Title: 'shiny' Applications for the 'tesselle' Packages
Version: 0.3.1
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Description: A collection of 'shiny' applications for the 'tesselle' packages https://www.tesselle.org/. This package provides applications for archaeological data analysis and visualization. These mainly, but not exclusively, include applications for chronological modelling (e.g. matrix seriation, aoristic analysis) and count data analysis (e.g. diversity measures, compositional data analysis).
License: GPL (≥ 3)
URL: https://codeberg.org/tesselle/kinesis, https://packages.tesselle.org/kinesis/, https://tesselle.r-universe.dev/kinesis
BugReports: https://codeberg.org/tesselle/kinesis/issues
Depends: R (≥ 4.2)
Imports: aion (≥ 1.5.0), arkhe (≥ 1.11.0), bslib (≥ 0.9.0), config (≥ 0.3.2), dimensio (≥ 0.14.1), grDevices, gt (≥ 1.0.0), isopleuros (≥ 1.4.0), kairos (≥ 2.3.0), khroma (≥ 1.16.0), mirai (≥ 2.5.0), nexus (≥ 0.6.0), sass (≥ 0.4.10), shiny (≥ 1.11.1), stats, tabula (≥ 3.3.2), utils
Suggests: tinytest
Encoding: UTF-8
RoxygenNote: 7.3.3
X-schema.org-applicationCategory: Archaeological Science
X-schema.org-isPartOf: https://www.tesselle.org
X-schema.org-keywords: archaeology, archaeological-science, archaeometry, shiny-apps, r-package
NeedsCompilation: no
Packaged: 2025-09-29 16:55:42 UTC; nfrerebeau
Author: Nicolas Frerebeau ORCID iD [aut, cre], Brice Lebrun ORCID iD [art] (Logo designer), Université Bordeaux Montaigne ROR ID [fnd], CNRS ROR ID [fnd]
Repository: CRAN
Date/Publication: 2025-09-29 17:10:02 UTC

kinesis: 'shiny' Applications for the 'tesselle' Packages

Description

logo

A collection of 'shiny' applications for the 'tesselle' packages https://www.tesselle.org/. This package provides applications for archaeological data analysis and visualization. These mainly, but not exclusively, include applications for chronological modelling (e.g. matrix seriation, aoristic analysis) and count data analysis (e.g. diversity measures, compositional data analysis).

Details

Version 0.3.1
License GPL-3
Zenodo DOI doi:10.5281/zenodo.14645671

Archéosciences Bordeaux (UMR 6034)
Maison de l'Archéologie
Université Bordeaux Montaigne
F-33607 Pessac cedex
France

Package options

kinesis uses the following options() to configure behavior:

Author(s)

Maintainer: Nicolas Frerebeau nicolas.frerebeau@u-bordeaux-montaigne.fr (ORCID)

Other contributors:

See Also

Useful links:

Aoristic Analysis Server

Description

Aoristic Analysis Server

Usage

aoristic_server(id, x, y)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive list (returned by time_interval_server())

Value

A reactive kairos::AoristicSum object.

See Also

aoristic_ui()

Other chronology modules: aoristic_ui(), seriate_server(), seriate_ui(), time_interval_server(), time_interval_ui()

Aoristic Analysis UI

Description

Aoristic Analysis UI

Usage

aoristic_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

aoristic_server()

Other chronology modules: aoristic_server(), seriate_server(), seriate_ui(), time_interval_server(), time_interval_ui()

Bertin Diagrams Server

Description

Bertin Diagrams Server

Usage

bertin_server(id, x, verbose = get_option("verbose", FALSE))

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame (typically returned by import_server()).

verbose

A logical scalar: should R report extra information on progress?

Value

No return value, called for side effects.

See Also

bertin_ui()

Other count data modules: bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Bertin Diagrams UI

Description

Bertin Diagrams UI

Usage

bertin_ui(id, title = NULL)

Arguments

id

A character vector to be used for the namespace.

title

A character string giving the plot title.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

bertin_server()

Other count data modules: bertin_server(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Build Numeric Input

Description

Build Numeric Input

Usage

build_numeric_input(id, x)

render_numeric_input(id)

Arguments

id

A character string specifying the namespace.

x

A reactive data.frame (typically returned by import_server()).

