Interactive Shiny app to tie a proxy record to an astronomical solution (tune live while tying)

A browser-based version of astro_anchor_interactive. One window shows three linked rows: the proxy record, the astronomical solution and, underneath, the record tuned to the current tie points together with a cycle extracted from it (and optionally the astronomical solution and the sedimentation rate). The tuned row is updated while tie points are made, moved or removed, so the effect of every change on the fit can be judged on the go. Tie points are numbered and colour coded in all rows and joined by lines between the two records.

Usage

astro_anchor_app(
  astro_solution = NULL,
  proxy_signal = NULL,
  proxy_min_or_max = "max",
  astrosolution_min_or_max = "max",
  pts = 3,
  ties = NULL,
  time_dir = TRUE,
  peaks_in_view = 12,
  tie_on = c("raw", "cycle"),
  proxy_flow = NULL,
  proxy_fhigh = NULL,
  proxy_roll = 3,
  inspect_flow = NULL,
  inspect_fhigh = NULL,
  inspect_roll = 3,
  sedrate_factor = 1,
  launch_browser = TRUE
)

Arguments

astro_solution: Astronomical solution to tie to (matrix or data frame with two columns: time/age (e.g. kyr) in column 1, value in column 2), or a named list of such solutions to choose from in the app (the first one is shown at the start). In the app the target can also be switched to a metronome (a cosine with a period, phase and time interval you set), or to a Laskar solution (eccentricity, obliquity, climatic precession or ETP of La2004, La2010a-d, La2011 eccentricity, or 65 N insolation) that is downloaded on request with getLaskar when you press the download button. Required, no default (Default=NULL gives an error).
proxy_signal: Proxy record to be tied (matrix or data frame with two columns: depth/time in column 1, proxy value in column 2; rows with NA are removed). Required, no default (Default=NULL gives an error).
proxy_min_or_max: Peaks offered when snapping on the proxy record (character): "max" (maxima) or "min" (minima). Default="max".
astrosolution_min_or_max: Peaks on which the tie points of the astronomical solution are placed (character): "max" (maxima) or "min" (minima). Default="max".
pts: Number of points to the left and right of a value that the peak detection (max_detect, min_detect) compares it with (integer, >= 1); larger values give fewer, more certain peaks. Default=3.
ties: Existing tie points to start from (data frame with the columns data_x (proxy depth/time) and insolation_x (astronomical age), otherwise the first two columns are used; e.g. the output of astro_anchor). The astronomical positions are moved to the nearest maximum/minimum, the proxy positions are used as given. NULL starts without tie points. Default=NULL.
time_dir: Direction of time in the proxy record (logical): TRUE if time increases with increasing depth/time values, FALSE if it decreases. Default=TRUE.
peaks_in_view: Approximate number of peaks shown in each window at the start (numeric, > 0). Default=12.
tie_on: Proxy record on which the tie points are placed at the start (character): "raw" (the raw record) or "cycle" (a cycle extracted from it with the Taner filter set by proxy_flow, proxy_fhigh and proxy_roll). Can be changed in the app. Default=c("raw", "cycle"), i.e. "raw".
proxy_flow, proxy_fhigh: Low and high cut-off frequencies of the Taner filter that extracts the proxy cycle, in cycles per depth/time unit of the proxy record (numeric, 0 < proxy_flow < proxy_fhigh; give both). NULL uses the strongest period of the wavelet spectrum of the proxy -/+ 25 percent. They can be changed in the app. Default=NULL.
proxy_roll: Roll-off of the proxy Taner filter as the exponent x of roll = 10^x (numeric; see taner). Default=3.
inspect_flow, inspect_fhigh: Low and high cut-off frequencies of the Taner filter that extracts the cycle from the tuned record, in cycles per time unit of the astronomical solution (numeric, 0 < inspect_flow < inspect_fhigh; give both). NULL uses the median spacing of the peaks of the astronomical solution -/+ 25 percent. Default=NULL.
inspect_roll: Roll-off of the Taner filter of the tuned record as the exponent x of roll = 10^x (numeric). Default=3.
sedrate_factor: Factor applied to the sedimentation rate (depth units per time unit) that is shown (numeric, > 0), for example 100 to go from m/kyr to cm/kyr. Default=1.
launch_browser: Open the app in the default web browser (logical, TRUE or FALSE); FALSE prints the local address (or uses the RStudio viewer when R is run there). Passed to shiny::runApp as launch.browser. Default=TRUE.

Value

A data frame with the tie points sorted by depth/time: data_x, data_y (proxy), insolation_x, insolation_y (astronomical solution). Without an interactive session and with ties the starting tie points are returned without starting the app (those on the astronomical solution moved to the nearest peak).

Details

What is tied. Tie points on the astronomical solution always sit on a maximum or minimum (see astrosolution_min_or_max). On the proxy side they can be placed on the raw record or on a cycle that is extracted from it with a Taner filter (taner; choose Cycle extracted from the proxy and give flow, fhigh and the exponent of the roll-off, roll = 10^x). The tuning is always applied to the raw record. Proxy tie points do not have to lie on a maximum or minimum: with Snap to peaks switched off they are placed exactly where you click, and every proxy tie point can be moved left and right with the buttons (fine and coarse steps), by typing its position, by typing its offset from the nearest maximum/minimum, or by dragging. The cycle shown in the tuned record is extracted with the same kind of Taner filter.

Tie a point: click one record (red) and then the other (in any order). Select a tie point by clicking it. Move it by clicking a free position of one of the records afterwards, by dragging over the record from the tie point to the new position, by the arrow buttons, or by editing the numbers. Untie it by double clicking it or with the Untie selected button. Tie points in the wrong order (the tuned time would run backwards) are marked with a black cross; the tuned row waits until they are fixed.

Target and windows. The card Astronomical solution selects the target (a provided solution, a metronome, or a Laskar solution), the time interval it spans and whether maxima or minima are tied. Two sliders above the plot show the visible window (from, to) of the proxy record and of the astronomical solution; type new numbers to set them. With the mouse, the wheel zooms the record under the pointer around the pointer and Shift + drag (or dragging with the right or middle mouse button) moves it from left to right. Sync brings the astronomical window to the partners of the tie points in the proxy window, Show both records in full resets both.

The sidebar also has buttons to undo changes and to finish (Done). Closing the browser tab also finishes and returns the tie points.

The app runs on the local computer only (a Shiny app started with runApp); nothing is sent to other servers. The package shiny has to be installed.

The result has the same four columns as the output of astro_anchor and can be used by plot_astro_anchor and anchor2time. data_y and insolation_y are the values of the records at the tie positions.

Examples

# \donttest{
# Without an interactive session (as here) the starting tie points are returned as they are.
astrosignal <- na.omit(astrosignal_example)
tie_start <- data.frame(data_x = c(155, 160, 165), insolation_x = c(5040, 5400, 5560))
proxy <- grey[grey[, 1] < 175, ]
astro_anchor_app(astro_solution = astrosignal, proxy_signal = proxy, ties = tie_start)
#>   data_x   data_y insolation_x insolation_y
#> 1    155 373.5227         5036    1.0902778
#> 2    160 373.6639         5393    0.6553615
#> 3    165 392.9241         5550    2.1563294
# in an interactive session, leave out 'ties' to start the app and tie the records with the mouse
# }