pemlm-class: PEM Linear Model Interface

In guenardg/MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps

PEM Linear Model Interface

Description

An interface to estimate a linear model

Usage

pemlm(formula, data, pem, ..., contrasts = NULL)

## S3 method for class 'pemlm'
print(x, ...)

## S3 method for class 'pemlm'
summary(object, ...)

## S3 method for class 'pemlm'
anova(object, ...)

## S3 method for class 'pemlm'
predict(
  object,
  newdata = data.frame(row.names = rownames(newloc)),
  newloc,
  se.fit = FALSE,
  interval = c("none", "confidence", "prediction"),
  level = 0.95,
  ...
)

Arguments

formula	An object of class "formula" (or one that can be coerced to that class): a symbolic description of the model to be fitted. (see 'details' in lm for further details on model specification.
data	An optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which pemlm is called.
pem	A PEM-class object.
...	Additional arguments to be passed to the low level regression fitting functions.
contrasts	An optional list. See the contrasts.arg of model.matrix.default.
x, object	A pemlm-class object.
newdata	An optional data frame containing auxiliary traits used for making predictions.
newloc	A data frame containing the graph locations of species targeted for making predictions.
se.fit	A logical specifying whether to return standard errors (default: FALSE).
interval	One of "none", "confidence", or "prediction") specifying the type of interval associated with the predictions.
level	Tolerance/confidence level (default: 0.95).

Format

A pemlm-class object contains:

auxModel

A lm-class object.

resetPEM

A function ...

getPEM

A function ...

aic

A function ...

getIncluded

A function ...

getCandidate

A function ...

scanCandidate

A function ...

forward

A function ...

promote

A function ...

pemModel

A function ...

Details

...

Value

pemlm

A pemlm-class object.

print.pemlm

NULL (invisibly).

summary.pemlm

A summary.lm-class object.

anova.pemlm

An anova-class data frame.

predict.pemlm

...

Functions

• pemlm(): PEM Linear Model

  Calculate a PEM-based linear model for estimating trait values.

• print(pemlm): Print PEM Linear Model

  A print method for pemlm-class objects.

• summary(pemlm): Summarize pemlm Model

  A summary method for pemlm-class objects.

• anova(pemlm): Anova of a pemlm Model

  An anova method for pemlm-class objects.

• predict(pemlm): Predict Trait Values

  A predict method for pemlm-class objects.

Author(s)

Guillaume Guénard [aut, cre] (<https://orcid.org/0000-0003-0761-3072>), Pierre Legendre [ctb] (<https://orcid.org/0000-0002-3838-3305>) Maintainer: Guillaume Guénard <[e-mail]>

References

Guénard, G., Legendre, P., and Peres-Neto, P. 2013. Phylogenetic eigenvector maps: a framework to model and predict species traits. Methods in Ecology and Evolution 4: 1120-1131

Examples

## Example here...

guenardg/MPSEM documentation built on April 14, 2025, 3:53 p.m.