# \[Breaking Change\] Intercept is now optional in regression and SKAT

**URL:** <https://discuss.hail.is/t/breaking-change-intercept-is-now-optional-in-regression-and-skat/597>\
**Category:** Updates\
**Created:** [August 6, 2018, 1:44pm UTC](https://discuss.hail.is/t/breaking-change-intercept-is-now-optional-in-regression-and-skat/597 "2018-08-06T13:44:00Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![jbloom](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/jbloom/32/109_2.png) [@jbloom](https://discuss.hail.is/u/jbloom)\
**Post date:** [August 6, 2018, 1:44pm UTC](https://discuss.hail.is/t/breaking-change-intercept-is-now-optional-in-regression-and-skat/597/1 "2018-08-06T13:44:01Z")

</div>

To give users more control, we’ve changed inclusion of an intercept from implicit to explicit in linear regression, logistic regression, and SKAT. Consider the linear regression model

```auto
y = b*x + b0 + b1*c1 + b2*c2 + e

```

where we are interested the effect size `b` on `x` per row of a matrix table `mt`, and `b0` represents an intercept.

**BEFORE** the intercept was implicitly added so you would write:

```auto
hl.linear_regression(y=mt.y, x=mt.x, covariates=[mt.c1, mt.c2]).

```

**NOW** the intercept must be included explicitly if desired so you should write:

```auto
hl.linear_regression(y=mt.y, x=mt.x, covariates=[1.0, mt.c1, mt.c2]).

```

Note that `1.0` is just a numeric expression (not special syntax) corresponding to a covariate that is `1.0` for every sample. This is equivalent to the model above, thought of as:

```auto
y = b*x + b0*1.0 + b1*c1 + b2*c2 + e

```

In sum: to get the same behavior as before, just add the covariate `1.0`.

**WARNING** : The first command will still run but give different results, since it now corresponds to the model without intercept:

```auto
y = b*x + b1*c1 + b2*c2 + e.

```

As another example, now simple linear regression

```auto
y = b*x + b_0 + e

```

corresponds to

```auto
hl.linear_regression(y=mt.y, x=mt.x, covariates=[1.0]).

```

We’ve also removed the empty default value for `covariates`, so to do even simpler linear regression (not even an intercept!)

```auto
y = b*x + e

```

explicitly write the empty list `[]` in

```auto
hl.linear_regression(y=mt.y, x=mt.x, covariates=[]).

```

These changes also makes the regression interface more consistent with the [linreg aggregator](https://hail.is/docs/devel/aggregators.html#hail.expr.aggregators.linreg) and LinearMixedModel class.