mlr3: Machine Learning in R - next generation

# mlr3 <img src="man/figures/logo.png" align="right" width = "120" />

Package website: [release](https://mlr3.mlr-org.com/) |
[dev](https://mlr3.mlr-org.com/dev/)

Efficient, object-oriented programming on the building blocks of machine
learning. Successor of [mlr](https://github.com/mlr-org/mlr).

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## Resources (for users and developers)

  - We *started* writing a [book](https://mlr3book.mlr-org.com/). This
    should be the central entry point to the package.
  - The [mlr-org website](https://mlr-org.com/) includes for example a
    [gallery](https://mlr-org.com/gallery.html) with case studies and a
    [blog](https://mlr-org.com/blog.html) (We are not the most frequent
    bloggers ;) )
  - [Reference manual](https://mlr3.mlr-org.com/reference/)
  - [FAQ](https://github.com/mlr-org/mlr3/wiki/FAQ)
  - Ask questions on [Stackoverflow (tag
    \#mlr3)](https://stackoverflow.com/questions/tagged/mlr3)
  - **Extension Learners**
      - Recommended core regression, classification, and survival
        learners are in
        [mlr3learners](https://github.com/mlr-org/mlr3learners)
      - All others are in
        [mlr3extralearners](https://github.com/mlr-org/mlr3extralearners)
      - Use the [learner search](https://mlr-org.com/learners.html) to
        get a simple overview
  - **Cheatsheets**
      - [Overview of cheatsheets](https://cheatsheets.mlr-org.com)
      - [mlr3](https://cheatsheets.mlr-org.com/mlr3.pdf)
      - [mlr3tuning](https://cheatsheets.mlr-org.com/mlr3tuning.pdf)
      - [mlr3pipelines](https://cheatsheets.mlr-org.com/mlr3pipelines.pdf)
  - **Videos**:
      - [useR2019 talk on
        mlr3](https://www.youtube.com/watch?v=wsP2hiFnDQs)
      - [useR2019 talk on mlr3pipelines and
        mlr3tuning](https://www.youtube.com/watch?v=gEW5RxkbQuQ)
      - [useR2020 tutorial on mlr3, mlr3tuning and
        mlr3pipelines](https://www.youtube.com/watch?v=T43hO2o_nZw)
      - [Recorded talk about mlr3spatiotempcv and mlr3spatial at
        OpenDataScience Europe Conference 2021 in Wageningen,
        NL](https://av.tib.eu/media/55271)
  - **Courses/Lectures**
      - The course [Introduction to Machine learning
        (I2ML)](https://slds-lmu.github.io/i2ml/) is a free and open
        flipped classroom course on the basics of machine learning.
        `mlr3` is used in the
        [demos](https://github.com/slds-lmu/lecture_i2ml/tree/master/code-demos-pdf)
        and
        [exercises](https://github.com/slds-lmu/lecture_i2ml/tree/master/exercises).
  - **Templates/Tutorials**
      - [mlr3-targets](https://github.com/mlr-org/mlr3-targets):
        Tutorial showcasing how to use {mlr3} with
        [targets](https://docs.ropensci.org/targets/) for reproducible
        ML workflow automation.
  - [List of extension packages](https://mlr-org.com/ecosystem.html)
  - [mlr-outreach](https://github.com/mlr-org/mlr-outreach) contains
    public talks and slides resources.
  - [Wiki](https://github.com/mlr-org/mlr3/wiki): Contains mainly
    information for developers.

