Package 'MRFtools'

Convert a MRF penalty object to a matrix

Description

Convert a MRF penalty object to a matrix

Usage

## S3 method for class 'mrf_penalty'
as.matrix(x, ...)

Arguments

x	an object inheriting from class "mrf_penalty"
...	arguments passed to other methods

Examples

p <- mrf_penalty(1:10)
as.matrix(p)

---

Extract configuration details of an MRF penalty

Description

Extract configuration details of an MRF penalty

Usage

get_config(penalty)

Arguments

penalty

an object of class "mrf_penalty"

Value

An object of class "mrf_config", a list.

---

Extract MRF node labels from an MRF penalty

Description

Extract MRF node labels from an MRF penalty

Usage

get_labels(penalty)

Arguments

penalty

an object of class "mrf_penalty"

---

Extract a fitted MRF

Description

Extract a fitted MRF

Usage

get_mrf(object, ...)

## S3 method for class 'bam'
get_mrf(object, ...)

## S3 method for class 'gamm'
get_mrf(object, ...)

## S3 method for class 'list'
get_mrf(object, ...)

## S3 method for class 'gam'
get_mrf(object, term, ...)

Arguments

object	An object from which to extract the fitted MRF. Currently only for objects of classes gam, bam, and gamm, and GAMMs fitted by gamm4::gamm4().
...	Arguments passed to other methods.
term	character; the MRF term to extract. Can be a partial match to a term, which is matched against the smooth label.

Value

A object representing the fitted MRF

---

Extract a MRF penalty matrix

Description

Extract a MRF penalty matrix

Usage

get_penalty(penalty, ...)

## S3 method for class 'mrf_penalty'
get_penalty(penalty, ...)

Arguments

penalty	an R object from which to extract the MRF penalty matrix.
...	arguments passed to other methods.

Value

A penalty matrix of class "matrix".

---

Extract the type of MRF from the penalty

Description

Extract the type of MRF from the penalty

Usage

get_type(object)

## S3 method for class 'mrf_penalty'
get_type(object)

## S3 method for class 'mrf_config'
get_type(object)

Arguments

object

an object of class "mrf_penalty" or "mrf_config".

Value

A length 1 character vector containing the type of MRF penalty.

---

Markov Random Field Penalty

Description

Markov Random Field Penalty

Usage

mrf_penalty(object, ...)

Arguments

object	an R object to create the MRF penalty from.
...	arguments passed to other methods.

---

MRF penalty from a dendrogram

Description

MRF penalty from a dendrogram

Usage

## S3 method for class 'dendrogram'
mrf_penalty(object, node_labels = NULL, add_delta = FALSE, ...)

Arguments

object	an R object to create the MRF penalty from.
node_labels	character; a vector of alternative labels for the levels of the factor.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
...	arguments passed to other methods.

---

Fully connected graph and random effect MRF penalties from a factor

Description

Fully connected graph and random effect MRF penalties from a factor

Usage

## S3 method for class 'factor'
mrf_penalty(
  object,
  type = c("full", "individual"),
  node_labels = NULL,
  add_delta = FALSE,
  ...
)

Arguments

object	an R object to create the MRF penalty from.
type	character; one of "full" or "individual" indicating if a fully connected graph ("full") or a random effect (random intercepts; "individual") penalty is created.
node_labels	character; a vector of alternative labels for the levels of the factor.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
...	arguments passed to other methods.

Examples

# a factor
fv <- factor(letters[1:10])

# create the MRF penalty for a fully connected graph
p <- mrf_penalty(fv, type = "full")
p
as.matrix(p)

# create the MRF penalty equivalent of random effects
p <- mrf_penalty(fv, type = "individual")
p
as.matrix(p)

---

MRF penalty from a hclust object

Description

MRF penalty from a hclust object

Usage

## S3 method for class 'hclust'
mrf_penalty(object, ...)

Arguments

object	an R object to create the MRF penalty from.
...	arguments passed to other methods.

---

First-order random walk MRF penalty from a numeric vector

Description

First-order random walk MRF penalty from a numeric vector

Usage

## S3 method for class 'numeric'
mrf_penalty(
  object,
  type = c("linear", "cyclic"),
  node_labels = NULL,
  add_delta = FALSE,
  end_points = NULL,
  ...
)

Arguments

object	an R object to create the MRF penalty from.
type	character; one of "linear" or "cyclic" indicating if the observations form a cyclic series or not.
node_labels	character; a vector of alternative labels for the levels of the factor.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
end_points	numeric; an optional vector of length 2 providing the end points of the period of cycle.
...	arguments passed to other methods.

Examples

# linear
p <- mrf_penalty(1:10)
as.matrix(p)

# cyclic
p <- mrf_penalty(1:10, type = "cyclic")
as.matrix(p)

# cyclic with user end points
p <- mrf_penalty(1:10, type = "cyclic", end_points = c(0,11))
as.matrix(p)

---

MRF penalty from a phylogeny

Description

MRF penalty from a phylogeny

Usage

## S3 method for class 'phylo'
mrf_penalty(object, node_labels = NULL, add_delta = FALSE, eps = 0, ...)

Arguments

object	an R object to create the MRF penalty from.
node_labels	character; a vector of alternative labels for the levels of the factor.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
eps	A value to add to the variance-covariance matrix diagonal to make it positive definite
...	arguments passed to other methods.

---

MRF penalty from polygon or multi-polygon simple features

Description

MRF penalty from polygon or multi-polygon simple features

Usage

## S3 method for class 'sf'
mrf_penalty(object, node_labels = NULL, buffer = NULL, add_delta = FALSE, ...)

Arguments

object	an R object to create the MRF penalty from.
node_labels	character; a vector of alternative labels for the levels of the factor.
buffer	numeric; buffer distance for all or for individual elements of the geometry. See argument dist in sf::st_buffer for details.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
...	arguments passed to other methods.

---

MRF penalty from a SpatialPolygons

Description

MRF penalty from a SpatialPolygons

Usage

## S3 method for class 'SpatialPolygons'
mrf_penalty(object, node_labels = NULL, buffer = NULL, add_delta = FALSE, ...)

Arguments

object	an R object to create the MRF penalty from.
node_labels	character; a vector of alternative labels for the levels of the factor.
buffer	numeric; buffer distance for all or for individual elements of the geometry. See argument dist in sf::st_buffer for details.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
...	arguments passed to other methods.

---

MRF penalty from a SpatialPoylgonsDataFrame

Description

MRF penalty from a SpatialPoylgonsDataFrame

Usage

## S3 method for class 'SpatialPolygonsDataFrame'
mrf_penalty(object, node_labels = NULL, buffer = NULL, add_delta = FALSE, ...)

Arguments

object	an R object to create the MRF penalty from.
node_labels	character; a vector of alternative labels for the levels of the factor.
buffer	numeric; buffer distance for all or for individual elements of the geometry. See argument dist in sf::st_buffer for details.
add_delta	numeric or logical; either the numeric value to add to the diagonal of the MRF penalty matrix, or a logical value indicating if such an adjustment should be made. The default is to not alter the diagonal of the penalty matrix.
...	arguments passed to other methods.

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