disagapp v0.0.1

Disagapp is an application written in R that can be used to perform disaggregation regression analyses using {disaggregation}. A version is deployed to https://disagapp.le.ac.uk/

Disagapp was built using the {shinyscholar} template which was itself forked from {wallace} v2.0.5 (CRAN, website)

Install disagapp via Github and run the application with the following R code.

install.packages("devtools")
devtools::install_github("simon-smart88/disagapp")
library(disagapp)
run_disagapp()

Components and modules

The application is divided in components that are steps in the analysis and modules that are possible options in each step of the analysis. Each of the modules calls a function of the same name, either in this package or in {disaggregation}.

Response - load the response data (resp)

• Combine spreadsheet and shapefile: upload both files and merge them
• Upload spreadsheet: upload the data and combine it with boundary data
• Upload shapefile: when the data is already merged in a shapefile
• Example datasets: load an example dataset
• Edit data: remove unwanted parts of the data
• Simplify polygons: simplify the geometries of the boundary data

Covariates - load covariates to use in the analysis (cov)

• Accessibility: The time required to travel to cities or healthcare. Provided by the Malaria Atlas Project via malariaAtlas
• Climate: Various bioclimatic variables relating to temperature and precipitation. Provided by Worldclim via {geodata}
• Land use: The percentage of land covered by different classes of land use. Provided by the Copernicus programme
• Nighttime lights: Satellite imagery of the intensity of nighttime lights. Provided by NASA via blackmarbler developed by the World Bank
• Distance to water: The distance to surface water. Provided by ESRI using data from USGS and ESA
• Population density: Population density provided by Worldpop
• Upload covariates: Upload your own covariates in the .tif format

Aggregation - load an aggregation raster (agg)

• Population count: Population counts provided by Worldpop
• Land use: The percentage of land covered by different classes of land use. Provided by the Copernicus programme
• Upload aggregation: Upload your own aggregation raster in the .tif format
• Uniform: Generate a uniform aggregation raster

Prepare - prepare the data for modelling (prep)

• Generate mesh: generate a spatial mesh from the response data
• Summarise and resample covariates: resample covariates so that they have the same resolution and extent
• Scale covariates: scales the covariates so that their coefficients can be compared fairly
• Covariate correlations: examine correlations between covariates
• Reduce covariate resolution: generate lower resolution covariates to speed up model fitting
• Finalise data preparation: combine all the data together

Fit - fit a disaggregation model (fit)

• Fit model: using either gaussian, binomial or poisson likelihood functions and logit, log or identity link functions

Predict - make predictions (pred)

• Make predictions: generate predictions from the model
• Transfer predictions: transfer predictions to a new area of interest

Reproduce - reproduce the analysis (rep)

• Download session code: download a .Rmd file that completely replicates the analysis
• Reproduce environment: use renv to capture dependencies, allowing the analysis to be reproduced exactly
• Download covariates: download copies of the covariate data
• Download package references: download a list of all the packages used in the analysis

Adding new modules

• This guide details how to develop a module from scratch, but depending on what the new module does, it may be easier to copy an existing module instead and use this as a guide to refactoring it.
• Install shinyscholar with devtools::install_github("simon-smart88/shinyscholar")
• Clone the repository using git clone https://github.com/simon-smart88/disagapp

Create module files

• Determine which component the module will be added to - the shorthand in the section titles above forms the first part of the module’s identifier.
• Use shinyscholar::create_module() to create the module files:
  • id is the module identifier formed from the component identifier (listed above) and a single word identifier for the module. We will use fit_improved as the identifier in this example.
  • dir is the root directory of the application.
  • map should be set to TRUE if the results of the module need to be plotted on the map.
  • result should be set to TRUE if the module produces graphs to be presented in the Results tab.
  • rmd should be set to TRUE if the module should be included in the reproducible Rmarkdown.
  • save should be set to TRUE if the module has inputs that should be saved and loaded when the app is saved.
  • download should be set to TRUE if the module will produce an output that you want the user to be able to download.
  • async should be set to TRUE if the the module takes more than a few seconds to run so that it operates asynchronously.
  • init should be left set as FALSE.
  • e.g. assuming you are in the root directory run:

shinyscholar::create_module(
  id = "fit_improved", 
  dir = ".", 
  map = FALSE,
  result = TRUE,
  rmd = TRUE,
  save = TRUE,
  download = TRUE,
  async = TRUE)`

