statim

A Declarative Interface for Statistical Inference

Package Overview: Simple Fun Fact

What does {statim} mean?

{statim} is a Latin word for “immediately, at once”. The name carries a double meaning:

• stat: as in statistics, the domain this package lives in

• im (statim): as in “immediate”, signalling that inference should be expressible as a direct declaration, not somewhat a sequence of mechanical steps

This simply means: you declare what statistical inference you want to perform, then {statim} immediately delivers how.

Why statim?

R has a rich statistical ecosystem. Statistical inference in general is served by an assortment of disconnected functions: the functions you’re looking for may exist but they are scattered across different packages.

R gained a grammar for graphics ({ggplot2}), and one for data manipulation ({dplyr}). And then there’s {statim}, an attempt to re-imagine the “grammar of statistical inference” from the ground up. The core idea of {statim} in general is it’s fully declarative, and that any inferential procedure can be described in three steps.

What makes {statim} composable for statistical workflows is the verbs and the accessibility of the methods you’re looking for. For example, you want to write a t-test pipeline, and you want to use the classical one and then the permutation method. {statim} lets you do that with via("<method_name>"), and while you can use t-test from default (classical), you can access its permutation method through ... |> via("permute") with one line of code only. You won’t need you to do a lot of work (which sometimes require rewriting your code), just a single addition to the syntax.

# Classical t-test
sleep |> 
    define_model(x_by(extra, group)) |> 
    prepare_test(TTEST) |> 
    conclude()

# Permutation t-test
sleep |> 
    define_model(x_by(extra, group)) |> 
    prepare_test(TTEST) |> 
    # Here, one line added, nothing else changes
    via("permute", n = 1000L) |>         
    conclude()

For a quick result, the eager form skips the piped syntax entirely:

# Only works for `stat_fn` functions
TTEST(x_by(extra, group), sleep)

The trade-off: eager forms cannot be recalibrated / switch off into different methods with via() and do not support post-execution output manipulation (see for more details).

Installation

The package is yet to be submitted into CRAN.

# Stable version (not yet released)
install.packages("statim")

For the time being, you can install the current implementation on GitHub:

# Development version from GitHub
# install.packages("pak")
pak::pak("s7-stats/statim")

General Usage

Let us start by loading {statim} first:

library(statim)

All you need to know is that the most usual usage of {statim} comes with three steps. Here’s the general anatomy of the main {statim} semantics:

# Data can be piped in or passed as argument to `define_model()`
... |>                                   # Possible extensions  
    define_model(
        <var_id>(var1, var2, ...), 
        data, ...
    ) |>                                 # 1. Model definition
    # ... |>                             # Possible extensions  
    prepare(<STAT_FN>) |>                # 2. Prepare method (lazy)
    via(...) |>                          # Optional: method variant  (*)
    state_null(<expr>) |>                # Optional: null hypothesis (*)
    # ... |>                             # Possible extensions  
    conclude() |>                        # 3. Execute
    <output_handler>()                   # e.g. tidy(), display()    

Explanation of the code above:

1. Model processor and definition, where defining the shape of model to be analyzed happens at the beginning during statistical inference. Typically, this step where supplying either a data frame or a <var_id> objects into define_model() occurs, and then some functions to be appended in the future updates.

2. Parameterization, where the estimation process of the statistical inference pipeline is defined lazily. Our usual statistical inference application can be a model-based inference (e.g. linear regression through prepare_model()), H-test inference (e.g. t-test through prepare_test()), or both with just prepare(). With that said, the execution is lazy-loaded, and only executed if needed. (The (*) mark means they are interchangeable. )

   state_null() is one of the reasons why {statim} — it’s astronomical way of writing null hypothesis expressed mathematically. Learn more about it on vignette("hypothesis-expressions", package = "statim").

3. Execution and retrieval, where the first 2 steps is (re-)executed and then retrieve the output. The most common function is conclude(). There are several techniques to retrieve the output, e.g. through tidy(). This is functional if there are available methods are registered, automatically or from a manual step.

The ... before the pipe above means the possible future extensions for this package. For more information, see through vignette("statim"), and learn more about how {statim} works.

Core Semantics

The package is designed around three ideas:

1. Composability: the simplest way to write {statim} has two forms: the eager form and the grammar/piped syntax form. The eager form skips the verbs and cannot be recalibrated, only skips to the output. On the other hand, the grammar/piped syntax form relies on verbs and lazy loading, which comes with the recalibration of the estimation method with a single via() call, and the execution of the lazy-loaded pipeline with conclude().

2. A shared grammar: Only applied on the main {statim} semantics: piped/grammar syntax. define_model() => prepare() => conclude() is the same shape for every inferential procedure. The <var_id> objects (x_by, rel, pairwise, …) describe the statistical structure of the problem; the verbs stay constant.

   Eager forms (TTEST(), CORTEST(), …) provide a shortcut when the full pipeline (in a form of piped syntax that reads like a sentence) is not needed.

3. Extensible by design: the {statim} pipeline is extensible. For instance, if you want to write new estimation method, an implementation is through filling up the stat_define() object (then store it within list of defs from STAT_CONSTRUCTOR() functions, saved as <STAT_FN>), then baseline() to write the default form of <STAT_FN> and variant() to extend the current <STAT_FN> form (only be accessed with via() only). With these, you can bring your own engine, your own method, your own implementation, or use them to extend the current ones.

License

MIT + file LICENSE

Contributing

We are sincerely grateful for contributions; they are beneficial for the project and for us as maintainers. Please read CONTRIBUTING.md for development setup, pull request guidelines, and workflow notes.

Code of Conduct

Please note that the statim project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.