---
myst:
  html_meta:
    description: Build design matrices from R formulas, name contrasts and check designs for problems before fitting, with CytePool.
---

# Designs and contrasts

A {class}`~cytepool.design.Design` joins a sample table, the fixed effects as an R
formula, optional random effects in lme4 notation and named contrasts. Its model
matrix has the columns and column names that R's `model.matrix` gives for the same
level order. Without explicit levels, factor levels are sorted by code point, as R
sorts them with `LC_COLLATE=C`; R's default follows the session's locale.
{meth}`~cytepool.design.Design.check` reports problems such as aliased columns before
anything is fitted.

```{eval-rst}
.. automodule:: cytepool.design
```

```{eval-rst}
.. py:data:: INTERCEPT
   :module: cytepool.design
   :value: '(Intercept)'

   The name of the intercept column of a model matrix, as R names it.
```

Column names and term labels write a variable name that is not syntactic in R between
backticks, as R does: a factor `cell type` gives columns such as `` `cell type`B ``,
and a contrast refers to them by the same names.

```{eval-rst}
.. autofunction:: cytepool.design.formula.quote_name
```