clustTMB {clustTMB} | R Documentation |
Fit a finite mixture model using TMB
Description
Fit a finite mixture model using TMB
Usage
clustTMB(
response = NULL,
expertformula = ~1,
gatingformula = ~1,
expertdata = NULL,
gatingdata = NULL,
family = gaussian(link = "identity"),
Offset = NULL,
G = 2,
rr = list(spatial = NULL, temporal = NULL, random = NULL),
covariance.structure = NULL,
Start = list(),
Map = list(),
initialization.args = list(control = init.options()),
spatial.list = list(loc = NULL, mesh = NULL, init.range = list(gating.range = NULL,
expert.range = NULL)),
projection.dat = NULL,
control = run.options()
)
Arguments
response |
A numeric vector, matrix, or data frame of observations. When data are multivariate, rows correspond to observations and columns correspond to the multivariate response. |
expertformula |
Formula defining expert model. This formula corresponds to the covariates included in the response densities. Defaults to intercept only (~1) when no covariates are used. |
gatingformula |
Formula defining gating model. This formula corresponds to the covariates included in the mixing proportions (logistic regression). Defaults to intercept only (~1) when no covariates are used. When a random effects term is included in the gating network, this formula will be updated so that the intercept term is removed. |
expertdata |
Data frame containing expert model covariates. |
gatingdata |
Data frame containing gating model covariates. |
family |
Statistical distribution and link function of observations. |
Offset |
Constant in expertformula only used to offset density expectation. |
G |
Integer specifying the number of clusters. |
rr |
List specifying dimension of rank reduction in spatial, temporal, and/or random effects. Dimension must be smaller than the total dimension of the response. Rank reduction is applied only to the expertformula random effects. The rank reduction reduces the dimensionality of a correlated multivariate response to a smaller dimension independent response. When used, the covariance structure of the response is switched to 'Diagonal.' Defaults to NULL, no rank reduction. If rank reduction is used in conjunction with a random effect, that random effect must also be specified in the expert formula. Currently, rank reduction on temporal random effects is disabled. |
covariance.structure |
A character string specifying the covariance structure of the response using mclust naming scheme. See description of modelNames under ?Mclust for details. |
Start |
Set initial values for random effects parameters (fixed and random terms) |
Map |
Vector indicating parameter maps, see ? |
initialization.args |
A list consisting of initialization settings used to generate initial values.
control Calls
|
spatial.list |
List of data objects needed when fitting a spatial GMRF model |
projection.dat |
Spatial Points class of projection coordinates or Spatial Points Dataframe containing projection coordinates and projection covariates |
control |
List controlling whether models are run and whether standard errors are calculated. |
Value
list of objects from fitted model
Examples
data("faithful")
m1 <- clustTMB(response = faithful, covariance.structure = "VVV")
plot(faithful$eruptions, faithful$waiting, pch = 16, col = m1$report$classification + 1)