Value

Correspondence Analysis Server

Description

Correspondence Analysis Server

Usage

ca_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame.

Value

A reactive dimensio::PCA object.

See Also

ca_ui()

Other multivariate analysis modules: ca_ui(), multivariate_server(), multivariate_ui(), pca_server(), pca_ui()

Correspondence Analysis UI

Description

Correspondence Analysis UI

Usage

ca_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

ca_server()

Other multivariate analysis modules: ca_server(), multivariate_server(), multivariate_ui(), pca_server(), pca_ui()

Updatable Checkbox Group

Description

Updatable Checkbox Group

Usage

checkbox_ui(id, label = "Choose", inline = TRUE)

Arguments

id

A character vector to be used for the namespace.

Value

A checkbox group control that can be added to a UI definition (see shiny::checkboxGroupInput()).

See Also

update_checkbox_colnames()

Bar Plot Server

Description

Bar Plot Server

Usage

coda_barplot_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive nexus::CompositionMatrix object.

Value

No return value, called for side effects.

See Also

coda_barplot_ui()

Other coda modules: coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Bar Plot UI

Description

Compositional Bar Plot UI

Usage

coda_barplot_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

coda_barplot_server()

Other coda modules: coda_barplot_server(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Hierarchical Clustering Server

Description

Compositional Data Hierarchical Clustering Server

Usage

coda_hclust_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive nexus::CompositionMatrix object.

Value

No return value, called for side effects.

See Also

coda_hclust_ui()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Hierarchical Clustering UI

Description

Compositional Data Hierarchical Clustering UI

Usage

coda_hclust_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

coda_hclust_server()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Histogram Server

Description

Compositional Histogram Server

Usage

coda_hist_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive nexus::CompositionMatrix object.

Value

No return value, called for side effects.

See Also

coda_hist_ui()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Histogram UI

Description

Compositional Histogram UI

Usage

coda_hist_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

coda_hist_server()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Outliers Server

Description

Compositional Data Outliers Server

Usage

coda_outliers_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive nexus::CompositionMatrix object.

Value

A reactive nexus::OutlierIndex object.

See Also

coda_outliers_ui()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Outliers UI

Description

Compositional Data Outliers UI

Usage

coda_outliers_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

coda_outliers_server()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Server

Description

Compositional Data Server

Usage

coda_server(id, demo = NULL, verbose = get_option("verbose", FALSE))

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

demo

A character string specifying the name of a dataset (see import_server()).

verbose

A logical scalar: should R report extra information on progress?

Value

A reactive nexus::CompositionMatrix object.

See Also

coda_ui()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Summary Server

Description

Compositional Data Summary Server

Usage

coda_summary_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive nexus::CompositionMatrix object.

Value

No return value, called for side effects.

See Also

coda_summary_ui()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_ui(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data Summary UI

Description

Compositional Data Summary UI

Usage

coda_summary_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

coda_summary_server()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_ui(), logratio_server(), logratio_ui()

Compositional Data UI

Description

Compositional Data UI

Usage

coda_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

coda_server()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), logratio_server(), logratio_ui()

Count Data Server

Description

Count Data Server

Usage

count_server(id, demo = NULL)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

demo

A character string specifying the name of a dataset (see import_server()).

Value

A reactive data.frame.

See Also

count_ui()

Other count data modules: bertin_server(), bertin_ui(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Count Data UI

Description

Count Data UI

Usage

count_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

count_server()

Other count data modules: bertin_server(), bertin_ui(), count_server(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Alpha Diversity Server

Description

Alpha Diversity Server

Usage

diversity_alpha_server(id, x, verbose = get_option("verbose", FALSE))

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame returned by diversity_server().

verbose

A logical scalar: should R report extra information on progress?

