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minibuoy-app's Introduction

The Mini Buoy App

The Mini Buoy measures hydrodynamics at the coast. Analysis of Mini Buoy data can be done within this App for a single deployment, or for comparing reference (e.g., established vegetation) vs target (e.g. planned restoration site) locations. There are three Mini Buoy designs to choose from; the B4, B4+ and Pendant.

Mini Buoys will calculate inundation duration, current velocity, and wave orbital velocity (B4+ only) along shallow intertidal areas. Hydrodynamics are calculated from acceleration (tilt) data, gathered by acceleration loggers housed inside bottom mounted floats.

Guidance on how to assemble, deploy, and analyse Mini Buoy data is available in the handbook here.

minibuoy-app's People

Contributors

mcwimm avatar ale0430 avatar cailadd90 avatar

Watchers

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minibuoy-app's Issues

unify.datetime() changed

unify.datetime has been changed in Aleschanges branch to a mutate(...) variation also using lubridate parse, including the two most common datetime formas of MSR and hobo files (mdy_HMS, ymd_HMS), though more formats could be added if needed.

unify.datetime() is a function to standardise 12 hr clock to 24 hr clock. as originally written, on R version 4.3.2 the function removes entirely the datetime column for MSR files, causing the app to fail.

ACTIONS: I'm now running only R v4.2.3, can someone call my branch and run the app using R v4.3.2 to assess the app performance with the changes on datetime?

Settings

I can't reproduce the problem mentioned in issue #12

image

H (Marie) - Loading icon over the “Download data” and “Download figure” buttons (or transparent white overlay on the plot) once clicked, so the user is aware data is downloading (or similar function for when “Apply filter” is clicked)

"Loading icon over the “Download data” and “Download figure” buttons (or transparent white overlay on the plot)": No good idea how to do this. We can show a notification (lower, right corner). See PR #48

Apply filter shows a spinner... but that one is connected to generating text output...
Also all spinners for figures are switched off by Plotly...

Global functions

Assign functions that are defined in server.r but used in any fun_...r script globally (<<-)

About page -> Open Handbook not working

The "open handbook" opens a blank RStudio blank graphics window instead of the Manual's link. Trying to solve this but noticed window.open() is a java based function (might my java not be working?) - updated java -> still did not work
I tried installing shinyjs-> did not work
tried changing code in the 'fun_ui_about.R' file to 'onclick="location.href='https://cailadd90.github.io/MiniBuoyHandbook/'" this opens the handbook on a new chrome window tab.

Action required -> change code in the master branch of the app (i did not implement this on an own branch yet)

What needs to be done

SETTINGS

UPLOAD - PR #46

  • H (Cai) - Add additional if statement to read separate date and time columns in B4
  • H (Cai) - Update the B4 classifier using LDA not QDA (improved results) and maybe higher-resolution Pendant classifier (test first)

FILTER

HYDRODYNAMICS

Later

  • All – Check if there’s a way to define whether differences in inundation duration and frequency are meaningfully
  • Cai - Check whether timezone corrections are needed
  • Cai - Add error terms in the results downloads

Done

  • H (Marie) - “Filename” option for assigning prefix to downloaded files isn’t working. “Example” is always given instead. See line 318 in fun.data.R
  • H (Marie) - The App crashes if “Use data” is clicked when there’s a mismatch between Mini Buoy data uploaded and the model selected (e.g. upload a Pendant dataset, but choose 'B4+' from the drop-down menu, and click the 'Use data' button). This should trigger a message like "Unable to read data. Does the Mini Buoy match the uploaded data?"
  • H (Marie) - Need to click upload twice for Target and Reference to be recognised in the top menu (even though the App still works)
  • #47
  • M (Marie) - Multiple messages appear when figures are downloaded. Maybe the same message code that only produces 1 message for ‘Download results’ in the Reference tab can be used as a template? - PR #49
  • Cai/Marie – Try making the App standalone
  • Marie - if one tries to upload a second dataset, the target/reference/comparison are locked on the first dataset. - PR #40
  • Marie - the date format in exported data is odd (e.g. 2022-01-31T00:01:00Z). Can T and Z be removed? - PR #36
  • Marie - Archive the summary text for the comparison page so that, for this version of the App, only the table is shown
  • Marie – Migrate Mini Buoy App Handbook to Ale’s repository
  • #53
  • Marie - Add a licence for the App within the repo
  • Marie - Option to overwrite downloaded data to the working directory (each new download gets a long identifier that gets confusing) - PR #38
  • Marie - When selecting 'Download results', can we have only 1 'File saved successfully!' message appear? - PR #39
  • Marie - Can the loading symbol in the 'Summary' be centred, to align with that in the 'Table' window?
  • Cai - Modify error bars in currents and wave plots to show 95% ranges
  • Cai - Find out why daily inundation doesn’t add up to the same as summary and event tables
  • Cai - Create example datasets that test the App
  • Cai - Update the Mini Buoy App Handbook (inc. adding a Troubleshooting chapter)
  • Cai - Use 95 upper and lower percentiles instead of peak (max/min) values for currents and waves
  • Cai - Check that all the short titles are appropriate
  • Cai - Check if pop-ups are needed anywhere to clarify inputs
  • Cai - Rename Velocity stage plot, and rename its x-axis to hours to high tide
  • Cai – Update default values used in analysing the data
  • Marie - Reference table appears to be missing the option to scroll the table to rows 11-18 (this is working for Target)
  • Marie – Check whether we include analyses done under the ‘Target’ and ‘Reference’ tabs automatically in ‘Comparison’ if ‘Target’ and ‘Reference’ are selected by the user before Comparison. This would save CPU
  • Marie - Hydro/Target/Ref/Results: show spinner when reloading results with overlapping time window
  • Marie - in custom settings, add limits to the possible values that can be entered into minimum tilt = 0 - 90
  • Cai/Marie - add legend to target/reference raw data plot + different colors? more constrast, different shapes? larger points
    • Inundation status: Blue = not inundated, Green = partially inundated, Navy = fully inundated
  • Marie - populate tables in the App's front-end with calculations from the 'get.summary.statistics(), which has superseded 'get.statistics()'
  • Cai - combine summary, daily, event, and tidal results into one excel file to export
  • Cai - update get.stats() so outlier detection is working and switch to only using U-tests
  • Cai/Marie - how to use ggplotly in shiny
  • Marie - integrate the velocity stage and violin plots
  • Cai - add x-axis annotations to differentiate flood and ebb tide on the stage velocity plot
  • Marie - Layout changes
  • Cai - "# add a message like: in theory any "no" means the site is unsuitable. Steps can be taken to modify the enviornment, e.g. see restoration manuals." what does this mean? (old comment in fun_hydrology.R)
  • Cai - check which packages are really required + add short description

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