Calls all other functions for the ContDataQC library.
ContDataQC(
fun.myData.Operation,
fun.myData.SiteID,
fun.myData.Type,
fun.myData.DateRange.Start,
fun.myData.DateRange.End,
fun.myDir.import = getwd(),
fun.myDir.export = getwd(),
fun.myConfig = "",
fun.myFile = "",
fun.myReport.format = "",
fun.myReport.Dir = "",
fun.CreateReport = TRUE,
fun.AddDeployCol = TRUE
)Operation to be performed; c("GetGageData","QCRaw", "Aggregate", "SummaryStats")
Station/SiteID.
data type; c("Air","Water","AW","Gage","AWG","AG","WG")
Start date for requested data. Format = YYYY-MM-DD.
End date for requested data. Format = YYYY-MM-DD.
Directory for import data. Default is current working directory.
Directory for export data. Default is current working directory.
Configuration file to use for this data analysis. The default is always loaded first so only "new" values need to be included. This is the easiest way to control time zones.
Single file (or vector of files) to perform functions. SiteID, Type, and Date Range not used when file name(s) provided.
Report format (docx or html). Default is specified in config.R (docx). Can be customized in config.R; ContData.env$myReport.Format.
Report (rmd) template folder. Default is the package rmd folder. Can be customized in config.R; ContData.env$myReport.Dir.
Boolean parameter to create reports or not. Default = TRUE.
Boolean for adding column name. Default = TRUE Can be customized in config.R; ContData.env$myName.LoggerDeployment.
Returns a csv into the specified export directory with additional columns for calculated statistics.
Below are the default data directories assumed to exist in the working directory. These can be created with code in the example.
./Data0_Original/ = Unmodified data logger files.
./Data1_RAW/ = Data logger files modified for use with library. Modifications for extra rows and file and column names.
./Data2_QC/ = Repository for library output for QCed files.
./Data3_Aggregated/ = Repository for library output for aggregated (or split) files.
./Data4_Stats/ = Repository for library output for statistical summary files.
It is possible to call the Aggregate file portion of the script to meld together files from multiple sites (e.g., all sites in a watershed or from different depths on a lake). The file will be named by the first file named with "Append_x" where "x" is the number of files that were aggregated. The purpose is to allow users to analyze the data in these files from a single file.
Pandoc is needed for docx reports (default). Pandoc comes packaged with RStudio. To install Pandoc on Windows use the `installr` package.
https://CRAN.R-project.org/package=installr
install.packages("installr") installr::install.pandoc()
The above won't work if don't have admin rights on your computer. Alternative = Download the msi file from the link below for the latest release. You may need to have your IT dept install it for you. https://github.com/jgm/pandoc/releases For help for installing via command window: http://www.intowindows.com/how-to-run-msi-file-as-administrator-from-command-prompt-in-windows/
# Examples of each operation
# 00. Set up
# Parameters
Selection.Operation <- c("GetGageData"
, "QCRaw"
, "Aggregate"
, "SummaryStats")
Selection.Type <- c("Air","Water","AW","Gage","AWG","AG","WG")
Selection.SUB <- c("Data0_Original"
, "Data1_RAW"
, "Data2_QC"
