# inti

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The **inti** package is part of the **inkaverse** project, which
develops tools and workflows for plant science, experimental design,
data analysis, and scientific writing. The package supports researchers
during experiment planning and field data collection through **Tarpuy**,
statistical analysis and visualization through **Yupana**, and the
preparation of scientific outputs.

More information about the project is available at
<https://inkaverse.com/>.

## Installation

The stable version of **inti** can be installed from CRAN:

``` r

install.packages("inti")
```

To install the latest development version directly from GitHub, it is
recommended to use **pak**:

``` r

if (!requireNamespace("pak", quietly = TRUE)) {
  install.packages("pak")
}

pak::pkg_install("flavjack/inti")
```

To install a specific version from CRAN (e.g., version 0.4.4):

``` r

if (!requireNamespace("pak", quietly = TRUE)) {
  install.packages("pak")
}

pak::pkg_install("inti@0.4.4")
```

After installation, load the package:

``` r

library(inti)
```

## Shiny Applications

The **inti** package includes two Shiny applications that provide
graphical interfaces for experimental design, data management,
statistical analysis, and result visualization.

### Installing Application Dependencies

The applications can be accessed directly from the **RStudio Addins**
menu or launched from the R console.

**Yupana** is an interactive environment for statistical analysis and
visualization of experimental data.

``` r

inti:::yupana_full()
```

**Tarpuy** is an interactive platform for experimental planning,
field-book generation, treatment organization, and data management.

``` r

inti:::tarpuy_full()
```

# Package index

## Yupana

Data analysis

- [`yupana()`](https://inkaverse.com/reference/yupana.md) : Interactive
  data analysis
- [`yupana_analysis()`](https://inkaverse.com/reference/yupana_analysis.md)
  : Fieldbook analysis report
- [`yupana_export()`](https://inkaverse.com/reference/yupana_export.md)
  : Graph options to export
- [`yupana_import()`](https://inkaverse.com/reference/yupana_import.md)
  : Import information from data summary
- [`yupana_mvr()`](https://inkaverse.com/reference/yupana_mvr.md) :
  Multivariate Analysis
- [`yupana_reshape()`](https://inkaverse.com/reference/yupana_reshape.md)
  : Fieldbook reshape
- [`plot_augmented_design()`](https://inkaverse.com/reference/plot_augmented_design.md)
  : Plot augmented fieldbook design
- [`plot_diag()`](https://inkaverse.com/reference/plot_diag.md) :
  Diagnostic plots
- [`plot_diagnostic()`](https://inkaverse.com/reference/plot_diagnostic.md)
  : Diagnostic plots
- [`plot_raw()`](https://inkaverse.com/reference/plot_raw.md) : Plot raw
  data
- [`plot_smr()`](https://inkaverse.com/reference/plot_smr.md) : Plot
  summary data
- [`plot_split_rcbd_design()`](https://inkaverse.com/reference/plot_split_rcbd_design.md)
  : Plot Splitplot-RCBD fieldbook design
- [`plot_standard_design()`](https://inkaverse.com/reference/plot_standard_design.md)
  : Plot standard fieldbook experimental designs

## Tarpuy

Experimental designs

- [`tarpuy()`](https://inkaverse.com/reference/tarpuy.md) : Interactive
  fieldbook designs
- [`tarpuy_design()`](https://inkaverse.com/reference/tarpuy_design.md)
  : Fieldbook experimental designs
- [`tarpuy_plex()`](https://inkaverse.com/reference/tarpuy_plex.md) :
  Fieldbook plan information
- [`tarpuy_plotdesign()`](https://inkaverse.com/reference/tarpuy_plotdesign.md)
  : Fieldbook plot experimental designs
- [`tarpuy_traits()`](https://inkaverse.com/reference/tarpuy_traits.md)
  : Field book traits

## Rticles

Write technical documents

- [`rticle()`](https://inkaverse.com/reference/rticle.md) : Convert a
  Markdown manuscript into a Quarto document
- [`include_pdf()`](https://inkaverse.com/reference/include_pdf.md) :
  Include PDF in markdown documents
- [`include_table()`](https://inkaverse.com/reference/include_table.md)
  : Table with footnotes
- [`footnotes()`](https://inkaverse.com/reference/footnotes.md) :
  Footnotes in tables
- [`web_table()`](https://inkaverse.com/reference/web_table.md) : HTML
  tables for markdown documents

## Plant breeding

Algorithms and calculations

- [`H2cal()`](https://inkaverse.com/reference/H2cal.md) : Broad-sense
  heritability in plant breeding
- [`metamorphosis()`](https://inkaverse.com/reference/metamorphosis.md)
  : Transform fieldbooks based in a dictionary
- [`outliers_remove()`](https://inkaverse.com/reference/outliers_remove.md)
  : Remove outliers
- [`remove_outliers()`](https://inkaverse.com/reference/remove_outliers.md)
  : Remove outliers using mixed models
- [`mean_comparison()`](https://inkaverse.com/reference/mean_comparison.md)
  : Mean comparison test
- [`design_augmented()`](https://inkaverse.com/reference/design_augmented.md)
  : Experimental design: Augmented
- [`design_noreps()`](https://inkaverse.com/reference/design_noreps.md)
  : Experimental design without replications
- [`design_repblock()`](https://inkaverse.com/reference/design_repblock.md)
  : Experimental design in CRD and RCBD
- [`design_split()`](https://inkaverse.com/reference/design_split.md) :
  Split-plot experimental designs
- [`design_split_rcbd()`](https://inkaverse.com/reference/design_split_rcbd.md)
  : Split-plot RCBD experimental design

## Datasets

- [`potato`](https://inkaverse.com/reference/potato.md) : Water use
  efficiency in 15 potato genotypes
- [`met`](https://inkaverse.com/reference/met.md) : Swedish cultivar
  trial data

## Miscellaneous

- [`split_folder()`](https://inkaverse.com/reference/split_folder.md) :
  Split folder

# Articles

### All vignettes

- [Apps](https://inkaverse.com/articles/apps.md):

  inti: interactive apps.

- [Broad-sense heritability in plant
  breeding](https://inkaverse.com/articles/heritability.md):

  How to calculate the heritability in plant breeding.

- [Inkaverse Privacy Policy](https://inkaverse.com/articles/policy.md):

- [Rticles](https://inkaverse.com/articles/rticles.md):

  Rticles: scientific documents with R.

- [Tarpuy](https://inkaverse.com/articles/tarpuy.md):

  Tarpuy: field-book experimental plans.

- [Yupana](https://inkaverse.com/articles/yupana.md):

  Yupana: experimental design analysis.