global.R, server.R, and ui.R need to be refactored for correctness and readability

[bryce-carson]

The server and UI code is chaotic and not written in a clear style using the syntax of R to its fullest. The server and UI code needs to be refactored so that it is more maintainable after I leave the project.

spatialEpisim/server.R

Lines 846 to 865 in df70041

	if(input$modelSelect == "SEIRD"){
	if (input$selectedCountry == "Czech Republic"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "CZE" & model == "SEIRD")[1,"lambda"])
	} else if (input$selectedCountry == "Nigeria"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "NGA" & model == "SEIRD")[1,"lambda"])}
	else if (input$selectedCountry == "Uganda"){
	lambdaValue <- 5}
	else if (input$selectedCountry == "Democratic Republic of Congo"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "COD" & model == "SEIRD")[1,"lambda"])}
	} else if (input$modelSelect == "SVEIRD"){
	if (input$selectedCountry == "Czech Republic"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "CZE" & model == "SVEIRD")[1,"lambda"])
	} else if (input$selectedCountry == "Nigeria"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "NGA" & model == "SVEIRD")[1,"lambda"])
	}
	else if (input$selectedCountry == "Uganda"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "COD" & model == "SVEIRD")[1,"lambda"])}
	else if (input$selectedCountry == "Democratic Republic of Congo"){
	lambdaValue <- as.numeric(filter(epiparms, ISONumeric == "COD" & model == "SVEIRD")[1,"lambda"])}
	}

If the names of the countries are added as a new column to the epiparms data file, these lines can be simplified to the following pipeline.

lambdaValue <-
filter(epiparms, model == input$modelSelect, country == input$selectedCountry)[1, "lambda"] |>
as.numeric()

[bryce-carson]

This is just an example of what can be improved in server.

[bryce-carson]

This is just an example of what can be improved in server.

To justify this issue being an example I am labelling it duplicate of the less specific #32 which represents the needed work to refactor the entire application architecture and implementation.

[bryce-carson]

I removed the duplicate label and renamed the issue to make it clearer that this issue was originally opened to track the refactoring of the server and UI code. At the time I opened this issue I was unaware that the contents of the R/ sub-folder would need to be refactored as well, so this issue tracks a separate but linked refactoring.

The server code will take advantage of the functionality provided by the functions defined in one or more files in the R/ sub-folder, so this issue is related to the refactoring occurring in #32 in that way and they will be closed at the same time when the unstable branch is merged in to main.

[bryce-carson]

As of today

Before

[bryce@fedora]~/Documents/src/r/spatialEpisim% scc --no-cocomo ~/src/r/spatialEpisim.stable/server.R 
───────────────────────────────────────────────────────────────────────────────
Language                 Files     Lines   Blanks  Comments     Code Complexity
───────────────────────────────────────────────────────────────────────────────
R                            1       792      129        53      610         84
───────────────────────────────────────────────────────────────────────────────
Total                        1       792      129        53      610         84
───────────────────────────────────────────────────────────────────────────────
Processed 28001 bytes, 0.028 megabytes (SI)
───────────────────────────────────────────────────────────────────────────────

After

[bryce@fedora]~/Documents/src/r/spatialEpisim% scc --no-cocomo server.R                             
───────────────────────────────────────────────────────────────────────────────
Language                 Files     Lines   Blanks  Comments     Code Complexity
───────────────────────────────────────────────────────────────────────────────
R                            1       614       86        81      447         50
───────────────────────────────────────────────────────────────────────────────
Total                        1       614       86        81      447         50
───────────────────────────────────────────────────────────────────────────────
Processed 23659 bytes, 0.024 megabytes (SI)
───────────────────────────────────────────────────────────────────────────────

[bryce-carson]

Global

Global needed to be cleaned up, so that the libraries that were loaded were only those that are actually used in the application and all of its dependencies. Files below the R/ folder, of course, should not be responsible for loading their own dependencies; it is difficult to track and maintain the files when that is done. It makes it difficult to study too.

The meat and potatoes of the application---its foundational SVEIRD simulation feature---is now documented and refactored in the package spatialEpisim.foundation. This will be hosted in a drat repository, and can then be installed quite easily by users (similarly to install_github from the devtools package).

Excerpt

spatialEpisim/global.R

Lines 1 to 42 in f5a7913

	options(conflicts.policy = list(warn = FALSE),
	scipen = 999)
	## FIXME: I have a strong feeling not all of these libraries are actually used
	## in spatialEpisim. TODO: remove all packages which are dependencies of
	## spatialEpisim.foundation; there's no need to load them twice.
	suppressPackageStartupMessages({
	library(av)
	library(bslib)
	library(cptcity)
	library(countrycode)
	library(deSolve) # ::solve?
	library(DT)
	library(leaflet)
	library(maps)
	library(plotly)
	library(readxl)
	library(writexl)
	library(terra)
	library(shiny)
	library(shinyalert)
	library(shinybusy)
	library(shinyhelper)
	library(shinyjs)
	library(shinyvalidate)
	library(shinyWidgets)
	library(tidyverse)
	library(here)
	})
	## TODO: include instructions in the README on installing the following package;
	## it's quite easy. DONT suppress messages from our own backend dependency.
	library(spatialEpisim.foundation)
	library(reactChartEditor)
	here::i_am("global.R")

[bryce-carson]

UI

The user interface, of course, was messy and has been rewritten. Things which were in server.R and didn't need to be, either because they could be refactored to not need to be, or just didn't belong there at all in any case, were moved to UI were they belonged.

[bryce-carson]

Server

See the previous comment.

Code which was written by chat bots, or which didn't perform the documented action have been rewritten for clarity and maintainability.