, "Data3_Aggregated"
, "Data4_Stats")
(myDir.BASE <- tempdir()) # create and print temp directory for example data
#> [1] "/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpZn7gXz"
# Create data directories
myDir.create <- file.path(myDir.BASE, Selection.SUB[1])
ifelse(dir.exists(myDir.create) == FALSE
, dir.create(myDir.create)
, "Directory already exists")
#> [1] TRUE
myDir.create <- file.path(myDir.BASE, Selection.SUB[2])
ifelse(dir.exists(myDir.create) == FALSE
, dir.create(myDir.create)
, "Directory already exists")
#> [1] TRUE
myDir.create <- file.path(myDir.BASE, Selection.SUB[3])
ifelse(dir.exists(myDir.create) == FALSE
, dir.create(myDir.create)
, "Directory already exists")
#> [1] TRUE
myDir.create <- file.path(myDir.BASE, Selection.SUB[4])
ifelse(dir.exists(myDir.create) == FALSE
, dir.create(myDir.create)
, "Directory already exists")
#> [1] TRUE
myDir.create <- file.path(myDir.BASE, Selection.SUB[5])
ifelse(dir.exists(myDir.create) == FALSE
, dir.create(myDir.create)
, "Directory already exists")
#> [1] TRUE
# Save example data (assumes myDir.BASE directory exists)
myData <- data_raw_test2_AW_20130426_20130725
write.csv(myData, file.path(myDir.BASE
, Selection.SUB[2]
, "test2_AW_20130426_20130725.csv"))
myData <- data_raw_test2_AW_20130725_20131015
write.csv(myData, file.path(myDir.BASE
, Selection.SUB[2]
, "test2_AW_20130725_20131015.csv"))
myData <- data_raw_test2_AW_20140901_20140930
write.csv(myData, file.path(myDir.BASE
, Selection.SUB[2]
, "test2_AW_20140901_20140930.csv"))
myData <- data_raw_test4_AW_20160418_20160726
write.csv(myData, file.path(myDir.BASE
, Selection.SUB[2]
, "test4_AW_20160418_20160726.csv"))
myFile <- "config.TZ.Central.R"
file.copy(file.path(path.package("ContDataQC"), "extdata", myFile)
, file.path(myDir.BASE, Selection.SUB[2], myFile))
#> [1] TRUE
# 01.A. Get Gage Data
myData.Operation <- "GetGageData" #Selection.Operation[1]
myData.SiteID <- "01187300" # Hubbard River near West Hartland, CT
myData.Type <- Selection.Type[4] #"Gage"
myData.DateRange.Start <- "2013-01-01"
myData.DateRange.End <- "2014-12-31"
myDir.import <- ""
myDir.export <- file.path(myDir.BASE, Selection.SUB[2])
ContDataQC(myData.Operation
, myData.SiteID
, myData.Type
, myData.DateRange.Start
, myData.DateRange.End
, myDir.import
, myDir.export)
#> [1] "Total items to process = 1"
#>
#> [1] "Getting available data; 01187300."
#>
#> agency_cd site_no station_nm site_tp_cd
#> 530 USGS 01187300 HUBBARD RIVER NEAR WEST HARTLAND, CT ST
#> 531 USGS 01187300 HUBBARD RIVER NEAR WEST HARTLAND, CT ST
#> 532 USGS 01187300 HUBBARD RIVER NEAR WEST HARTLAND, CT ST
#> dec_lat_va dec_long_va coord_acy_cd dec_coord_datum_cd alt_va alt_acy_va
#> 530 42.0375 -72.93933 H NAD83 594.57 0.01
#> 531 42.0375 -72.93933 H NAD83 594.57 0.01
#> 532 42.0375 -72.93933 H NAD83 594.57 0.01
#> alt_datum_cd huc_cd data_type_cd parm_cd stat_cd ts_id loc_web_ds
#> 530 NGVD29 01080207 uv 00010 <NA> 66869 NA
#> 531 NGVD29 01080207 uv 00060 <NA> 66866 NA
#> 532 NGVD29 01080207 uv 00065 <NA> 66867 NA
#> medium_grp_cd parm_grp_cd srs_id access_cd begin_date end_date count_nu
#> 530 wat <NA> 1645597 0 2015-11-04 2018-08-08 1008
#> 531 wat <NA> 1645423 0 1990-10-01 2022-12-22 11770
#> 532 wat <NA> 17164583 0 2007-10-01 2022-12-22 5561
#>
#>
#> [1] "Processing item 1 of 1, COMPLETE, 01187300."
#>
#> [1] "Task COMPLETE; 0.23 min."