Developing the function

• Develop the new functionality outside of Shiny first e.g. in an Rmarkdown file using example data.
• Open fit_improved_f.R in the R/ directory and copy the code you have developed into the fit_improved function.
• If the function will run synchronously:
  • Add a logger parameter as the last parameter that is set to NULL by default.
• If the function will run asynchronously:
  • The function will only run asynchronously inside the app, not when used in the Rmarkdown, so the function needs to be flexible to both use cases.
  • Add an async parameter as the last parameter that is set to FALSE by default.
  • Any rasters used inside the function need to be wrapped before they are passed to the function, unwrapped inside it, wrapped if they are to be returned and then unwrapped inside the app. Use if (async) blocks to unwrap rasters using terra::unwrap() at the start of the function and wrap them at the end using terra::wrap()
  • If there are any messages that you want to pass to the logger when the function runs successfully, these should be stored in a list() along with the main output
• Add checks at the start of the function that check that inputs are in the correct format and pass the errors to writeLog or asyncLog depending on whether the function is synchronous or asynchronous respectively e.g.:

  if (!inherits(shape, "sf")){
    logger |> writeLog(type = "error", "shape must be an sf object")
    return()
  }
  
  if (!inherits(shape, "sf")){
    return(async |> asyncLog(type = "error", "shape must be an sf object"))
  }

• Document the function using roxygen2 tags - see other functions in the R/ directory for examples.
• Open the test-fit_improved.R file in the tests/testthat/ directory and add tests that check the error handling checks function correctly and that the function produces the desired results.
• You can find various example data objects in tests/testthat/helper_data.R that may help to test the function.
• Document the package using devtools::document() and then install with devtools::install()
• Open the test file and click the “Run Tests” in the top right of the window pane.
• Once the tests are all passing you can begin to develop the Shiny module.

Shiny module

• The shiny module consists of four files in the inst/shiny/modules/ directory named with the module identifier and ending in .yml, .R, .md and .Rmd

Configuration

• The .yml file is a configuration file and contains five lines:
  • component contains the component the module belongs to e.g. "fit"
  • short_name contains a short name for the module and is used in the user interface so should be formatted accordingly e.g. "Fit improved model”
  • long_name contains a longer name for the module and is also used in the user interface e.g. "Fit an improved model using the new method"
  • authors contains your name: e.g. "Simon E H Smart"
  • package contains a list of packages used in the module inside square brackets and without quotes e.g. [terra, disaggregation]
  • Add an extra line at the end of the file called class: and then add mandatory, choice or optional after it (without quotes) depending on whether it is mandatory to use the module, it is one of several of choices but one must be used or it is optional. Depending on the function of the module, you may need to update the .yml of other modules in the component, for example currently the fit_fit module is mandatory but if we were to add a new module to the component that could be changed to choice.

UI and server

• Data is passed between modules and loaded after being saved through the common object, defined in the common.R file in the inst/shiny/ directory. If the module uses data created by previous modules you need to find the name of these objects in that file, for example the response data is stored in common$shape and the unprepared covariates in common$covs. If the module produces a new type of object then you need to add a new object to the common data structure by editing the common.R file. This is not necessary if, for example the module adds a new method for uploading response data or another covariate as these would add their results to common$shape and common$covs respectively.
• The .R file is the main module file and contains several sections:
  • The <identifier>_module_ui function contains the *Input elements which should correspond with the parameters of the function. See https://shiny.posit.co/r/components/ for available input widgets you can use. The input ids need wrapping inside ns() to create ids that are unique to the module. The template contains an actionButton() which when clicked runs the code inside the *_module_server function.
  • The <identifier>_module_server function contains an observeEvent() which is run when the actionButton() in the UI is clicked.
  • The structure of the code inside the module server differs depending on whether the module runs synchronously or asynchronously. For synchronous modules:
    • In the warning block, examine inputs to check that they are as expected and issue warnings if not using common$logger |> writeLog(). These checks are distinct from those inside the function as they are checking that the state of the app is correct - for example if the module requires the data to have been prepared, you should check that common$prep is not NULL. See the documentation of shinyscholar::writeLog() for more details.
    • In the function call block, pass the inputs to the module function.
    • In the load into common block, store the result(s) of the function call in the relevant common object.
    • The metadata block can be left blank for now.
    • In the trigger block, trigger() is called which can be used to trigger actions elsewhere in the module or app using watch(). This should not need editing.
    • In the result block, use the relevant common objects to produce outputs like plots using render* objects which will be passed to the _module_result function. Inside each render* function you should add a req() containing the common object created by the module to stop it executing before the object exists and a watch() to trigger the execution once the object is created.
    • The return block, block can be left blank for now.
  • For asynchronous modules, the principles are the same but the button only triggers the function to start and a separate results section waits for the results and processes them. Much of the setup is handled automatically in the template module.
    • Add checks in the warning block as before
    • Rather than passing the inputs to the function directly, pass them instead to for example common$tasks$fit_improved$invoke()
    • Wrap any SpatRaster objects are present in the function inputs using terra::wrap()
    • Inside the results section, you should check the class of the object returned by the function and only load the result into common if it is the correct type. If an error is returned it will be sent to the logger.
    • Unwrap any SpatRaster objects in the returned object using terra::unwrap()
  • The <identifier>_module_result function contains the *Output() functions that render the results created in the result block of the module server. As in the *_module_ui function, the object ids need wrapping inside ns().
  • The <identifier>_module_map function updates the leaflet map. map is a leafletProxy() object created in the main server function so leaflet functions can be piped to it e.g. map |> addRasterImage(). There are several functions in the package that facilitate adding objects to the map e.g. raster_map() and shape_map() which you can either use directly or modify to suit your needs. If you are unfamiliar with leaflet, it is probably sensible to develop this function outside of Shiny.
  • The *_module_rmd function can be left blank for now.