Value

A reactive data.frame (see tabula::diversity()).

See Also

diversity_alpha_ui()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Alpha Diversity UI

Description

Alpha Diversity UI

Usage

diversity_alpha_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

diversity_alpha_server()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Beta Diversity Server

Description

Beta Diversity Server

Usage

diversity_beta_server(id, x, quanti, quali)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame returned by diversity_server().

quanti

A reactive data.frame returned by diversity_alpha_server().

quali

A reactive data.frame (typically returned by import_server()).

Value

No return value, called for side effects.

See Also

diversity_beta_ui()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Beta Diversity UI

Description

Beta Diversity UI

Usage

diversity_beta_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

diversity_beta_server()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Diversity Definitions UI

Description

Diversity Definitions UI

Usage

diversity_docs_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_server(), diversity_ui(), occurrence_server(), occurrence_ui()

Alpha Diversity Server

Description

Alpha Diversity Server

Usage

diversity_server(id, x, verbose = get_option("verbose", FALSE))

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame (typically returned by import_server()).

verbose

A logical scalar: should R report extra information on progress?

Value

A reactive data.frame (see tabula::diversity()).

See Also

diversity_ui()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_ui(), occurrence_server(), occurrence_ui()

Diversity UI

Description

Diversity UI

Usage

diversity_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

diversity_server()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), occurrence_server(), occurrence_ui()

Default Value for Falsy

Description

Replaces a falsy value with a default value.

Usage

x %|||% y

Arguments

x, y

An object.

Value

If x is not truthy, returns y; otherwise returns x.

Description

Footer Server

Usage

footer_server(id)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

Value

No return value, called for side effects.

See Also

footer_ui()

Other page modules: footer_ui(), home_server(), home_ui()

Description

Footer UI

Usage

footer_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A list that can be converted into an HTML ⁠<footer>⁠ tag (see htmltools::tags()).

See Also

footer_server()

Other page modules: footer_server(), home_server(), home_ui()

Read Configuration Values

Description

Read Configuration Values

Usage

get_config(app, file = NA, active = NA, use_parent = TRUE)

Arguments

app

A character string specifying the Shiny application to run (see run_app()).

file

A character string specifying the configuration file to read from. If NA (the default), use the value of the KINESIS_CONFIG_FILE environment variable ("config.yml" if the variable does not exist). If NULL, use the build-in configuration file.

active

A character string specifying the name of configuration to read from. If NA (the default), use the value of the KINESIS_CONFIG_ACTIVE environment variable ("default" if the variable does not exist).

use_parent

A logical scalar: should parent directories be scanned for configuration files if the specified config file isn't found?

Value

A list of configuration values.

Author(s)

N. Frerebeau

Get App Options

Description

Get App Options

Usage

get_option(name = NULL, default = NULL)

Arguments

name

A character string specifying the name of an option to get. If NULL (the default), all options are returned.

default

A value to be returned if the option is not currently set.

Value

The value of a Shiny option (see shiny::getShinyOption()).

Author(s)

N. Frerebeau

Graphical Parameters Server

Description

Graphical Parameters Server

Usage

graphics_server(id)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

Value

A reactiveValues object with elements:

col_quali, col_quant

A palette function that when called with a single argument returns a character vector of colors.

pch

A palette function that when called with a single argument returns a character vector of symbols.

lty

A palette function that when called with a single argument returns a character vector of symbols.

cex

A palette function that when called with a single argument returns a numeric vector giving the amount by which plotting text and symbols should be magnified relative to the default.

asp

See Also

graphics_ui()

Other plot modules: graphics_ui(), scatter_server(), scatter_ui(), ternary_server(), ternary_ui()

Graphical Parameters UI

Description

Graphical Parameters UI

Usage

graphics_ui(
  id,
  col_quali = TRUE,
  col_quant = TRUE,
  pch = TRUE,
  lty = TRUE,
  cex = TRUE,
  asp = FALSE
)

Arguments

id

A character vector to be used for the namespace.

Value

A list of UI elements.

