# MixedModels v2.0.0

**URL:** <https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858>\
**Category:** Package Announcements\
**Tags:** announcement\
**Created:** [July 26, 2019, 5:10pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858 "2019-07-26T17:10:23Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![dmbates](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dmbates/32/44_2.png) [@dmbates](https://discourse.julialang.org/u/dmbates)\
**Post date:** [July 26, 2019, 5:10pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/1 "2019-07-26T17:10:23Z")

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I plan to release v"2.0.0" of the [`MixedModels` package](https://github.com/dmbates/MixedModels.jl) on Aug. 1. This version is compatible with `StatsModels` v"0.6.0" (a.k.a. Terms2.0), which allows for much greater flexibility in formula specification. Also, the internals have been rewritten extensively but that should not be obvious to users.

If you use the MixedModels package I would appreciate it if you could install and test the master branch to let me know of difficulties in advance of the release.

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**Author:** ![Christopher\_Fisher](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/christopher_fisher/32/26132_2.png) [@Christopher\_Fisher](https://discourse.julialang.org/u/Christopher_Fisher)\
**Post date:** [July 26, 2019, 6:20pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/2 "2019-07-26T18:20:58Z")

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I encountered some version conflicts with Distributions when I tried to switch to master:

```julia
(v1.1) pkg> add MixedModels #master
  Updating git-repo `https://github.com/dmbates/MixedModels.jl.git`
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package Distributions [31c24e10]:
 Distributions [31c24e10] log:
 ├─possible versions are: [0.1.0-0.1.4, 0.2.0-0.2.13, 0.3.0, 0.6.4-0.6.7, 0.7.0-0.7.6, 0.8.0-0.8.10, 0.9.0, 0.10.0-0.10.2, 0.11.0-0.11.1, 0.12.0-0.12.5, 0.13.0, 0.14.0-0.14.2, 0.15.0, 0.16.0-0.16.4, 0.17.0, 0.18.0, 0.19.1-0.19.2, 0.20.0, 0.21.0] or uninstalled
 ├─restricted to versions [0.11.0-0.11, 0.12.0-0.12, 0.13.0-0.13, 0.14.0-0.14, 0.15.0-0.15, 0.16.0-0.16, 0.17.0-0.17, 0.18.0-0.18, 0.19.0-0.19, 0.20.0-0.20] by MixedModels [ff71e718], leaving only versions [0.11.0-0.11.1, 0.12.0-0.12.5, 0.13.0, 0.14.0-0.14.2, 0.15.0, 0.16.0-0.16.4, 0.17.0, 0.18.0, 0.19.1-0.19.2, 0.20.0]
 │ └─MixedModels [ff71e718] log:
 │ ├─possible versions are: 2.0.0 or uninstalled
 │ └─MixedModels [ff71e718] is fixed to version 2.0.0
 └─restricted to versions 0.21.0 by an explicit requirement — no versions left

(v1.1) pkg> st Distributions
    Status `~/.julia/environments/v1.1/Project.toml`
  [31c24e10] Distributions v0.21.0
  [1fd47b50] QuadGK v2.1.0
  [2913bbd2] StatsBase v0.31.0
  [4c63d2b9] StatsFuns v0.8.0

```

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**Author:** ![dmbates](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dmbates/32/44_2.png) [@dmbates](https://discourse.julialang.org/u/dmbates)\
**Post date:** [July 26, 2019, 6:46pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/3 "2019-07-26T18:46:09Z")

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Thanks for the report. The `Project.toml` file for `MixedModels#master` allows up to v"0.20" of `Distributions` and I have just pushed a commit to allow v"0.21" but on my systems I still have `Distributions` at v"0.19.2".

It looks as if `MixedModels` depends on some other package that restricts the version of `Distributions`. Can anyone suggest how I would determine the reverse dependencies of `Distributions` and intersect that with the direct and implied dependencies of `MixedModels`.