Guidance

• The .md file contains the module guidance.
• The background section should explain what the module does and what the scientific basis for it is.
• The implementation section should explain how the module works (e.g. which functions it uses) and how the user can use it i.e. what do they need to click.
• Add any relevant references in the references section.

Reproducibility

• The .Rmd file contains the Rmarkdown required to reproduce the module. Leave this blank for now.

Changes to other files

• If you have added a resp, cov or agg module, some other modules need updating to listen for changes made by the module by adding e.g. watch("fit_improved"). Modules to update are as follows:
  • For resp modules update resp_simplify.R, prep_mesh.R and prep_final.R. You should also add watch("resp_edit") to your own module underneath the existing watch() line.
  • For cov modules update prep_summary.R and rep_covs.R.
  • For agg modules update prep_summary.R and rep_covs.R.
• Open the global.R file in the inst/shiny/ directory and navigate to the line that creates base_module_configs. Add a new line to the object in the relevant position to load the new module. The order of modules is important as this object defines the order of chunks in the Rmarkdown and so modules must be placed after any modules that they use the results of. For example if our fit_improved module used the results of the fit_fit module, it needs to be placed after it in the list.
• If your module created new objects in common that contain a SpatRaster, the core_save.R and core_load.R files need to be edited to wrap and unwrap them. Use wrap_terra() and unwrap_terra() for this as they can handle cases where the objects are NULL e.g. when your module has not been used. Objects need wrapping before saving, unwrapping after saving and unwrapping after loading. There are many other lines already doing this for other objects.

Manual checks

• Now you can run the app and check your module works. It may be helpful to create a save file of the app at a stage immediately prior to running your module so that you can reload it quickly if the app crashes. If you create a variable called load_file_path that contains the path to the load file, it will be loaded automatically when the app starts.

Reproducibility

• Once the module is running correctly run shinyscholar::save_and_load(".", "fit_improved") to add lines of code to the module that save and load the inputs and then shinyscholar::metadata(".", "fit_improved") to add lines to the metadata block in the module server, the module_rmd function and to the .Rmd file.
• Edit the .Rmd to use the input variables to call the module function. The variables are added automatically by shinyscholar::metadata() and take the form of e.g. {{fit_improved_input1}}. The curly brackets are required for the input values to be transferred when the user reproduces their analysis. The common objects have corresponding variables inside the .Rmd files of the modules and these need to used so that the chunk of the new module can be linked to previous chunks. For example common$prep containing the prepared data is replaced by prepared_data in the .Rmd files.

End-to-end tests

• Create an end-to-end test using shinytest2. You are probably best of using an existing test as a template.
• They consist of two files - a helper file e.g. helper-fit_improved.R which runs the app and saves it after running the module and the module test file which you created earlier to test the module’s function. This architecture is necessary because saving the app in tests fails erratically and this setup allows the test to be rerun until it saves successfully.
• In the helper-fit_improved.R you start the app, set any necessary input values and then run the module. Add a section to test-fit_improved.R that calls then function defined in the helper function using e.g. rerun_test_setup("fit_improved_test") and which then reads the saved file and checks that the common object modified or created in the module is in the correct state. Note that if the module runs asynchronously you need to wait for it to complete by adding app$wait_for_value(input = "fit_improved-complete") before saving the app.
• Run all the tests using devtools::test().

Finally

• Commit your changes, push to Github and create a pull request to add the module.

Updating deployments

To update deployments running on shinyserver it is necessary to update the package and also copy the contents of /inst into the /apps directory.

Install the updated version package

R -e "remotes::install_github('simon-smart88/disagapp')"

Update the app directory

Because the repository contains the package files as well as the app, we need to update the local copy of the package and then update the app files.

cd /local/disagapp
git pull
cp -rf inst/shiny/. /local/shiny/apps/disagapp

Restart shinyserver

sudo systemctl restart shiny-server