# 01.B. Get Gage Data (central time zone)
myData.Operation <- "GetGageData" #Selection.Operation[1]
myData.SiteID <- "07032000" # Mississippi River at Memphis, TN
myData.Type <- Selection.Type[4] #"Gage"
myData.DateRange.Start <- "2013-01-01"
myData.DateRange.End <- "2014-12-31"
myDir.import <- ""
myDir.export <- file.path(myDir.BASE, Selection.SUB[2])
# include path if not in working directory
myConfig <- file.path(myDir.BASE, Selection.SUB[2]
, "config.TZ.central.R")
ContDataQC(myData.Operation
, myData.SiteID
, myData.Type
, myData.DateRange.Start
, myData.DateRange.End
, myDir.import
, myDir.export
, myConfig)
#> [1] "Total items to process = 1"
#>
#> [1] "Getting available data; 07032000."
#>
#> agency_cd site_no station_nm site_tp_cd dec_lat_va
#> 360 USGS 07032000 MISSISSIPPI RIVER AT MEMPHIS, TN ST 35.12315
#> 361 USGS 07032000 MISSISSIPPI RIVER AT MEMPHIS, TN ST 35.12315
#> dec_long_va coord_acy_cd dec_coord_datum_cd alt_va alt_acy_va alt_datum_cd
#> 360 -90.07759 S NAD83 184 21 NAVD88
#> 361 -90.07759 S NAD83 184 21 NAVD88
#> huc_cd data_type_cd parm_cd stat_cd ts_id loc_web_ds medium_grp_cd
#> 360 08010100 uv 00060 <NA> 131634 NA wat
#> 361 08010100 uv 00065 <NA> 131635 NA wat
#> parm_grp_cd srs_id access_cd begin_date end_date count_nu
#> 360 <NA> 1645423 0 2014-10-01 2022-12-22 3004
#> 361 <NA> 17164583 0 2011-05-09 2022-12-22 4245
#>
#>
#> [1] "Processing item 1 of 1, COMPLETE, 07032000."
#>
#> [1] "Task COMPLETE; 0.01 min."
# 02.A. QC Raw Data
myData.Operation <- "QCRaw" #Selection.Operation[2]
myData.SiteID <- "test2"
myData.Type <- Selection.Type[3] #"AW"
myData.DateRange.Start <- "2013-01-01"
myData.DateRange.End <- "2014-12-31"
myDir.import <- file.path(myDir.BASE, Selection.SUB[2]) #"Data1_RAW"
myDir.export <- file.path(myDir.BASE, Selection.SUB[3]) #"Data2_QC"
myReport.format <- "docx"
ContDataQC(myData.Operation
, myData.SiteID
, myData.Type
, myData.DateRange.Start
, myData.DateRange.End
, myDir.import
, myDir.export
, fun.myReport.format = myReport.format)
#> [1] "Total files to process = 6"
#> [1] "Processing item 1 of 6, SKIPPED (Non-Match, SiteID), 01187300_Gage_20130101_20150101.csv."
#> [1] "Processing item 2 of 6, SKIPPED (Non-Match, SiteID), 07032000_Gage_20140930_20141231.csv."
#> [1] "Processing item 3 of 6, WORKING (QC Tests and Flags - WaterTemp), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 3 of 6, WORKING (QC Tests and Flags - AirTemp), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 3 of 6, WORKING (QC Tests and Flags - WaterP), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 3 of 6, WORKING (QC Tests and Flags - AirP), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 3 of 6, WORKING (QC Tests and Flags - SensorDepth), test2_AW_20130426_20130725.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 9.081066 secs."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2013-04-26 to 2013-07-25)."
#> [1] "Processing item 3 of 6, COMPLETE, test2_AW_20130426_20130725.csv."
#> [1] "Processing item 4 of 6, WORKING (QC Tests and Flags - WaterTemp), test2_AW_20130725_20131015.csv."
#> [1] "Processing item 4 of 6, WORKING (QC Tests and Flags - AirTemp), test2_AW_20130725_20131015.csv."
