In parsnip: A Common API to Modeling and Analysis Functions

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r descr_models("pls", "mixOmics")

Tuning Parameters

#| label: mixOmics-param-info
#| echo: false
defaults <- 
  tibble::tibble(parsnip = c("num_comp", "predictor_prop"),
                 default = c("2L",           "see below"))

param <-
  pls() |> 
  set_engine("mixOmics") |> 
  set_mode("regression") |> 
  make_parameter_list(defaults)

This model has r nrow(param) tuning parameters:

#| label: mixOmics-param-list
#| echo: false
#| results: asis
param$item

Translation from parsnip to the underlying model call (regression)

r uses_extension("pls", "mixOmics", "regression")

#| label: mixOmics-reg
library(plsmod)

pls(num_comp = integer(1), predictor_prop = double(1)) |>
  set_engine("mixOmics") |>
  set_mode("regression") |>
  translate()

[plsmod::pls_fit()] is a function that:

Determines the number of predictors in the data.
Adjusts num_comp if the value is larger than the number of factors.
Determines whether sparsity is required based on the value of predictor_prop.
Sets the keepX argument of mixOmics::spls() for sparse models.

Translation from parsnip to the underlying model call (classification)

r uses_extension("pls", "mixOmics", "classification")

#| label: mixOmics-cls
library(plsmod)

pls(num_comp = integer(1), predictor_prop = double(1)) |>
  set_engine("mixOmics") |>
  set_mode("classification") |>
  translate()

In this case, [plsmod::pls_fit()] has the same role as above but eventually targets mixOmics::plsda() or mixOmics::splsda().

Installing mixOmics

This package is available via the Bioconductor repository and is not accessible via CRAN. You can install using:

#| eval: false
  if (!require("remotes", quietly = TRUE)) {
    install.packages("remotes")
  }

  remotes::install_bioc("mixOmics")

Preprocessing requirements

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Case weights

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Prediction types

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parsnip:::get_from_env("pls_predict") |>
  dplyr::select(mode, type)

References

Rohart F and Gautier B and Singh A and Le Cao K-A (2017). "mixOmics: An R package for 'omics feature selection and multiple data integration." PLoS computational biology, 13(11), e1005752.