fibre: Fit a 'fibre'

In rdinnager/fibre: Fast Evolutionary Trait Modelling on Phylogenies using Branch Regression Models

Fit a fibre

Description

fibre() fits a model.

Usage

fibre(x, ...)

## Default S3 method:
fibre(x, ...)

## S3 method for class 'data.frame'
fibre(
  x,
  y,
  intercept = TRUE,
  engine = c("inla", "glmnet", "torch"),
  engine_options = list(),
  ncores = NULL,
  verbose = 0,
  fit = TRUE,
  ...
)

## S3 method for class 'matrix'
fibre(
  x,
  y,
  intercept = TRUE,
  engine = c("inla", "glmnet", "torch"),
  engine_options = list(),
  ncores = NULL,
  verbose = 0,
  fit = TRUE,
  ...
)

## S3 method for class 'formula'
fibre(
  formula,
  data,
  intercept = TRUE,
  family = "gaussian",
  engine = c("inla", "glmnet", "torch"),
  engine_options = list(),
  ncores = NULL,
  verbose = 0,
  fit = TRUE,
  ...
)

## S3 method for class 'recipe'
fibre(
  x,
  data,
  intercept = TRUE,
  engine = c("inla", "glmnet", "torch"),
  engine_options = list(),
  ncores = NULL,
  verbose = 0,
  fit = TRUE,
  ...
)

Arguments

x	Depending on the context: A data frame of predictors. A matrix of predictors. A recipe specifying a set of preprocessing steps created from recipes::recipe().
...	Not currently used, but required for extensibility.
y	When x is a data frame or matrix, y is the outcome specified as: A data frame with 1 numeric column. A matrix with 1 numeric column. A numeric vector.
intercept	A logical. Should an intercept be included in the model?
engine	A single character. The engine to use for fitting the model.
engine_options	A list of options to pass to the engine.
ncores	An integer. The number of cores to use for parallel processing.
verbose	An integer. The level of verbosity.
fit	A logical. Should the model be fit? If FALSE, the model is not fit and instead a list of data is returned that can be used to fit the model later. Useful for debugging or for fitting the model using a custom model design or currently unsupported engine.
formula	A formula specifying the outcome terms on the left-hand side, and the predictor terms on the right-hand side.
data	When a recipe or formula is used, data is specified as: A data frame containing both the predictors and the outcome.

Value

A fibre object.

Examples

predictors <- mtcars[, -1]
outcome <- mtcars[, 1]

# XY interface
#mod <- fibre(predictors, outcome)

# Formula interface
#mod2 <- fibre(mpg ~ ., mtcars)

# Recipes interface
#library(recipes)
#rec <- recipe(mpg ~ ., mtcars)
#rec <- step_log(rec, disp)
#mod3 <- fibre(rec, mtcars)

rdinnager/fibre documentation built on Dec. 14, 2024, 10:33 a.m.