addDataQuality: Add Data Quality Matrix to PyPam NetCDF
In PAMscapes: Tools for Summarising and Analysing Soundscape Data

addDataQuality

R Documentation

Add Data Quality Matrix to PyPam NetCDF

Description

Add or modify the existing data quality matrix data in a PyPam (or similar) hybrid millidecade NetCDF output. This data adds or modifies the "quality_flag" variable of a NetCDF file, which is a matrix of numbers 1,2,3, or 4 that is the same dimensions as the hybrid millidecade outputs. The input NetCDF files are modified unless preview=TRUE

Usage

addDataQuality(
  x,
  annotation = NULL,
  platformColumn = NULL,
  updateUnknown = FALSE,
  preview = FALSE,
  plot = FALSE,
  reset = FALSE,
  verbose = FALSE
)

formatDQDf(annotation)

Arguments

`x`	one or more NetCDF files or a folder containing NetCDF files. If `x` is a folder, all files with extension ".nc" will be listed from the first level of the folder (non-recursive)
`annotation`	a dataframe of annotations specifying the time-frequency bounds and quality flags to be changed. Columns for time bounds must be called `start` and `end`, must be in UTC timezone, and either POSIXct format or in YYYY-MM-DD HH:MM:SS. Columns for frequency bounds must be called `freqMin` and `freqMax` and have numeric frequency values in Hz. Column for quality code must be called `quality` and have numeric values from 1,2,3,4. Can also have additional column `file` specifying that a given annotation only applies to a specific file, or a column to match the "platform" attribute of the NetCDF file (see `platformColumn`)
`platformColumn`	NetCDF files should contain a "platform" global attribute, this can be used to specify that certain rows of `annotation` only apply to certain files in `x`. This value specifies the name of the column in `annotation` should be used (e.g. "deployment_code" means `annotation$deployment_code` contains values that will match the "platform" global attribute)
`updateUnknown`	if `FALSE`, then existing quality flags of "2" will not be changed, otherwise flags of "2" will be updated to this value (must be one of 1, 3, or 4)
`preview`	if `TRUE`, then no changes are applied to the NetCDF files, instead only plots are shown. It is recommended to run with `preview=TRUE` first to check that annotations appear to be applied properly
`plot`	if `TRUE`, a plot of the quality matrix is shown. If `"new"`, the plot is only shown if any annotations have been applied to the file. If `FALSE` no plot is created
`reset`	if `TRUE`, all quality flag flags are reset to a value of "2" before applying further annotations. Can be useful if incorrect annotations were previously applied. If `reset=TRUE` and `annotation=NULL`, then all quality code values will be "2"
`verbose`	logical flag to show or hide some messages

Value

TRUE or FALSE to indicate whether or not any annotations were applied. If x is multiple files or a folder of files, the returned vector has names equal to the file names