## Installation

Install the last release from CRAN:

``` r
install.packages("mlr3")
```

Install the development version from GitHub:

``` r
remotes::install_github("mlr-org/mlr3")
```

If you want to get started with `mlr3`, we recommend installing the
[mlr3verse](https://mlr3verse.mlr-org.com/) meta-package which installs
`mlr3` and some of the most important extension packages:

``` r
install.packages("mlr3verse")
```

## Example

### Constructing Learners and Tasks

``` r
library(mlr3)

# create learning task
task_penguins = as_task_classif(species ~ ., data = palmerpenguins::penguins)
task_penguins
```

    ## <TaskClassif:palmerpenguins::penguins> (344 x 8)
    ## * Target: species
    ## * Properties: multiclass
    ## * Features (7):
    ##   - int (3): body_mass_g, flipper_length_mm, year
    ##   - dbl (2): bill_depth_mm, bill_length_mm
    ##   - fct (2): island, sex

``` r
# load learner and set hyperparameter
learner = lrn("classif.rpart", cp = .01)
```

### Basic train + predict

``` r
# train/test split
split = partition(task_penguins, ratio = 0.67)

# train the model
learner$train(task_penguins, split$train_set)

# predict data
prediction = learner$predict(task_penguins, split$test_set)

# calculate performance
prediction$confusion
```

    ##            truth
    ## response    Adelie Chinstrap Gentoo
    ##   Adelie       146         5      0
    ##   Chinstrap      6        63      1
    ##   Gentoo         0         0    123

``` r
measure = msr("classif.acc")
prediction$score(measure)
```

    ## classif.acc 
    ##   0.9651163

### Resample

``` r
# 3-fold cross validation
resampling = rsmp("cv", folds = 3L)

# run experiments
rr = resample(task_penguins, learner, resampling)

# access results
rr$score(measure)[, .(task_id, learner_id, iteration, classif.acc)]
```

    ##                     task_id    learner_id iteration classif.acc
    ## 1: palmerpenguins::penguins classif.rpart         1   0.9391304
    ## 2: palmerpenguins::penguins classif.rpart         2   0.9478261
    ## 3: palmerpenguins::penguins classif.rpart         3   0.9298246

``` r
rr$aggregate(measure)
```

    ## classif.acc 
    ##    0.938927

## Extension Packages

<a href="https://raw.githubusercontent.com/mlr-org/mlr3/main/man/figures/mlr3verse.svg?sanitize=true"><img src="man/figures/mlr3verse.svg" /></a>

Consult the
[wiki](https://github.com/mlr-org/mlr3/wiki/Extension-Packages) for
short descriptions and links to the respective repositories.

For beginners, we strongly recommend to install and load the
[mlr3verse](https://mlr3verse.mlr-org.com/) package for a better user
experience.

## Why a rewrite?

[mlr](https://github.com/mlr-org/mlr) was first released to
[CRAN](https://cran.r-project.org/package=mlr) in 2013. Its core design
and architecture date back even further. The addition of many features
has led to a [feature
creep](https://en.wikipedia.org/wiki/Feature_creep) which makes
[mlr](https://github.com/mlr-org/mlr) hard to maintain and hard to
extend. We also think that while mlr was nicely extensible in some parts
(learners, measures, etc.), other parts were less easy to extend from
the outside. Also, many helpful R libraries did not exist at the time
[mlr](https://github.com/mlr-org/mlr) was created, and their inclusion
would result in non-trivial API changes.