#> [1] "Processing item 4 of 6, WORKING (QC Tests and Flags - WaterP), test2_AW_20130725_20131015.csv."
#> [1] "Processing item 4 of 6, WORKING (QC Tests and Flags - AirP), test2_AW_20130725_20131015.csv."
#> [1] "Processing item 4 of 6, WORKING (QC Tests and Flags - SensorDepth), test2_AW_20130725_20131015.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 7.8039 secs."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2013-07-25 to 2013-10-15)."
#> [1] "Processing item 4 of 6, COMPLETE, test2_AW_20130725_20131015.csv."
#> [1] "Processing item 5 of 6, WORKING (QC Tests and Flags - WaterTemp), test2_AW_20140901_20140930.csv."
#> [1] "Processing item 5 of 6, WORKING (QC Tests and Flags - AirTemp), test2_AW_20140901_20140930.csv."
#> [1] "Processing item 5 of 6, WORKING (QC Tests and Flags - WaterP), test2_AW_20140901_20140930.csv."
#> [1] "Processing item 5 of 6, WORKING (QC Tests and Flags - AirP), test2_AW_20140901_20140930.csv."
#> [1] "Processing item 5 of 6, WORKING (QC Tests and Flags - SensorDepth), test2_AW_20140901_20140930.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 7.146763 secs."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2014-09-01 to 2014-09-30)."
#> [1] "Processing item 5 of 6, COMPLETE, test2_AW_20140901_20140930.csv."
#> [1] "Processing item 6 of 6, SKIPPED (Non-Match, SiteID), test4_AW_20160418_20160726.csv."
#> [1] "Task COMPLETE; 0.48 min."
# 02.B. QC Raw Data (offset collection times for air and water sensors)
myData.Operation <- "QCRaw" #Selection.Operation[2]
myData.SiteID <- "test4"
myData.Type <- Selection.Type[3] #"AW"
myData.DateRange.Start <- "2016-04-28"
myData.DateRange.End <- "2016-07-26"
myDir.import <- file.path(myDir.BASE, Selection.SUB[2]) #"Data1_RAW"
myDir.export <- file.path(myDir.BASE, Selection.SUB[3]) #"Data2_QC"
myReport.format <- "html"
ContDataQC(myData.Operation
, myData.SiteID
, myData.Type
, myData.DateRange.Start
, myData.DateRange.End
, myDir.import
, myDir.export
, fun.myReport.format = myReport.format)
#> [1] "Total files to process = 6"
#> [1] "Processing item 1 of 6, SKIPPED (Non-Match, SiteID), 01187300_Gage_20130101_20150101.csv."
#> [1] "Processing item 2 of 6, SKIPPED (Non-Match, SiteID), 07032000_Gage_20140930_20141231.csv."
#> [1] "Processing item 3 of 6, SKIPPED (Non-Match, SiteID), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 4 of 6, SKIPPED (Non-Match, SiteID), test2_AW_20130725_20131015.csv."
#> [1] "Processing item 5 of 6, SKIPPED (Non-Match, SiteID), test2_AW_20140901_20140930.csv."
#> [1] "Processing item 6 of 6, WORKING (QC Tests and Flags - WaterTemp), test4_AW_20160418_20160726.csv."
#> [1] "Processing item 6 of 6, WORKING (QC Tests and Flags - AirTemp), test4_AW_20160418_20160726.csv."
#> [1] "Processing item 6 of 6, WORKING (QC Tests and Flags - WaterP), test4_AW_20160418_20160726.csv."
#> [1] "Processing item 6 of 6, WORKING (QC Tests and Flags - AirP), test4_AW_20160418_20160726.csv."
#> [1] "Processing item 6 of 6, WORKING (QC Tests and Flags - SensorDepth), test4_AW_20160418_20160726.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 13.06512 secs."
#> [1] "User defined parameters: SiteID (test4), Data Type (Aw), Date Range (2016-04-18 to 2016-07-26)."
