Package index • symbolizer

Package

symbolizer symbolizer-package: symbolizer: Symbolic Specifications, Interpretations, and Teachable Stories for Statistical Models

First-time entry

One call that does it all, plus the plain-English summary of a symbolized_model.

explain(): One-call explainer for a fitted model
summary(<symbolized_model>): Plain-English summary of a symbolized model

Teaching bundle (one-call)

model_card collects equation, assumptions, readings, extraction calls, recommended plots in one S3 object.

model_card(): One-call teaching bundle for a symbolized model

Build the structured symbolic object

The product. Renderers consume it; users override symbols, units, context here.

symbolize(): Symbolize a fitted statistical model
symbolize(<drmTMB>): Symbolize a drmTMB fit (Gaussian and bivariate Gaussian, v0.1)
symbolize(<gllvmTMB>): Symbolize a gllvmTMB fit (Gaussian and binomial latent-variable models)
symbolize(<glmmTMB>): Symbolize a glmmTMB fit (Gaussian, v0.7 first slice)
symbolize(<brmsfit>): Symbolize a brms fit (Gaussian, v0.8 first slice)
symbolize(<MCMCglmm>): Symbolize an MCMCglmm fit (Gaussian, v0.9 first slice)
symbolize(<lm>): Symbolize a base R lm() fit (Gaussian, v0.10 first slice)
symbolize(<glm>): Symbolize a base R glm() fit (Gaussian / binomial / poisson, v0.10 first slice)
symbolize(<lmerMod>): Symbolize an lme4 lmer() fit (Gaussian, v0.10 first slice)
symbolize(<glmerMod>): Symbolize an lme4 glmer() fit (binomial / poisson, v0.11 first slice)
symbolize(<sdmTMB>): Symbolize an sdmTMB fit (Gaussian, v0.12 first slice)
symbolize(<rma.uni>): Symbolize a metafor rma.uni fit (meta-analysis / meta-regression, v0.13 first slice)
symbolize(<rma.mv>): Symbolize a metafor rma.mv fit (multilevel / multivariate meta-analysis, v0.13.1)
symbolize(<gam>) symbolize(<bam>): Symbolize an mgcv gam / bam fit (additive grammar, v0.14 first slice)
symbolize(<phylolm>): Symbolize a phylolm fit (Gaussian PGLS, v0.21.4 first slice)
symbolize(<psem>): Symbolize a piecewiseSEM psem fit
symbolizer_capabilities(): Symbolizer capability registry

Read both notations

Educator-facing bridge between index and matrix forms.

notation_bridge(): Index vs matrix notation bridge

See the data flow

Numeric arrays behind the symbols, and the three-views widget — interactive HTML and static PDF.

expand(): Expand a symbolized_model to its underlying numeric arrays
as_html_three_views(): Three-views HTML rendering of a symbolized_model
as_pdf_three_views(): PDF rendering of a symbolized_model in three stacked sections

Render the equations

LaTeX surface. Lines come from the symbolized_model; renderers only choose the layout.

equations(): Equation rows from a symbolized_model
as_latex(): Render a symbolized_model as LaTeX

Render the tables

Symbols (with dimensions), assumptions (stated / implied / not checked), R-syntax-to-math bridge.

symbol_table(): Symbol dictionary as a reader-friendly table
assumption_table(): Assumption table for a symbolized model
formula_bridge(): Formula bridge table for a symbolized model

Interpret the coefficients

Per-parameter readings on link, natural, variance, and biological scales.

parameter_interpretation(): Per-parameter interpretations for a symbolized model

Factors & dummy coding

Demystify treatment / contrast coding for multi-level factors and interactions — in one call, or an interactive widget.

explain_factors(): Explain a model's factors and dummy coding in one call
as_html_factor_views(): Interactive HTML widget for a model's factors and dummy coding

Marginal estimates

The group_* family — per-group means, per-group slopes, and pairwise / vs-reference contrasts via emmeans. Confidence bands, no p-values.

group_means(): Per-group marginal means for a symbolized model
group_slopes(): Per-group slopes for a continuous predictor
group_contrasts(): Pairwise and reference contrasts between factor levels

Variance components

Where the variation lives, and how repeatable a trait is (ICC / repeatability).

variance_partition(): Where the variation lives: a variance partition for a mixed model
icc(): Intraclass correlation (repeatability) for a mixed model

Compare two models

Structural diff between two symbolized_model objects: which submodels, which terms, which assumption statuses differ.

compare_symbolic(): Structural comparison of two symbolized models

Draft a Methods paragraph

Turn a symbolized_model into a draft Methods-section paragraph (opt-in, template-based, never LLM).

methods_text(): Methods-section paragraph from a symbolized model

Per-fit warnings

Conditions symbolize() flagged when building the object (e.g., Wald CI with few RE groups). Templated from inst/extdata/warning-templates.csv.

warning_table(): Per-fit prose warnings for a symbolized model

Model diagram

Render the structural model as a DAG (nodes for response, parameters, predictors, groups, random effects). Returns a list with DOT (GraphViz), Mermaid (Markdown / Quarto), and TikZ (LaTeX) representations.

as_dag(): Model diagram for a symbolized model

Simulation recipe

Pseudocode + runnable R code describing how to simulate from a fitted model.

simulate_recipe(): Simulation recipe for a symbolized model

Internal: term-grammar bridge

The R formula <-> model matrix <-> biological symbol layer that every renderer reads.

extract_terms(): Build the term-grammar / model-matrix bridge for one submodel
get_parameterization(): Get the family parameterization contract

Internal: capability registry

The gate deciding which (class, family, component) tuples symbolize() supports, plus the human-readable status words.

capability_check(): Check whether a (class, family, component) tuple is supported
friendly_status(): Map an assumption-status key to a friendlier display label

Internal: template loader

Reads and caches the prose / LaTeX templates in inst/extdata/*.csv that every renderer draws from.

load_template(): Load a template CSV from inst/extdata
clear_template_cache(): Clear the template cache

Internal: formula helpers

Low-level formula-parsing and LaTeX-environment utilities shared across the extractors and renderers.

formula_lhs(): Get the left-hand side of a formula
formula_rhs(): Get the right-hand side of a formula
formula_vars(): All variable names appearing in a formula RHS
wrap_aligned(): Wrap a vector of equation lines in aligned environment
align_at(): Insert an alignment marker before = or \\sim
wrap_env(): Wrap aligned LaTeX equation lines in a chosen environment

Internal: object construction

S3 constructor and validator. Useful only for advanced users hand-building symbolized_model objects.

new_symbolized_model(): Construct a symbolized_model object
validate_symbolized_model(): Validate a symbolized_model object