Version:	0.4.2
Title:	A Template for Creating Reproducible 'shiny' Applications
Description:	Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE). A guide to developing applications can be found on the package website.
Depends:	R (≥ 4.1.0), bslib, gargoyle, leaflet (≥ 2.0.2), shiny (≥ 1.8.1)
Imports:	curl, devtools, glue, knitr, tools, zip
Suggests:	DT (≥ 0.5), dplyr (≥ 1.0.2), httr2, knitcitations, leaflet.extras (≥ 1.0.0), markdown, mirai, R6, RColorBrewer, renv, rintrojs, rmarkdown, shinyAce, shinyalert, shinybusy, shinyjs, shinytest2, shinyWidgets (≥ 0.6.0), terra, testthat, xml2, withr
SystemRequirements:	pandoc is required for generating reproducible reports
License:	GPL-3
URL:	https://simon-smart88.github.io/shinyscholar/
BugReports:	https://github.com/simon-smart88/shinyscholar/issues
Encoding:	UTF-8
RoxygenNote:	7.3.2
NeedsCompilation:	no
Packaged:	2025-06-01 18:51:05 UTC; simon
Author:	Simon E. H. Smart [aut, cre, cph], Tim Lucas [aut], Jamie M. Kass [ctb], Gonzalo E. Pinilla-Buitrago [ctb], Andrea Paz [ctb], Bethany A. Johnson [ctb], Valentina Grisales-Betancur [ctb], Dean Attali [ctb], Matthew E. Aiello-Lammens [ctb], Cory Merow [ctb], Mary E. Blair [ctb], Robert P. Anderson [ctb], Sarah I. Meenan [ctb], Olivier Broennimann [ctb], Peter J. Galante [ctb], Brian S. Maitner [ctb], Hannah L. Owens [ctb], Sara Varela [ctb], Bruno Vilela [ctb], Robert Muscarella [ctb]
Maintainer:	Simon E. H. Smart <simon.smart@cantab.net>
Repository:	CRAN
Date/Publication:	2025-06-01 23:20:06 UTC

shinyscholar: A modular platform for creating reproducible applications

Description

shinyscholar is a template for creating reproducible shiny applications to academic standards. shinyscholar is forked from 'wallace' and provides a template for producing applications that are interactive, reproducible, adaptable and built to high standards. It was created to ease the process of creating complex workflows in a single, streamlined GUI interface. In addition, executable session code (R Markdown format) can be downloaded to share with others or use as supplementary information for scientific papers and reports. An example application is run via the function run_shinyscholar and requires install.packages("shinyscholar", dependencies = TRUE).

asyncLog

Description

For internal use. Similar to writeLog but for use inside async functions

Usage

asyncLog(async, ..., type = "default")

Arguments

Value

No return value, called for side effects

Check whether suggested packages are installed

Description

Checks whether all the packages in Suggests are installed and stops execution if not or returns FALSE when example = TRUE

Usage

check_suggests(testing = FALSE, example = FALSE)

Arguments

Value

No return value, called for side effects unless example is TRUE in which case FALSE is returned if the Suggests are not installed or TRUE if they are installed.

Author(s)

Simon Smart simon.smart@cantab.net

check_url

Description

For internal use. Checks whether a URL is live

Usage

check_url(url)

Arguments

Value

An httr2 response if the URL is live

close_loading_modal

Description

For internal use. Close the modal once loading is complete

Usage

close_loading_modal(session = getDefaultReactiveDomain())

Arguments

Value

No return value, called for side effects

Create a shinyscholar module

Description

Create the template of a new shinyscholar module.

Usage

create_module(
  id,
  dir,
  map = FALSE,
  result = FALSE,
  rmd = FALSE,
  save = FALSE,
  download = FALSE,
  async = FALSE,
  init = FALSE
)

Arguments

Value

No return value, called for side effects

See Also

register_module

Create a skeleton application containing empty modules

Description

Creates a skeleton app containing empty modules with options controlling objects in common and whether to include a map, code and tables

Usage

create_template(
  path,
  name,
  common_objects,
  modules,
  author,
  include_map = TRUE,
  include_table = TRUE,
  include_code = TRUE,
  install = FALSE,
  logger = NULL
)

Arguments

Value

No return value, called for side effects

Author(s)

Simon E. H. Smart simon.smart@cantab.net

Examples

td <- tempfile()
dir.create(td, recursive = TRUE)

modules <- data.frame(
"component" = c("data", "data", "plot", "plot"),
"long_component" = c("Load data", "Load data", "Plot data", "Plot data"),
"module" = c("user", "database", "histogram", "scatter"),
"long_module" = c("Upload your own data", "Query a database to obtain data",
"Plot the data as a histogram", "Plot the data as a scatterplot"),
"map" = c(TRUE, TRUE, FALSE, FALSE),
"result" = c(FALSE, FALSE, TRUE, TRUE),
"rmd" = c(TRUE, TRUE, TRUE, TRUE),
"save" = c(TRUE, TRUE, TRUE, TRUE),
"download" = c(FALSE, FALSE, TRUE, TRUE),
"async" = c(TRUE, FALSE, FALSE, FALSE))

common_objects = c("raster", "histogram", "scatter")

create_template(path = td, name = "demo",
common_objects = common_objects, modules = modules,
author = "Simon E. H. Smart", include_map = TRUE, include_table = TRUE,
include_code = TRUE, install = FALSE)

