Format miniDOT concatenate (cat) output

Format miniDOT concatenate (cat) output for use with `ContDataQC` package. Works on single files. Imports, modifies, and saves the new file.

format_minidot(
  fun.myFile = NULL,
  fun.myDir.import = getwd(),
  fun.myDir.export = getwd(),
  fun.myConfig = NULL
)

Arguments

fun.myFile

Single file (or vector of files) to perform functions.

fun.myDir.import

Directory for import data. Default is current working directory.

fun.myDir.export

Directory for export data. Default is current working directory.

fun.myConfig

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.

Value

No data frames are returned. A CSV file ready for use with the ContDataQC QC function will be generated in the specified output directory.

Details

1. Imports a miniDOT cat output file from a folder. Can also use ContDataQC::minidot_cat function.

2. Reformats it using defaults from the ContDataQC config file

3. Exports a CSV to the provided folder for use with ContDataQC

Below are the default data directories assumed to exist in the working directory. These can be created with code in the example. Using this function as an example, files will be imported from Data0_Original and exported to Data1_RAW.

* ./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.

Examples

# Create Folders
myDir.BASE <- tempdir()
myDir.create <- file.path(myDir.BASE, "Data0_Original")
  ifelse(dir.exists(myDir.create) == FALSE
         , dir.create(myDir.create)
         , "Directory already exists")
#> [1] "Directory already exists"
myDir.create <- file.path(myDir.BASE, "Data1_RAW")
  ifelse(dir.exists(myDir.create) == FALSE
         , dir.create(myDir.create)
         , "Directory already exists")
#> [1] "Directory already exists"
myDir.create <- file.path(myDir.BASE, "Data2_QC")
  ifelse(dir.exists(myDir.create) == FALSE
         , dir.create(myDir.create)
         , "Directory already exists")
#> [1] "Directory already exists"

# Data
dn_input <- file.path(system.file("extdata", package = "ContDataQC")
                      , "minidot")
dn_export <- file.path(myDir.BASE, "Data0_Original")
filename <- "test_minidot.csv"

# Create miniDOT concatenate file
minidot_cat(folderpath = dn_input
            , savetofolder = dn_export)

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# FORMAT
myFiles <- "7392-354869.csv"
myDir.BASE <- tempdir()
myDir.import <- file.path(myDir.BASE, "Data0_Original")
myDir.export <- file.path(myDir.BASE, "Data1_RAW")

# Run Function (with default config)
format_minidot(myFiles, myDir.import, myDir.export)
#> Working on item (1/1); 7392-354869.csv
#> Task complete.

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# QC newly created file
myData.Operation <- "QCRaw"
myFile <- "7392-354869.csv"
myDir.BASE <- tempdir()
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 = 1"
#> [1] "Processing item 1 of 1, WORKING (QC Tests and Flags - WaterTemp), 7392-354869.csv."
#> [1] "Processing item 1 of 1, WORKING (QC Tests and Flags - DO, mg/L), 7392-354869.csv."
#> [1] "Processing item 1 of 1, WORKING (QC Tests and Flags - DO, pct sat), 7392-354869.csv."
#> [1] "Task COMPLETE. QC Report.  Total time = 3.253127 secs."
#> [1] "User defined parameters: File Name (7392-354869.csv)."
#> [1] "Processing item 1 of 1, COMPLETE, 7392-354869.csv."
#> [1] "Task COMPLETE; 0.06 min."