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GroundWater Spatiotemporal Data Analysis Tool (GWSDAT) R-Shiny implementation.

Home Page: https://stats-glasgow.shinyapps.io/GWSDAT

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shiny contamination-detection groundwater-flow plume spatio-temporal-analysis

gwsdat's Introduction

GWSDAT

This is the R Shiny application of the GroundWater Spatiotemporal Data Analysis Tool (GWSDAT) for the analysis of groundwater monitoring data. This package can be run locally or can be deployed on a Shiny Server. For more background see http://www.gwsdat.net.

Install and Run

For latest development version, install from github using the devtools R package:

devtools::install_github("WayneGitShell/GWSDAT")
options(shiny.useragg = FALSE) #to avoid artefacts in spatial plots
GWSDAT::launchApp()

Or install from CRAN:

install.packages("GWSDAT")
options(shiny.useragg = FALSE) #to avoid artefacts in spatial plots
GWSDAT::launchApp()

A couple of example data sets are already pre-loaded. See full options for interactive data input in section 6.1 of the GWSDAT user manual: http://www.gwsdat.net/gwsdat_manual

Data input directly from R.

Install the package as above and pass a GWSDAT_Options list to launchApp(). The method GWSDAT::createOptions() creates this GWSDAT_Options list. The GWSDAT_Options list must either contain the WellData and WellCoords data.frames:

library(GWSDAT)
# Define GWSDAT_Options
opt <- createOptions("Site Name")
opt$WellData <- read.csv(system.file("extdata","ComprehensiveExample_WellData.csv",package="GWSDAT"))
opt$WellCoords <- read.csv(system.file("extdata","ComprehensiveExample_WellCoords.csv",package="GWSDAT"))
launchApp(opt)

or the location of input csv files WellDataFilename and WellCoordsFilename.

library("GWSDAT")
# Define GWSDAT_Options
GWSDAT_Options <- createOptions("Example Site")
GWSDAT_Options$WellDataFilename <- system.file("extdata","BasicExample_WellData.csv",package="GWSDAT")
GWSDAT_Options$WellCoordsFilename <- system.file("extdata","BasicExample_WellCoords.csv",package="GWSDAT")
launchApp(GWSDAT_Options)

Save & Load Session File

Inside the Shiny app, a data analysis session can be saved inside the Analysis panel, in the top navigation bar under More -> Save Session. This creates a .rds file that can be loaded with the launchApp() method:

GWSDAT::launchApp(session_file = "path_to_file.rds")

Deploy on Posit Connect

Create the file app.R with the following content and publish to Posit Connect server in the usual manner:

library("GWSDAT")
launchApp()

Beta: Deploy as API on Posit Connect

Create the file app.R with the following content and publish to Posit Connect server in the usual manner:

library("GWSDAT")
launchApp(createOptions())

GWSDAT input arguments can be included in the URL. This example here passes the location of the csv well and well coordinates data. This example here passes the location of an Excel GWSDAT Input data file. This functionality is still in development.

gwsdat's People

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mrecos rainbow729 drroad kadambala sumank792 turbaevsky iafm4jesus

gwsdat's Issues

"Show GW contour" and GW flow arrows not displayed in contour plot.

Disappeared after adding aggregate function.

Show GW Contour lines do not show up when option actived in contour plot.

Make simple httpuv script. Attempt to attach Shiny.

Change of 'Time Step' slider should change time interval displayed in ImagePlot (contour) and Traffic Light table.

Add 'Display Table' control into 'Smooth Time-Series' tabPanel.

This control allows to enable "Threshold" display.

It will be also added to the 'Traffic Light' tabPanel.

Playback of Contour Plot faulty, jumps back and forth after slider is moved.

And the playback never stops.. maybe something with the time_step variable.

Pass error back from init script, instead of tcltk popup error message.

This involves all calls to tkmessageBox() inside GWSDAT_Run_shiny.R.

PlumeUnitHandlingFunc() not found when enabling 'PlumeDiagnostic' in Plot options.