See Also

graphics_server()

Other plot modules: graphics_server(), scatter_server(), scatter_ui(), ternary_server(), ternary_ui()

Home Server

Description

Home Server

Usage

home_server(id)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

Value

No return value, called for side effects.

See Also

home_ui()

Other page modules: footer_server(), footer_ui(), home_ui()

About UI

Description

About UI

Usage

home_ui(id, package = NULL)

Arguments

id

A character vector to be used for the namespace.

package

A character vector of package names to be cited.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

home_server()

Other page modules: footer_server(), footer_ui(), home_server()

Import Data Server

Description

Import Data Server

Usage

import_server(id, demo = NULL)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

demo

A character string specifying the name of a dataset from folio or datasets.

Value

A reactive data.frame.

See Also

import_ui()

Other generic modules: import_ui(), prepare_server(), prepare_ui()

Import Data UI

Description

Import Data UI

Usage

import_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A list of UI elements.

See Also

import_server()

Other generic modules: import_server(), prepare_server(), prepare_ui()

Linear Model Server

Description

Linear Model Server

Usage

lm_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame.

Value

A reactive lm object.

See Also

lm_ui()

Other modeling modules: lm_ui()

Linear Model UI

Description

Linear Model UI

Usage

lm_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

lm_server()

Other modeling modules: lm_server()

Log-Ratio Server

Description

Log-Ratio Server

Usage

logratio_server(id, x, method)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive nexus::CompositionMatrix object.

method

A character string specifying the log-ratio to be computed.

Value

A reactive nexus::LogRatio object.

See Also

logratio_ui()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_ui()

Log-Ratio UI

Description

Log-Ratio UI

Usage

logratio_ui(id, title)

Arguments

id

A character vector to be used for the namespace.

title

A character string giving the sidebar title.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

logratio_server()

Other coda modules: coda_barplot_server(), coda_barplot_ui(), coda_hclust_server(), coda_hclust_ui(), coda_hist_server(), coda_hist_ui(), coda_outliers_server(), coda_outliers_ui(), coda_server(), coda_summary_server(), coda_summary_ui(), coda_ui(), logratio_server()

MCD Server

Description

MCD Server

Usage

mcd_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame (typically returned by import_server()).

Value

No return value, called for side effects.

See Also

mcd_ui()

Other ceramic data modules: mcd_ui()

MCD UI

Description

MCD UI

Usage

mcd_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

mcd_server()

Other ceramic data modules: mcd_server()

Multivariate Analysis Server

Description

Multivariate Analysis Server

Usage

multivariate_server(id, x, y)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive dimensio::MultivariateAnalysis object.

y

A reactive matrix-like object use to compute the multivariate analysis.

Value

No return value, called for side effects.

See Also

multivariate_ui

Other multivariate analysis modules: ca_server(), ca_ui(), multivariate_ui(), pca_server(), pca_ui()

Mutlivariate Analysis UI

Description

Mutlivariate Analysis UI

Usage

multivariate_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A tab that can be passed to shiny::tabsetPanel().

A navigation container (see bslib::navset_card_pill()).

See Also

multivariate_server()

Other multivariate analysis modules: ca_server(), ca_ui(), multivariate_server(), pca_server(), pca_ui()

Co-Occurrence Server

Description

Co-Occurrence Server

Usage

occurrence_server(id, x, verbose = get_option("verbose", FALSE))

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame returned by diversity_server().

verbose

A logical scalar: should R report extra information on progress?

Value

No return value, called for side effects.

See Also

occurrence_ui()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_ui()

Co-Occurrence UI

Description

Co-Occurrence UI

Usage

occurrence_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

occurrence_server()

Other count data modules: bertin_server(), bertin_ui(), count_server(), count_ui(), diversity_alpha_server(), diversity_alpha_ui(), diversity_beta_server(), diversity_beta_ui(), diversity_docs_ui(), diversity_server(), diversity_ui(), occurrence_server()

Plot UI

Description

Plot UI

Usage

output_plot(id, ..., tools = NULL, title = NULL, note = NULL)

Arguments

id

A character vector to be used for the namespace.

