Package {StabilityApp}

Type:	Package
Title:	Interactive Stability Analysis of Multi-Environment Trials
Version:	1.0.0
Date:	2026-11-03
Description:	A 'shiny' application for the stability analysis of multi-environment trials of plant breeding with the package 'stability': analyses of variance, Eberhart and Russell's and Finlay and Wilkinson's regression, Wricke's, Shukla's, Kang's and Fox's statistics, Eskridge's safety-first indices, Annicchiarico's, Lin and Binns' and Huehn's statistics, AMMI analysis and stability values, and the GGE biplot. Every analysis comes with its tables, plots, the R code that repeats it and an interpretation specific to the method, computed from the results; an optional longer written interpretation can be requested from an external text service with the user's own key.
License:	GPL-3
URL:	https://myaseen208.com/StabilityApp/, https://github.com/myaseen208/StabilityApp
BugReports:	https://github.com/myaseen208/StabilityApp/issues
Encoding:	UTF-8
Language:	en-US
Depends:	R (≥ 4.2)
Imports:	bslib, commonmark, data.table, DT, ggplot2, htmltools, httr2, shiny, stability (≥ 1.0.0), utils
Suggests:	knitr, pkgload, quarto, R.rsp, svglite, testthat (≥ 3.0.0), withr
VignetteBuilder:	quarto, R.rsp
Config/Needs/website:	pkgdown (>= 2.1.0)
Config/testthat/edition:	3
Config/skill/prefix:	sa
RoxygenNote:	7.3.1
NeedsCompilation:	no
Packaged:	2026-11-10 04:30:19 UTC; myaseen208
Author:	Muhammad Yaseen [aut, cre, cph], Kent Eskridge [aut, ctb]
Maintainer:	Muhammad Yaseen <myaseen208@gmail.com>
Repository:	CRAN
Date/Publication:	2026-11-10 09:20:09 UTC

StabilityApp: Interactive Stability Analysis of Multi-Environment Trials

Description

StabilityApp runs the analyses of the package stability in a web browser (StabilityApp()), with an interpretation of every result specific to its method and, optionally, a longer written interpretation from an external text service (sa_prompt(), sa_ask(), sa_services()).

Author(s)

Muhammad Yaseen (myaseen208@gmail.com), Kent M. Eskridge (keskridge1@unl.edu)

See Also

Useful links:

• https://myaseen208.com/StabilityApp/

• https://github.com/myaseen208/StabilityApp

• Report bugs at https://github.com/myaseen208/StabilityApp/issues

Stability analysis of multi-environment trials in a web browser

Description

StabilityApp() starts the application: load a trial (the example ge_data of stability or a CSV file with one row per plot), choose the columns, and run any of the twenty analyses of stability. Each analysis shows an interpretation written for its method and computed from its results (stability::stab_interpret()), its tables (with CSV and Excel export), its plots (PNG and PDF), and the R code that repeats it. A longer written interpretation can be requested from an external text service with your own key (sa_services(); optional).

Usage

StabilityApp(launch.browser = interactive(), ...)

sa_app()

Arguments

Details

The analyses: means and rankings, interaction effects; analysis of variance in each environment, combined, and Eberhart and Russell's; Finlay and Wilkinson's regression, variance measures, Shukla's stability variance with Kang's yield-stability statistic, Kang's rank-sum, Fox's top third; AMMI analysis, AMMI biplots, AMMI stability value, modified AMMI stability value, AMMI stability distance; GGE biplot (which won where, mean against stability, discrimination).

The key of a text service is typed on the Settings page (it stays in the session and is not saved) or read from the environment variable named in sa_services().

Value

Called for its side effect; returns the value of shiny::runApp() when the application is closed. sa_app() returns the application object (for shiny::runApp(), shiny::testServer() or deployment).

Author(s)

Muhammad Yaseen (myaseen208@gmail.com), Kent M. Eskridge (keskridge1@unl.edu)

See Also

sa_prompt, sa_services

Examples

if (interactive()) {
  StabilityApp(
      launch.browser = TRUE
    )
}

The request for a written interpretation of one analysis

Description

sa_prompt() builds the text sent to an external text service (sa_ask()) for a written interpretation of one result of the package stability. It is specific to the method: it contains how the statistics of that method are read, what to concentrate on, the interpretation computed by stability::stab_interpret() (to be kept to), the facts behind it and the first rows of the main table.

Usage

sa_prompt(x, higher_better = TRUE, trait = NULL, rows = 15L)

Arguments

Details

The text has two parts: system (the role and the rules: use only the numbers given, keep to the computed findings, name genotypes and environments as given, say when something cannot be concluded) and user (the material and the task: four sections, Statistical interpretation, Key agronomic findings, Recommendations and Next steps, at most about 350 words). Because the computed findings are part of the request, the written text cannot contradict the tests and rankings of the analysis without contradicting its own material, which the rules forbid.

Value

A list with system and user (character strings) and interpretation (the result of stability::stab_interpret()).

Author(s)

Muhammad Yaseen (myaseen208@gmail.com)

See Also

sa_ask, StabilityApp

Examples

fit <-
  stability::ammi(
      .data = stability::ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
p <-
  sa_prompt(
      x             = fit
    , higher_better = TRUE
    , trait         = "grain yield (kg/ha)"
    , rows          = 15
    )
cat(p$user)

External text services for a written interpretation

Description

sa_services() lists the external text services the application can ask for a longer written interpretation, and sa_ask() sends one request to such a service and returns its text. Using a service is optional: the application always shows the interpretation of stability::stab_interpret(), which is computed from the results and needs no connection.

Usage

sa_services()

sa_ask(
  service,
  prompt,
  model = NULL,
  key = "",
  max_tokens = 1500,
  timeout = 90
)

Arguments

Details

The services are read from the file services.csv of the package (columns id, label, format, url, model, key_env, and header, an extra header name=value). Three request formats are supported: "messages", "chat" and "generate", the formats of the three services in the file. The key is taken from the argument key or, when it is empty, from the environment variable named in key_env, so that it need not be typed into the application. The request is sent over HTTPS to the service's own address; the key is never stored by the package.

What is sent is the text built by sa_prompt(): the name of the analysis, the trait, the size of the trial, the interpretation of stab_interpret(), its facts and the first rows of the main table. No data file is sent.

Value

sa_services(): a data frame of the services. sa_ask(): the text of the answer (character), or an error with the message of the service.

Author(s)

Muhammad Yaseen (myaseen208@gmail.com)

See Also

sa_prompt, StabilityApp

Examples

sa_services()[, c("id", "format", "model")]
## Not run: 
fit <-
  stability::stab_reg(
      .data = stability::ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
p <-
  sa_prompt(
      x             = fit
    , higher_better = TRUE
    , trait         = NULL
    , rows          = 15L
    )
sa_ask(
    service    = sa_services()$id[1]
  , prompt     = p
  , model      = sa_services()$model[1]
  , key        = ""
  , max_tokens = 1500
  , timeout    = 90
  )

## End(Not run)