# Reference

Use this section when you know what you need and want a precise answer.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Analysis matrix
:link: analysis-matrix
:link-type: doc

Model types, endpoints, methods, outputs, maturity, and explicit execution
boundaries in one table.
:::

:::{grid-item-card} All 56 capabilities
:link: capability-catalog
:link-type: doc

Every registry entry with maturity, implementation state, reproducibility,
evidence artifacts, limitations, and open gates.
:::

:::{grid-item-card} Command-line interface
:link: cli
:link-type: doc

Every command, argument, family name, file contract, and exit code.
:::

:::{grid-item-card} Warnings and errors
:link: ../warnings
:link-type: doc

Stable code families, structured records, exceptions, and automation guidance.
:::

:::{grid-item-card} Formula and data
:link: ../user-guide/data-and-formulas
:link-type: doc

Input adapters, missingness contracts, grammar, transformations, factors, and
rank checks.
:::

:::{grid-item-card} Interoperability
:link: ../interoperability/index
:link-type: doc

Compatibility reports and conservative import/export boundaries for R,
NONMEM, PharmML, SBML, and SED-ML.
:::

:::{grid-item-card} Glossary
:link: glossary
:link-type: doc

Definitions for statistical, numerical, pharmacometric, and provenance terms
used throughout PyMixEF.
:::

:::{grid-item-card} Aliases
:link: ../api/aliases
:link-type: doc

Searchable mapping for `Normal`, `NB2`, `dry_run`, `model_diff`, PK aliases,
backend aliases, and `pymixef.load`.
:::

:::{grid-item-card} Complete API
:link: ../api/index
:link-type: doc

Task-oriented public symbol map plus one generated reference page per public
module.
:::
::::

```{toctree}
:maxdepth: 1

analysis-matrix
capability-catalog
cli
glossary
../concepts/conventions
../concepts/model-ir
../interoperability/index
```