#> [1] "Processing item 6 of 6, COMPLETE, test4_AW_20160418_20160726.csv."
#> [1] "Task COMPLETE; 0.27 min."
# 03. Aggregate Data
myData.Operation <- "Aggregate" #Selection.Operation[3]
myData.SiteID <- "test2"
myData.Type <- Selection.Type[3] #"AW"
myData.DateRange.Start <- "2013-01-01"
myData.DateRange.End <- "2014-12-31"
myDir.import <- file.path(myDir.BASE, Selection.SUB[3]) #"Data2_QC"
myDir.export <- file.path(myDir.BASE, Selection.SUB[4]) #"Data3_Aggregated"
#Leave off myReport.format and get default (docx).
ContDataQC(myData.Operation
, myData.SiteID
, myData.Type
, myData.DateRange.Start
, myData.DateRange.End
, myDir.import
, myDir.export)
#> [1] "Total files to process = 4"
#> [1] "Task COMPLETE. QC Report. Total time = 7.931497 secs."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2013-01-01 to 2014-12-31)."
#> [1] "Processing item 1 of 4, COMPLETE, QC_test2_Aw_20130426_20130725.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 10.34814 secs."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2013-01-01 to 2014-12-31)."
#> [1] "Processing item 2 of 4, COMPLETE, QC_test2_Aw_20130725_20131015.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 11.03408 secs."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2013-01-01 to 2014-12-31)."
#> [1] "Processing item 3 of 4, COMPLETE, QC_test2_Aw_20140901_20140930.csv."
#> [1] "Processing item 4 of 4, SKIPPED (Non-Match, SiteID), QC_test4_Aw_20160418_20160726.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 10.71593 secs."
#> [1] "User defined parameters: File Name (test2_Aw_20130101_20141231.csv)."
#> [1] "Processing of 4 of 4 files complete."
#> [1] "Processing of items (n=4) finished. Total time = 41.93611 secs."
#> [1] "Items COMPLETE = 3."
#> [1] "Items SKIPPPED = 1."
#> [1] "User defined parameters: SiteID (test2), Data Type (Aw), Date Range (2013-01-01 to 2014-12-31)."
#> [1] "No other data type files exist for this SiteID and Date Range.\n No combining across data types is possible."
# 04. Summary Stats
myData.Operation <- "SummaryStats" #Selection.Operation[4]
myData.SiteID <- "test2"
myData.Type <- Selection.Type[3] #"AW"
myData.DateRange.Start <- "2013-01-01"
myData.DateRange.End <- "2014-12-31"
myDir.import <- file.path(myDir.BASE, Selection.SUB[4]) #"Data3_Aggregated"
myDir.export <- file.path(myDir.BASE, Selection.SUB[5]) #"Data4_Stats"
#Leave off myReport.format and get default (docx).
ContDataQC(myData.Operation
, myData.SiteID
, myData.Type
, myData.DateRange.Start
, myData.DateRange.End
, myDir.import
, myDir.export)
#> [1] "Total items to process = 3:"
#> [1] "Water.Temp.C" "Air.Temp.C" "Sensor.Depth.ft"
#> [1] "Processing item 1 of 3; Water.Temp.C"
#> [1] "Processing item 2 of 3; Air.Temp.C"
#> [1] "Processing item 3 of 3; Sensor.Depth.ft"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# File Versions
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 02.Alt. QC Data
myData.Operation <- "QCRaw" #Selection.Operation[2]
#myFile <- "test2_AW_20130426_20130725.csv"
myFile <- c("test2_AW_20130426_20130725.csv"
, "test2_AW_20130725_20131015.csv"
, "test2_AW_20140901_20140930.csv")
myDir.import <- file.path(myDir.BASE, "Data1_RAW")
myDir.export <- file.path(myDir.BASE, "Data2_QC")
myReport.format <- "docx"
ContDataQC(myData.Operation
, fun.myDir.import = myDir.import
, fun.myDir.export = myDir.export
, fun.myFile = myFile
, fun.myReport.format = myReport.format)
#> [1] "Total files to process = 3"
#> [1] "Processing item 1 of 3, WORKING (QC Tests and Flags - WaterTemp), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 1 of 3, WORKING (QC Tests and Flags - AirTemp), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 1 of 3, WORKING (QC Tests and Flags - WaterP), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 1 of 3, WORKING (QC Tests and Flags - AirP), test2_AW_20130426_20130725.csv."