...

Further parameters to be passed to shiny::plotOutput().

tools

A (list of) input elements.

title

A character string giving the card title.

note

A character string giving a note to be placed in the footer.

Value

A htmltools::div() tag.

See Also

Other widgets: render_plot()

Principal Components Analysis Server

Description

Principal Components Analysis Server

Usage

pca_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame.

Value

A reactive dimensio::PCA object.

See Also

pca_ui()

Other multivariate analysis modules: ca_server(), ca_ui(), multivariate_server(), multivariate_ui(), pca_ui()

Principal Components Analysis UI

Description

Principal Components Analysis UI

Usage

pca_ui(id, center = TRUE, scale = TRUE, help = NULL)

Arguments

id

A character vector to be used for the namespace.

center

A logical scalar: should the variables be shifted to be zero centered?

scale

A logical scalar: should the variables be scaled to unit variance?

help

A character string giving a short help text.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

pca_server()

Other multivariate analysis modules: ca_server(), ca_ui(), multivariate_server(), multivariate_ui(), pca_server()

Prepare Data Server

Description

Prepare Data Server

Usage

prepare_server(id, demo = NULL)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

demo

A character string specifying the name of a dataset (see import_server()).

Value

A reactive data.frame.

See Also

prepare_ui()

Other generic modules: import_server(), import_ui(), prepare_ui()

Prepare Data UI

Description

Prepare Data UI

Usage

prepare_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

prepare_server()

Other generic modules: import_server(), import_ui(), prepare_server()

Plot Server

Description

Plot Server

Usage

render_plot(id, x, ...)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive function recording the plot.

...

Further parameters to be passed to shiny::renderPlot().

Value

No return value, called for side effects.

See Also

Other widgets: output_plot()

Run an App

Description

A wrapper for shiny::shinyAppDir().

Usage

run_app(
  app = c("diversity", "seriation", "aoristic", "mcd", "source", "scatter", "ternary",
    "ca", "pca"),
  options = list(launch.browser = interactive())
)

Arguments

app

A character string specifying the Shiny application to run (see details). Any unambiguous substring can be given.

options

A list of named options that should be passed to the shiny::shinyAppDir() call.

Details

Application name Keyword
Aoristic Analysis aoristic
Correspondence Analysis ca
Principal Components Analysis pca
Diversity Measures diversity
Mean Ceramic Date mcd
Scatter Plot scatter
Matrix Seriation seriation
Compositional Data Analysis source
Ternary Plot ternary

Value

A shiny application object.

Author(s)

N. Frerebeau

Examples

if (interactive()) {
 run_app("seriation")
}

Scatter Plot Server

Description

Scatter Plot Server

Usage

scatter_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame.

Value

No return value, called for side effects.

See Also

scatter_ui()

Other plot modules: graphics_server(), graphics_ui(), scatter_ui(), ternary_server(), ternary_ui()

Scatter Plot UI

Description

Scatter Plot UI

Usage

scatter_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

scatter_server()

Other plot modules: graphics_server(), graphics_ui(), scatter_server(), ternary_server(), ternary_ui()

Updatable Select List

Description

Updatable Select List

Usage

selectize_ui(id, label = "Choose", multiple = FALSE)

Arguments

id

A character string specifying the namespace.

Value

A select list control that can be added to a UI definition (see shiny::selectizeInput()).

See Also

update_selectize_colnames(), update_selectize_rownames()

CA Seriation Server

Description

CA Seriation Server

Usage

seriate_server(id, x, order)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame (typically returned by import_server()).

order

A reactive R object (coercible by kairos::as_seriation()).

Value

A reactive kairos::AveragePermutationOrder object.

See Also

seriate_ui()

Other chronology modules: aoristic_server(), aoristic_ui(), seriate_ui(), time_interval_server(), time_interval_ui()

CA Seriation UI

Description

CA Seriation UI

Usage

seriate_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

seriate_server()

Other chronology modules: aoristic_server(), aoristic_ui(), seriate_server(), time_interval_server(), time_interval_ui()

Ternary Plot Server

Description

Ternary Plot Server

Usage

ternary_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive matrix-like object.

