Interactive bulk removal editor

Opens a Shiny application for quickly trimming the start and/or end of a continuous monitoring deployment across every parameter at once, typically because a sensor was out of the water before it started recording or after it was retrieved. Removal is always linked so that a selection made while viewing one parameter removes the same timestamps from every other parameter. Unlike editASRflag, no QC flags are computed and no DQO thresholds are involved. This is a coarse first pass meant to run before other QC processes.

Usage

editASRbulk(cont, removed = NULL)

Arguments

cont

contdat data frame returned by readASRcont, or the contdat element of a previous editASRbulk result for iterative editing.

removed

Optional data frame: the removed element returned by a previous call to editASRbulk (or a compatible removed data frame from editASRflag, since both share the same Parameter/DateTime/Value columns). When supplied, the corresponding timestamps are pre-populated as removed (excluded from the plot, shown in the Removed Points table) without any new action.

Value

A list with two elements, invisibly returned after the app closes:

contdat

A data frame with the same structure as the input cont (sorted by DateTime), where every parameter at a removed timestamp is replaced with NA. Rows are retained with only DateTime populated.

removed

A data frame of all removed observations across all parameters, with columns Parameter, DateTime, and Value. Can be passed as the removed argument to a later editASRbulk.

Details

This tool is intended only for trimming the edges of a deployment. A bad stretch in the middle of a record (e.g., the sensor was pulled for cleaning and redeployed mid-deployment) should be reviewed and removed with editASRflag instead.

How to select a range

Zooming and panning with the plot toolbar is recommended to more easily identify the portion to remove. Hover over the plot and choose the Box Select or Lasso Select tool from the menu on the top right, then click and drag (box) or click and encircle (lasso) the points to remove. The removal applies to every parameter at those timestamps, not just the one currently displayed.

Only trim contiguous stretches at the very start or end of the record. Do not use this app to remove a stretch from the middle of a deployment, e.g., a period when the sensor was pulled for cleaning and redeployed; review and remove that kind of gap with editASRflag instead.

Controls

• Parameter: drop-down selector to switch between parameters. Removed timestamps are shared across all parameters, so switching parameters never changes what has been removed.

• Undo Last Removal: restores the most recently removed selection, across every parameter.

• Start Over: undoes all removals made in the current session, reverting to the state the app was in when it opened. Any removals passed in via the removed argument are preserved.

• Export Progress: saves the current cleaned data as an Excel file in a ZIP archive. If any points have been removed, a removed-observations file is included as well.

• Done / Close: stops the app. Choosing Close, save edits returns the filtered data for all parameters whereas choosing Close, discard edits returns the original unmodified data. Closing the browser tab or window directly (without clicking Done / Close) also saves edits, equivalent to Close, save edits. Refreshing the page has the same effect.

Examples

if (FALSE) { # \dontrun{
contpth <- system.file("extdata/ExampleCont1.xlsx", package = "AquaSensR")
contdat <- readASRcont(contpth)

# First session: trim obvious out-of-water stretches
trimmed <- editASRbulk(contdat)
} # }