#> [1] "Processing item 1 of 3, WORKING (QC Tests and Flags - SensorDepth), test2_AW_20130426_20130725.csv."
#> [1] "ERROR; no such file exists. Cannot create QC Report."
#> [1] "PATH = /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpZn7gXz/Data2_QC"
#> [1] "FILE = QC_test2_AW_20130426_20130725.csv"
#> Error in fun.Report.File(strFile, fun.myDir.export, fun.myDir.export, strFile.Out.Prefix, fun.myReport.format, fun.myReport.Dir): Bad file.
# 03.Alt. Aggregate Data
myData.Operation <- "Aggregate" #Selection.Operation[3]
myFile <- c("QC_test2_Aw_20130426_20130725.csv"
, "QC_test2_Aw_20130725_20131015.csv"
, "QC_test2_Aw_20140901_20140930.csv")
myDir.import <- file.path(myDir.BASE, "Data2_QC")
myDir.export <- file.path(myDir.BASE, "Data3_Aggregated")
myReport.format <- "html"
ContDataQC(myData.Operation
, fun.myDir.import = myDir.import
, fun.myDir.export = myDir.export
, fun.myFile = myFile
, fun.myReport.format = myReport.format)
#> [1] "Total files to process = 3"
#> [1] "Processing item 1 of 3, COMPLETE, QC_test2_Aw_20130426_20130725.csv."
#> [1] "Processing item 2 of 3, COMPLETE, QC_test2_Aw_20130725_20131015.csv."
#> [1] "Processing item 3 of 3, COMPLETE, QC_test2_Aw_20140901_20140930.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 13.57352 secs."
#> [1] "User defined parameters: File Name (QC_test2_Aw_20130426_20140930.csv)."
#> [1] "Processing of 3 of 3 files complete."
#> [1] "Processing of items (n=3) finished. Total time = 15.78808 secs."
#> [1] "Items COMPLETE = 3."
#> [1] "Items SKIPPPED = 0."
#> [1] "User defined parameters: File Output(DATA_QC_test2_Aw_20130426_20140930.csv)."
# 04. Alt. Summary Stats
myData.Operation <- "SummaryStats" #Selection.Operation[4]
myFile <- "QC_test2_AW_20130426_20130725.csv"
#myFile <- c("QC_test2_AW_20130426_20130725.csv"
# , "QC_test2_AW_20130725_20131015.csv"
# , "QC_test2_AW_20140901_20140930.csv")
myDir.import <- file.path(myDir.BASE, "Data2_QC")
myDir.export <- file.path(myDir.BASE, "Data4_Stats")
#Leave off myReport.format and get default (docx).
ContDataQC(myData.Operation
, fun.myDir.import = myDir.import
, fun.myDir.export = myDir.export
, fun.myFile = myFile)
#> [1] "Total files to process = 1"
#> [1] "ERROR; no such file exits. Cannot generate summary statistics."