Value

No return value, called for side effects.

See Also

ternary_ui()

Other plot modules: graphics_server(), graphics_ui(), scatter_server(), scatter_ui(), ternary_ui()

Ternary Plot UI

Description

Ternary Plot UI

Usage

ternary_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

ternary_server()

Other plot modules: graphics_server(), graphics_ui(), scatter_server(), scatter_ui(), ternary_server()

Bootstrap Theme

Description

Bootstrap Theme

Usage

theme_ui(version = "5", ...)

Arguments

version

A character string specifying the major version of Bootstrap to use.

...

Extra parameters to be passed to bslib::bs_theme().

Value

Returns a sass::sass_bundle() object (see bslib::bs_theme()).

Aoristic Analysis Server

Description

Aoristic Analysis Server

Usage

time_interval_server(id, x)

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

x

A reactive data.frame.

Value

A reactive list.

See Also

time_interval_ui()

Other chronology modules: aoristic_server(), aoristic_ui(), seriate_server(), seriate_ui(), time_interval_ui()

Time Intervals UI

Description

Time Intervals UI

Usage

time_interval_ui(id)

Arguments

id

A character vector to be used for the namespace.

Value

A nav item that may be passed to a nav container (e.g. bslib::navset_tab()).

See Also

time_interval_server()

Other chronology modules: aoristic_server(), aoristic_ui(), seriate_server(), seriate_ui(), time_interval_server()

Update a Checkbox Group with Column Names

Description

Update a Checkbox Group with Column Names

Usage

update_checkbox_colnames(id, x, exclude = reactive(NULL), select = TRUE)

Arguments

id

A character string specifying the namespace.

x

A reactive matrix-like object.

exclude

A reactive character vector of values to be excluded from choices.

select

A logical scalar: should all choices be selected?

Value

A reactive character vector of column names.

Side effect: change the value of a checkbox group on the client.

See Also

checkbox_ui()

Update an Input Control with Column Names

Description

Update an Input Control with Column Names

Usage

update_input(
  control,
  id,
  x,
  choices = colnames,
  exclude = reactive(NULL),
  select = TRUE,
  placeholder = FALSE
)

Arguments

control

An UI input updater.

id

A character string specifying the namespace.

x

A reactive matrix-like object.

choices

A function that takes x as a single argument and returns a character vector.

exclude

A reactive character vector of values to be excluded from choices.

select

A logical scalar: should all choices be selected?

placeholder

A logical scalar: should a placeholder be added?

Value

A reactive character vector of column names.

Side effect: change the value of an input control on the client.

See Also

update_checkbox_colnames(), update_selectize_colnames(), update_selectize_rownames()

Update a Select List with Column Names

Description

Update a Select List with Column Names

Usage

update_selectize_colnames(
  id,
  x,
  exclude = reactive(NULL),
  select = FALSE,
  placeholder = TRUE
)

Arguments

id

A character string specifying the namespace.

x

A reactive matrix-like object.

exclude

A reactive character vector of values to be excluded from choices.

select

A logical scalar: should all choices be selected?

placeholder

A logical scalar: should a placeholder be added?

Value

A reactive character vector of column names.

Side effect: change the value of a select list on the client.

See Also

selectize_ui()

Update a Select List with Row Names

Description

Update a Select List with Row Names

Usage

update_selectize_rownames(
  id,
  x,
  exclude = reactive(NULL),
  select = FALSE,
  placeholder = TRUE
)

Arguments

id

A character string specifying the namespace.

x

A reactive matrix-like object.

exclude

A reactive character vector of values to be excluded from choices.

select

A logical scalar: should all choices be selected?

placeholder

A logical scalar: should a placeholder be added?

Value

A reactive character vector of row names.

Side effect: change the value of a select list on the client.

See Also

selectize_ui()