Fetch a token from the NASA Earthdata API

Description

Uses the Earthdata API to fetch a token using the user's username and password

Usage

get_nasa_token(username, password)

Arguments

Value

A character string containing the token

Author(s)

Simon Smart simon.smart@cantab.net

Add metadata lines to modules

Description

Adds lines to modules and their associated rmarkdown files to semi-automate reproducibility. By default all the modules in the application are edited or you can specify a single module. If metadata lines are already present, the file will not be edited. This function is currently experimental and only semi-automates the process. To ensure that the code is functional complete the following steps:

• Check that any inputs created by packages other than 'shiny' are included

• Add any inputs created dynamically i.e. those without an explicit line of code to generate them, for example those created inside a loop in a renderUI or from a 'leaflet' or 'DT' object.

• Use the objects in each .Rmd file to call the module's function.

Usage

metadata(folder_path, module = NULL)

Arguments

Value

No return value, called for side effects

Author(s)

Simon E. H. Smart simon.smart@cantab.net

Examples

td <- tempfile()
dir.create(td, recursive = TRUE)

modules <- data.frame(
  "component" = c("demo"),
  "long_component" = c("demo"),
  "module" = c("demo"),
  "long_module" = c("demo"),
  "map" = c(FALSE),
  "result" = c(TRUE),
  "rmd" = c(TRUE),
  "save" = c(TRUE),
  "download" = c(TRUE),
  "async" = c(FALSE))

create_template(path = td, name = "demo",
                common_objects = c("demo"), modules = modules,
                author = "demo", include_map = FALSE,
                include_table = FALSE, include_code = FALSE, install = FALSE)

test_files <- list.files(
  system.file("extdata", package = "shinyscholar"),
  pattern = "test_test*", full.names = TRUE)

module_directory <- file.path(td, "demo", "inst", "shiny", "modules")
file.copy(test_files, module_directory, overwrite = TRUE)

metadata(file.path(td, "demo"), module = "test_test")

Extract values from a raster to produce a histogram

Description

Called by the plot_hist module in the example app and extracts values from a raster image, returning a histogram of density

Usage

plot_hist(raster, bins, palette, name, logger = NULL)

Arguments

Value

a function that generates a histogram

Author(s)

Simon Smart simon.smart@cantab.net

Examples

if (check_suggests(example = TRUE)) {
  raster <- terra::rast(ncol = 8, nrow = 8)
  raster[] <- sapply(1:terra::ncell(raster), function(x){
    rnorm(1, ifelse(x %% 8 != 0, x %% 8, 8), 3)})
  histogram <- plot_hist(raster, bins = 10, palette = "Greens", name = "Example")
  histogram()
} else {
  message('reinstall with install.packages("shinyscholar", dependencies = TRUE)
  to run this example')
}

Extract values from a raster to produce a scatterplot

Description

Called by the plot_scatter module in the example app and samples values from a raster along with either the x or y coordinates of the points sampled

Usage

plot_scatter(raster, sample, axis, name, logger = NULL)

Arguments

Value

a function that generates a scatterplot

Author(s)

Simon Smart simon.smart@cantab.net

Examples

if (check_suggests(example = TRUE)) {
  raster <- terra::rast(ncol = 8, nrow = 8)
  raster[] <- sapply(1:terra::ncell(raster), function(x){
     rnorm(1, ifelse(x %% 8 != 0, x %% 8, 8), 3)})
  scatterplot <- plot_scatter(raster, sample = 10, axis = "Longitude", name = "Example")
  scatterplot()
} else {
  message('reinstall with install.packages("shinyscholar", dependencies = TRUE)
  to run this example')
}

printVecAsis

Description

For internal use. Print objects as character string

Usage

printVecAsis(x)

Arguments

Value

A character string to reproduce the object

Register a shinyscholar module

Description

Currently disabled as cannot be used with apps created by shinyscholar. Before running the shinyscholar application with run_shinyscholar(), you can register your own modules to be used in shinyscholar.

Usage

register_module(config_file)

Arguments

Value

No return value, called for side effects

See Also

create_module

reset_data

Description

For internal use. Clears the common structure of data, resets the map and any plots

Usage

reset_data(common)

Arguments

Run shinyscholar Application

Description

This function runs the shinyscholar application in the user's default web browser.

Usage

run_shinyscholar(
  launch.browser = TRUE,
  port = getOption("shiny.port"),
  load_file = NULL
)

Arguments

Value

No return value, called for side effects

Author(s)

Jamie Kass jkass@gradcenter.cuny.edu

Gonzalo E. Pinilla-Buitrago gpinillabuitrago@gradcenter.cuny.edu

Simon E. H. Smart simon.smart@cantab.net

Examples

if(interactive()) {
run_shinyscholar()
}

Adds lines to modules to save and load input values.

