format_minidot: Format miniDOT concatenate (cat) output

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

Format miniDOT concatenate (cat) output

Description

Format miniDOT concatenate (cat) output for use with 'ContDataQC' package. Works on single files. Imports, modifies, and saves the combined new file. Data columns with all NA values are removed.

Usage

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.

Details

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

2. Reformat using defaults from the ContDataQC config file.

3. As a QC step, to prevent issues with ContDataQC function, any columns that are all NA will be removed.

4. 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.

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.

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")
myDir.create <- file.path(myDir.BASE, "Data1_RAW")
  ifelse(dir.exists(myDir.create) == FALSE
         , dir.create(myDir.create)
         , "Directory already exists")
myDir.create <- file.path(myDir.BASE, "Data2_QC")
  ifelse(dir.exists(myDir.create) == FALSE
         , dir.create(myDir.create)
         , "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)

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 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)

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