## Design principles

  - Only the basic building blocks for machine learning are implemented
    in this package.
  - Focus on computation here. No visualization or other stuff. That can
    go in extra packages.
  - Overcome the limitations of R’s [S3
    classes](https://adv-r.hadley.nz/s3.html) with the help of
    [R6](https://cran.r-project.org/package=R6).
  - Embrace [R6](https://cran.r-project.org/package=R6) for a clean
    OO-design, object state-changes and reference semantics. This might
    be less “traditional R”, but seems to fit `mlr` nicely.
  - Embrace
    [`data.table`](https://cran.r-project.org/package=data.table) for
    fast and convenient data frame computations.
  - Combine `data.table` and `R6`, for this we will make heavy use of
    list columns in data.tables.
  - Defensive programming and type safety. All user input is checked
    with [`checkmate`](https://cran.r-project.org/package=checkmate).
    Return types are documented, and mechanisms popular in base R which
    “simplify” the result unpredictably (e.g., `sapply()` or `drop`
    argument in `[.data.frame`) are avoided.
  - Be light on dependencies. `mlr3` requires the following packages at
    runtime:
      - [`parallelly`](https://cran.r-project.org/package=parallelly):
        Helper functions for parallelization. No extra recursive
        dependencies.
      - [`future.apply`](https://cran.r-project.org/package=future.apply):
        Resampling and benchmarking is parallelized with the
        [`future`](https://cran.r-project.org/package=future)
        abstraction interfacing many parallel backends.
      - [`backports`](https://cran.r-project.org/package=backports):
        Ensures backward compatibility with older R releases. Developed
        by members of the `mlr` team. No recursive dependencies.
      - [`checkmate`](https://cran.r-project.org/package=checkmate):
        Fast argument checks. Developed by members of the `mlr` team. No
        extra recursive dependencies.
      - [`mlr3misc`](https://cran.r-project.org/package=mlr3misc):
        Miscellaneous functions used in multiple mlr3 [extension
        packages](https://mlr-org.com/ecosystem.html). Developed by the
        `mlr` team.
      - [`paradox`](https://cran.r-project.org/package=paradox):
        Descriptions for parameters and parameter sets. Developed by the
        `mlr` team. No extra recursive dependencies.
      - [`R6`](https://cran.r-project.org/package=R6): Reference class
        objects. No recursive dependencies.
      - [`data.table`](https://cran.r-project.org/package=data.table):
        Extension of R’s `data.frame`. No recursive dependencies.
      - [`digest`](https://cran.r-project.org/package=digest) (via
        `mlr3misc`): Hash digests. No recursive dependencies.
      - [`uuid`](https://cran.r-project.org/package=uuid): Create unique
        string identifiers. No recursive dependencies.
      - [`lgr`](https://cran.r-project.org/package=lgr): Logging
        facility. No extra recursive dependencies.
      - [`mlr3measures`](https://cran.r-project.org/package=mlr3measures):
        Performance measures. No extra recursive dependencies.
      - [`mlbench`](https://cran.r-project.org/package=mlbench): A
        collection of machine learning data sets. No dependencies.
      - [`palmerpenguins`](https://cran.r-project.org/package=palmerpenguins):
        A classification data set about penguins, used on examples and
        provided as a toy task. No dependencies.
  - [Reflections](https://en.wikipedia.org/wiki/Reflection_%28computer_programming%29):
    Objects are queryable for properties and capabilities, allowing you
    to program on them.
  - Additional functionality that comes with extra dependencies:
      - To capture output, warnings and exceptions,
        [`evaluate`](https://cran.r-project.org/package=evaluate) and
        [`callr`](https://cran.r-project.org/package=callr) can be used.

## Contributing to mlr3

This R package is licensed under the
[LGPL-3](https://www.gnu.org/licenses/lgpl-3.0.en.html). If you
encounter problems using this software (lack of documentation,
misleading or wrong documentation, unexpected behavior, bugs, …) or just
want to suggest features, please open an issue in the [issue
tracker](https://github.com/mlr-org/mlr3/issues). Pull requests are
welcome and will be included at the discretion of the maintainers.

Please consult the [wiki](https://github.com/mlr-org/mlr3/wiki/) for a
[style guide](https://github.com/mlr-org/mlr3/wiki/Style-Guide), a
[roxygen guide](https://github.com/mlr-org/mlr3/wiki/Roxygen-Guide) and
a [pull request
guide](https://github.com/mlr-org/mlr3/wiki/PR-Guidelines).

## Citing mlr3

If you use mlr3, please cite our [JOSS
article](https://doi.org/10.21105/joss.01903):

    @Article{mlr3,
      title = {{mlr3}: A modern object-oriented machine learning framework in {R}},
      author = {Michel Lang and Martin Binder and Jakob Richter and Patrick Schratz and Florian Pfisterer and Stefan Coors and Quay Au and Giuseppe Casalicchio and Lars Kotthoff and Bernd Bischl},
      journal = {Journal of Open Source Software},
      year = {2019},
      month = {dec},
      doi = {10.21105/joss.01903},
      url = {https://joss.theoj.org/papers/10.21105/joss.01903},
    }
