MovingAMaxT
#> 1 22.2375 24.48967
(ST.roc <- T_rateofchange(sitedata))
#> SiteInfo RC1 RC2 RC3 RC4 RC5 RC6 RC7 RC8 RC9
#> 1 Test2 NaN NaN NaN NaN 0.4328067 0.1452781 0.3250758 1.093146 0.1784598
#> RC10 RC11 RC12 RCsp RCsu RCfa RCwi
#> 1 NaN NaN NaN NaN 1.093146 NaN NaN
(ST.tim <- T_timing(sitedata))
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> SiteInfo JDmaxMaxT1 JDmaxMaxT2 JDmaxMaxT3 JDmaxMaxT4 JDmaxMaxT5 JDmaxMaxT6
#> 1 Test2 NaN NaN NaN NaN 150 178
#> JDmaxMaxT7 JDmaxMaxT8 JDmaxMaxT9 JDmaxMaxT10 JDmaxMaxT11 JDmaxMaxT12
#> 1 197 223 262 NaN NaN NaN
#> JDminMinT1 JDminMinT2 JDminMinT3 JDminMinT4 JDminMinT5 JDminMinT6 JDminMinT7
#> 1 NaN NaN NaN NaN 132 154 210
#> JDminMinT8 JDminMinT9 JDminMinT10 JDminMinT11 JDminMinT12 JDmaxMeanT1
#> 1 226 265 NaN NaN NaN NaN
#> JDmaxMeanT2 JDmaxMeanT3 JDmaxMeanT4 JDmaxMeanT5 JDmaxMeanT6 JDmaxMeanT7
#> 1 NaN NaN NaN 150 178 198
#> JDmaxMeanT8 JDmaxMeanT9 JDmaxMeanT10 JDmaxMeanT11 JDmaxMeanT12 JDmaxMaxTSp
#> 1 223 243 NaN NaN NaN NaN
#> JDminMinTSp JDmaxMeanTSp JDmaxMaxTSu JDminMinTSu JDmaxMeanTSu JDmaxMaxTFa
#> 1 NaN NaN 223 226 223 NaN
#> JDminMinTFa JDmaxMeanTFa JDmaxMaxTWi JDminMinTWi JDmaxMeanTWi JDM30MAMeanT
#> 1 NaN NaN NaN NaN NaN 209
#> JDM30MAMaxT JDM30MADRT JDM21MAMeanT JDM21MAMaxT JDM21MADRT JDM14MAMeanT
#> 1 210 269 214 215 272 218
#> JDM14MAMaxT JDM14MADRT JDM7MAMeanT JDM7MAMaxT JDM7MADRT JDM3MAMeanT
#> 1 219 278 221 222 283 222
#> JDM3MAMaxT JDM3MADRT
#> 1 261 283
(ST.var <- T_variability(sitedata))
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> Warning: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique
#> SiteInfo ADrange1 ADrange2 ADrange3 ADrange4 ADrange5 ADrange6 ADrange7
#> 1 Test2 NaN NaN NaN NaN 2.417323 2.289167 1.751656
#> ADrange8 ADrange9 ADrange10 ADrange11 ADrange12 Rmean1 Rmean2 Rmean3 Rmean4
#> 1 2.177774 2.038 NaN NaN NaN NaN NaN NaN NaN
#> Rmean5 Rmean6 Rmean7 Rmean8 Rmean9 Rmean10 Rmean11 Rmean12 CVDmax1
#> 1 7.790521 2.905562 3.575833 4.372583 5.175333 NaN NaN NaN NaN
#> CVDmax2 CVDmax3 CVDmax4 CVDmax5 CVDmax6 CVDmax7 CVDmax8
#> 1 NaN NaN NaN 0.008014304 0.003303075 0.004120679 0.004063426
#> CVDmax9 CVDmax10 CVDmax11 CVDmax12 CVDmin1 CVDmin2 CVDmin3 CVDmin4
#> 1 0.01108073 NaN NaN NaN NaN NaN NaN NaN
#> CVDmin5 CVDmin6 CVDmin7 CVDmin8 CVDmin9 CVDmin10 CVDmin11
#> 1 0.007500157 0.003100429 0.003020969 0.004748352 0.005618307 NaN NaN
#> CVDmin12 CVDmean1 CVDmean2 CVDmean3 CVDmean4 CVDmean5 CVDmean6
#> 1 NaN NaN NaN NaN NaN 0.007422009 0.002948373
#> CVDmean7 CVDmean8 CVDmean9 CVDmean10 CVDmean11 CVDmean12 RmaxSp
#> 1 0.003403629 0.003707559 0.005513046 NaN NaN NaN NaN
#> RminSp RmeanSp RmaxSu RminSu RmeanSu RmaxFa RminFa RmeanFa RmaxWi RminWi
#> 1 NaN NaN 6.129 6.095 4.372583 NaN NaN NaN NaN NaN
#> RmeanWi Max30MovingADRT DiffExtreme6.30 Max21MovingADRT DiffExtreme5.21
#> 1 NaN 2.818533 1.82021 3.277714 0
#> Max14MovingADRT DiffExtreme4.14 Max7MovingADRT DiffExtreme2.7 Max3MovingADRT
#> 1 3.204357 1.616734 5.034571 0.01802083 9.707667
#> DiffExtreme1.3
#> 1 0
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 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)
#> [1] TRUE
## 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)
#> Error: NoSuchMethodError (Java): org.apache.xmlbeans.XmlCursor.close()V
writeWorksheet(wb, Notes.Summary, sheet = "NOTES", startRow=20)
#> Error: NoSuchMethodError (Java): org.apache.xmlbeans.XmlCursor.close()V
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)