#> [1] "PATH = /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpZn7gXz/Data2_QC"
#> [1] "FILE = QC_test2_AW_20130426_20130725.csv"
#> Error in fun.Stats.File(fun.myFile, fun.myDir.import, fun.myDir.export, fun.myReport.format, fun.myReport.Dir): Bad file.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Summary Stats from Other Data
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 05. Gage Data
# Get Gage Data via the dataRetrieval package from USGS 01187300 2013
# (~4 seconds)
data.gage <- dataRetrieval::readNWISuv("01187300"
, "00060"
, "2013-01-01"
, "2014-12-31")
head(data.gage)
#> agency_cd site_no dateTime X_00060_00000 X_00060_00000_cd tz_cd
#> 1 USGS 01187300 2013-01-10 05:00:00 22.3 A UTC
#> 2 USGS 01187300 2013-01-10 05:15:00 22.5 A UTC
#> 3 USGS 01187300 2013-01-10 05:30:00 22.5 A UTC
#> 4 USGS 01187300 2013-01-10 05:45:00 22.3 A UTC
#> 5 USGS 01187300 2013-01-10 06:00:00 22.3 A UTC
#> 6 USGS 01187300 2013-01-10 06:15:00 22.3 A UTC
# Rename fields
myNames <- c("Agency"
, "SiteID"
, "Date.Time"
, "Discharge.ft3.s"
, "Code"
, "TZ")
names(data.gage) <- myNames
# Add Date and Time
data.gage[,"Date"] <- as.Date(data.gage[,"Date.Time"])
data.gage[,"Time"] <- strftime(data.gage[,"Date.Time"], format="%H:%M:%S")
# Add "flag" fields that are added by QC function.
Names.Flags <- paste0("Flag.",c("Date.Time", "Discharge.ft3.s"))
data.gage[,Names.Flags] <- "P"
# Save File
myFile <- "01187300_Gage_20130101_20141231.csv"
write.csv(data.gage, file.path(myDir.BASE, myFile), row.names=FALSE)
# Run Stats (File)
myData.Operation <- "SummaryStats"
myDir.import <- myDir.BASE
myDir.export <- myDir.BASE
ContDataQC(myData.Operation
, fun.myDir.import = myDir.import
, fun.myDir.export = myDir.export
, fun.myFile = myFile)
#> [1] "Total files to process = 1"
#> [1] "Total items to process = 1:"
#> [1] "Discharge.ft3.s"
#> [1] "Processing item 4 of 1; Discharge.ft3.s"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Lake Data, Aggregate
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(myDir.BASE <- tempdir()) # create and print temp directory for example data
#> [1] "/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpZn7gXz"
# 06. Lake Data
# Save example data (assumes directory exists)
myFile <- c("QC_Ellis--1.0m_Water_20180524_20180918.csv"
, "QC_Ellis--3.0m_Water_20180524_20180918.csv")
file.copy(file.path(system.file("extdata", package="ContDataQC"), myFile)
, file.path(myDir.BASE, "Data2_QC", myFile))
#> [1] TRUE TRUE
# Aggregate Data
myData.Operation <- "Aggregate" #Selection.Operation[3]
myFile <- myFile
myDir.import <- file.path(myDir.BASE, "Data2_QC")
myDir.export <- file.path(myDir.BASE, "Data3_Aggregated")
myReport.format <- "html"
ContDataQC(myData.Operation
, fun.myDir.import = myDir.import
, fun.myDir.export = myDir.export
, fun.myFile = myFile
, fun.myReport.format = myReport.format)
#> [1] "Total files to process = 2"
#> [1] "Processing item 1 of 2, COMPLETE, QC_Ellis--1.0m_Water_20180524_20180918.csv."
#> [1] "Processing item 2 of 2, COMPLETE, QC_Ellis--3.0m_Water_20180524_20180918.csv."
#> [1] "Task COMPLETE. QC Report. Total time = 2.43078 secs."
#> [1] "User defined parameters: File Name (QC_Ellis--1.0m_Water_20180524_20180918.csv)."
#> [1] "Processing of 2 of 2 files complete."
#> [1] "Processing of items (n=2) finished. Total time = 2.905718 secs."
#> [1] "Items COMPLETE = 2."
#> [1] "Items SKIPPPED = 0."
#> [1] "User defined parameters: File Output(DATA_QC_Ellis--1.0m_Water_20180524_20180918.csv)."