Description

Converts 'shiny' ⁠*Input⁠ functions to lines of code required to store and reload the values when the app is saved or loaded. By default all the modules in the application are edited. Currently only input functions from 'shiny' and shinyWidgets::materialSwitch are supported.

Usage

save_and_load(folder_path, module = NULL)

Arguments

Value

No return value, called for side effects

Author(s)

Simon E. H. Smart simon.smart@cantab.net

Examples

td <- tempfile()
dir.create(td, recursive = TRUE)

modules <- data.frame(
  "component" = c("demo"),
  "long_component" = c("demo"),
  "module" = c("demo"),
  "long_module" = c("demo"),
  "map" = c(FALSE),
  "result" = c(TRUE),
  "rmd" = c(TRUE),
  "save" = c(TRUE),
  "download" = c(TRUE),
  "async" = c(FALSE))

create_template(path = td, name = "demo",
                common_objects = c("demo"), modules = modules,
                author = "demo", include_map = FALSE,
                include_table = FALSE, include_code = FALSE, install = FALSE)

test_files <- list.files(
  system.file("extdata", package = "shinyscholar"),
  pattern = "test_test*", full.names = TRUE)

module_directory <- file.path(td, "demo", "inst", "shiny", "modules")
file.copy(test_files, module_directory, overwrite = TRUE)

save_and_load(file.path(td, "demo"), module = "test_test")

Load FAPAR data from NASA asynchronously

Description

Called by the select_async module in the example app and loads an FAPAR raster for the selected area via the Earthdata API. This function is identical to select_query but can be run asynchronously

Usage

select_async(poly, date, token, async = FALSE)

Arguments

Value

A list containing:

Author(s)

Simon Smart simon.smart@cantab.net

Examples

## Not run: 
 if (check_suggests(example = TRUE)) {
   poly <- matrix(c(0.5, 0.5, 1, 1, 0.5, 52, 52.5, 52.5, 52, 52), ncol = 2)
   colnames(poly) <- c("longitude", "latitude")
   date <- "2023-06-20"
   token <- get_nasa_token(username = "<username>", password = "<password>")
   ras <- select_async(poly, date, token)
 } else {
   message('reinstall with install.packages("shinyscholar", dependencies = TRUE)
   to run this example')
 }
 
## End(Not run)

Load FAPAR data from NASA

Description

Called by the select_query module in the example app and loads an FAPAR raster for the selected area via the Earthdata API.

Usage

select_query(poly, date, token, logger = NULL)

Arguments

Value

a SpatRaster object

Author(s)

Simon Smart simon.smart@cantab.net

Examples

## Not run: 
 if (check_suggests(example = TRUE)) {
   poly <- matrix(c(0.5, 0.5, 1, 1, 0.5, 52, 52.5, 52.5, 52, 52), ncol = 2)
   colnames(poly) <- c("longitude", "latitude")
   date <- "2023-06-20"
   token <- get_nasa_token(username = "<username>", password = "<password>")
   ras <- select_query(poly, date, token)
 } else {
   message('reinstall with install.packages("shinyscholar", dependencies = TRUE)
   to run this example')
 }
 
## End(Not run)

Load a raster image

Description

Called by the select_user module in the example app and loads a .tif file as a SpatRaster

Usage

select_user(raster_path, logger = NULL)

Arguments

Value

a SpatRaster object

Author(s)

Simon Smart simon.smart@cantab.net

Examples

if (check_suggests(example = TRUE)) {
  raster_path <- list.files(system.file("extdata", "wc", package = "shinyscholar"),
  full.names = TRUE)
  raster <- select_user(raster_path)
} else {
  message('reinstall with install.packages("shinyscholar", dependencies = TRUE)
  to run this example')
}

show_loading_modal

Description

For internal use. Show a modal when something is loading

Usage

show_loading_modal(message)

Arguments

Value

No return value, called for side effects

show_map

Description

For internal use. Switches the view to the Map tab

Usage

show_map(parent_session)

Arguments

Value

No return value, called for side effects

show_results

Description

For internal use. Switches the view to the Results tab

Usage

show_results(parent_session)

Arguments

Value

No return value, called for side effects

show_table

Description

For internal use. Switches the view to the Table panel

Usage

show_table(parent_session)

Arguments

Value

No return value, called for side effects

Spurious package call to avoid note of functions outside R folder

Description

For internal use.

Usage

spurious(x)

Arguments

Value

No return value, called for side effects

tidy_purl

Description

Knits and purls an Rmd file into a format which can be written to an R file.

Usage

tidy_purl(params)

Arguments

Author(s)

Simon E. H. Smart simon.smart@cantab.net

writeLog

Description

For internal use. Add text to a logger

Usage

writeLog(logger, ..., type = "default")

Arguments

Value

No return value, called for side effects