As one might expect, I only use `Distributions` in one place and that usage is for a call that has been part of the package since its inception.

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**Author:** ![Nosferican](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nosferican/32/9275_2.png) [@Nosferican](https://discourse.julialang.org/u/Nosferican)\
**Post date:** [July 28, 2019, 9:45pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/4 "2019-07-28T21:45:38Z")

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Will the

```julia
fit(LinearMixedModel,
    @formula(Y ~ 1 + A + B + (1|G)),
    data)

```

syntax be supported in MixedModels `v2.0.0` or just the

```julia
fit!(LinearMixedModel(@formula(Y ~ 1 + A + B + (1|G)),
                      data))

```

syntax?

On that note, it seems the ability to pass contrasts has been removed on master.

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**Author:** ![dmbates](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dmbates/32/44_2.png) [@dmbates](https://discourse.julialang.org/u/dmbates)\
**Post date:** [July 29, 2019, 3:25pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/5 "2019-07-29T15:25:57Z")

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The reason I prefer the `fit!(LinearMixedModel(@formula(...), ...)` form is because there are arguments to the `fit!` method that are don’t apply to the model construction. Things like `verbose`, `maxiter`, …

Also the user can modify the form of the model between the time that it is constructed and its being `fit!`. For a `LinearMixedModel` the user can switch to REML estimation. For a `GeneralizedLinearMixedModel`, `nAGQ`, the number of quadrature points in the adaptive Gauss-Hermite evaluation can be changed.

In the vanilla case, it seems to me that there is little overhead in writing `fit!(LinearMixedModel(@formula(...), ...)` compared to `fit(LinearMixedModel, @formula(...), ...)`, but I will admit that I sometimes botch the first form myself by typing a comma after `LinearMixedModel`.

It probably wouldn’t be a big deal to allow the `fit(LinearMixedModel, @formula(...), ...)` form as an alternative in the vanilla case. Do you think it is worthwhile?

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**Author:** ![Nosferican](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nosferican/32/9275_2.png) [@Nosferican](https://discourse.julialang.org/u/Nosferican)\
**Post date:** [July 29, 2019, 3:41pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/6 "2019-07-29T15:41:28Z")

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I do agree that it is nice to separate arguments that are part of the model being created from those used in the fitting process from a design approach. However, I think there shouldn’t be ambiguity among arguments through a `fit` method. Since the arguments are passed as keyword arguments the `fit` method should easily pass the model builder arguments and fitting process without issues. For users, it might be easier to not have to worry about determining if in one implementation an argument is considered part of the model or of the fitting process which may vary depending on the implementation and internals. I tend to favor smart/robust which might take a bit more logic from the developer side, but make it closer to fool-proof for end-users.

The other point which makes the `fit` method very nice is that it allows for a seamless interface with other packages. For example, a package may decide to use one model type based on features of the `Formula`, but if one implementation only provides `fit!` it requires a more elaborate handling.

Lastly, in case only `fit!` is provided, the `fit` method should throw the default no hasn’t been implemented for the type exception rather than the current error behavior.

Disclosure, losing the `fit` method would force me to update the code in Bioequivalence.jl so I would rather just handle it at the MixedModels level for the next release. 🙂

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**Author:** ![Juan](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/juan/32/7657_2.png) [@Juan](https://discourse.julialang.org/u/Juan)\
**Post date:** [July 29, 2019, 7:43pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/7 "2019-07-29T19:43:29Z")

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Any changes related with the ability to manage datasets larger than the RAM memory?

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**Author:** ![Nosferican](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nosferican/32/9275_2.png) [@Nosferican](https://discourse.julialang.org/u/Nosferican)\
**Post date:** [July 29, 2019, 8:16pm UTC](https://discourse.julialang.org/t/mixedmodels-v2-0-0/26858/8 "2019-07-29T20:16:09Z")

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Popular request at JuliaCon for the whole stats ecosystem… I don’t think anything has happened just yet, but we are well aware of the need…