Interactive editor for continuous monitoring data

Opens a Shiny application displaying the QC flag plot from anlzASRflag for each parameter in contdat and allows the user to interactively select and remove data points. Points are removed by clicking or drawing a selection using the box or lasso tool on the plot. A running table of removed points (including their flag assignments) is shown in the sidebar and is specific to the currently displayed parameter. Individual removal batches can be undone, or all parameters can be fully reset. Clicking Done / Close stops the app; choose Close, save edits to return the filtered data or Close, discard edits to return the original unmodified data.

Usage

editASRflag(cont, dqo, removed = NULL, ext = NULL)

Arguments

cont: contdat data frame returned by readASRcont, or the contdat element of a previous editASRflag result for iterative editing.
dqo: dqodat data frame returned by readASRdqo, or the dqodat element of a previous editASRflag result.
removed: Optional data frame: the removed element returned by a previous call to editASRflag. When supplied, previously removed observations are pre-populated in the app (shown in the removed-points table and excluded from the plot) and original values are restored before re-flagging so that QC checks are not affected by the gaps. Passing all three elements of a prior result enables fully iterative editing.
ext: Optional external data frame returned by readASRcont, with a DateTime column plus one or more parameter columns from a second file (e.g. a separate logger not otherwise included in cont). When supplied, each column is added as an additional entry in the Overlay drop-down (see Controls below) so it can be plotted alongside any parameter. Its DateTime column is aligned to cont's time zone and clipped to cont's date range. Entries are omitted entirely if the two do not overlap.

Value

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

contdat: A data frame with the same structure as the input contdat (sorted by DateTime), where values removed by the user are replaced with NA. Rows in which every parameter was removed are retained with only DateTime populated.
dqodat: A data frame with the same structure as the input dqo, reflecting any threshold edits made in the DQO Settings panel. If no edits were made the values are identical to the input.
removed: A data frame of all removed observations across all parameters, with columns Parameter, DateTime, Value, gross_flag, spike_flag, roc_flag, and flat_flag.

Details

QC flags are computed internally via utilASRflagall.

How to select points

Zooming and panning with the plot toolbar is recommended to more easily identify points for removal. These options are available in the menu on the top right when hovering over the plot.

Points can be selected for removal three ways. First, individual points can be removed by clicking. Second and third, use the box or lasso selection tool by hovering over the plot and selecting the desired tool from the menu on the top right. Click and drag over the desired area for the box selection or click and encircle the points with the lasso tool to add the points to the removal table. Double-click the plot background to remove the selected area if present after removal.

Controls

Parameter: drop-down selector to switch between parameters. Edits to each parameter are preserved independently when switching.
Overlay: optional drop-down to display a second parameter from contdat on a right-side y-axis, useful for spotting co-occurring changes across parameters. If an ext argument was supplied, one additional entry per column in that file is also available, labeled with an "[External File]" suffix.
USGS Overlay: enter a USGS site number and select a parameter type, then click Load to fetch continuous data from NWIS and display it on the secondary y-axis. Loading USGS data clears any Overlay selection and selecting an Overlay entry clears the USGS data. Site numbers can be found at the NWIS Mapper (https://apps.usgs.gov/nwismapper).
Linked Removal: optional checkbox. When checked (default), any timestamps removed from the current parameter are simultaneously removed from all other parameters. Undo restores the current parameter and all other parameters together as a single operation, regardless of which parameter is active when undo is clicked.
Undo Last Removal: restores the most recently removed point or batch of points. If the removal was linked, all affected parameters are restored together.
Start Over: undoes all removals and DQO edits made in the current session, reverting every parameter to the state it was in when the app opened. Any removals passed in via the removed argument are preserved.
Export Progress: saves the current cleaned data and DQO thresholds as Excel files 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 datasets for all parameters. 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 and ends the session, since a refresh disconnects the browser from the running app. If any points have been removed or DQO thresholds edited in the current session, closing or refreshing this way triggers the browser's own "leave site?" confirmation as a warning. Dismissing that warning by declining it keeps the session open. This warning does not appear when closing via Done / Close, since that choice is already explicit.

DQO Settings panel

A collapsible panel on the right side of the plot exposes the numeric QC thresholds for the currently selected parameter. Each of the four checks (gross range, spike, rate of change, flatline) shows independent Suspect and Fail threshold columns.

Apply: re-computes flags for the current parameter using the edited thresholds. Previously removed points are retained.
Reset to original: reverts the inputs to the values supplied in dqo and re-computes flags. Any points already removed are retained.

Threshold edits are per-parameter and independent; switching parameters shows that parameter's current thresholds without affecting others.

The app is constructed inline so that flag data are available directly to the server without file I/O. shiny::runApp() blocks until shiny::stopApp() is called, either by the Done button or by session$onSessionEnded() when the browser tab/window is closed or refreshed without using Done / Close; its return value becomes the function return value.

Examples

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

# First session
cleaned <- editASRflag(contdat, dqodat)

# Second session: picks up where the first left off
cleaned2 <- editASRflag(cleaned$contdat, cleaned$dqodat, cleaned$removed)

# Optional external overlay from a second file
extpth <- system.file("extdata/ExampleFlow1.xlsx", package = "AquaSensR")
extdat <- readASRcont(extpth)
cleaned3 <- editASRflag(contdat, dqodat, ext = extdat)
} # }