Active tab: Contour Plot

Plot_ImagePlot(): panel$tempTotalPlumeDetails saved but panel not passed back.

panel is updated inside plotting function, but currently Plot_ImagePlot() does not return the panel (unlike in GWSDAT MakePanel.R).

When I needed, update it. Better would be to recalculate panel$tempTotalPlumeDetails outside the plot function.

Accumulate GWSDAT_Warning() objects in a list.

So several warning messages returned from a function can be displayed/evaluated.

Import basic sample data into shiny script.

Do it manually to have the data available.

TRY OUT: Install R-Server on Linux and run Shiny on it.

See instruction here: https://www.rstudio.com/products/shiny/download-server

Note: the free version says it has no (1) user authentification and (2) no multi-processor support.

Is it still do-able with ptly and sqlite (see the User Authentificatin card) [How to link to another issue btw.?)
Serious issue considering that many users will access the service? Needs to be tested. Maybe there are other (free) server options.

Add 'Traffic Light' Plot in 3rd tabPanel.

Show 'Color Key' image. See Button 'Color Key' in tcltk.

Show Pop-up image.

Execute TclTK windows stuff when GWSDAT is run stand-alone.

This will show the usual progress windows, main window, etc..

If GWSDAT runs with Shiny, we don't want these windows to be created. Instead, all tk*() status messages are passed back to the Shiny server.

Insert 'Edit Thresholds' Button like control.

This affects Time-Series plot and Traffic Light table.

In tcltk it is done in a separate table, for each solute.

Add controls to sidebar, same as in the tcltk panel.

Click on Smooth Time-Series Plot opens image (png) window with Save button.

Add list with available data sets on Analyse page in Server Mode.

Get rid of TclTK panel (rp.control) for Shiny, but not Stand-Alone.

The function rp.control() creates the panel variable and a TK window. This is the basic call to create the TclTK window panel:

panel = rp.control(title = "", size = c(100, 100), panelname, background, ...)

Right now all the drawing related variables (DRV) are passed directly to this function (in the "..." part).
For Shiny I would not need rp.control. Instead only an object that holds all DRV, e.g.

DRV$Cont.Data
DRV$Well
etc.

To make it combatible with Stand-Alone I could pass this 'DRV' object to rp.control():

# Stand-Alone (TclTK)
panel = rp.control(title = "", size = c(100, 100), panelname, background, DRV)
# panel$DRV to access drawing stuff

and with Shiny I could just assign it directly to panel.

# Shiny
panel = 0
panel$DRV = DRV

Insert "Import Data" Option, upload .csv via browser select window.

Display Smooth Time Series plot in shiny UI.

TRY OUT: User authentification with dply and SQLite inside Shiny.

Check out this: http://shiny.rstudio.com/gallery/authentication-and-database.html

No need for httpuv?

Insert data info and link to data on top of Analysis tab.

Update smooth time-series plot as soon as any control changes value.

Display output from plot.GWSDAT.Data() inside Shiny UI, instead of TK Window.

GWSDAT_Init(): Set values of 'dlines' and 'ScaleCols' (both checkbox ctrls) based on Default.Values if present.

Pushing playback jumps 1 -> 2 -> 1 -> .. indefinitely after changing aggregation data.

Some data has not been set accordingly after the aggregation function has been called.

Make high-definition plots (see tk start option).

How to simulate 'Subset Plot' Button for Traffic Light table?

Requires a subset selection of

solutes
wells
Redraws traffic light table.

Load "Basic Example" data, if this is good, load "Extended Example".

TRY OUT: shinydashboard for clean UI.

test backlog card

Threshold does not adapt to different concentration units.

As default threshold = 500 (mg/l). But when the unit is changed to ng/l or mg/l, the threshold value is not adapted but stays at '500'.

Add Readme.md with basic information on running the App.

Loading Comprehensive Example generates error in Contour plot.

Not all wells are shown.

GWSDATpnl object contain data, model, and draw (panel) related stuff. Need to untangle?

I need to separate data&model stuff from the drawing related stuff.

Right now rpanel calls use the rp.control() object GWSDATpnl that also includes data and model. But for shiny I would only need the model and data but not the drawing related stuff, since this is done differently in shiny. But confirm this, before doing any hard splits.