covmatrix.SSN2 {SSN2}

Create a covariance matrix

Description

Create a covariance matrix from a fitted model object.

Usage

## S3 method for class 'ssn_lm'
covmatrix(object, newdata, cov_type, ...)

## S3 method for class 'ssn_glm'
covmatrix(object, newdata, cov_type, ...)

Arguments

object

A fitted model object (e.g., ssn_lm() or ssn_glm()).

newdata

If omitted, the covariance matrix of the observed data is returned. If provided, newdata is a data frame or sf object that contains coordinate information required to construct the covariance between newdata and the observed data. If a data frame, newdata must contain variables that represent coordinates having the same name as the coordinates from the observed data used to fit object. If an sf object, coordinates are obtained from the geometry of newdata.

cov_type

The type of covariance matrix returned. If newdata is omitted, the n \times n covariance matrix of the observed data is returned, where n is the sample size used to fit object. If newdata is provided and cov_type is "pred.obs" (the default), the m \times n covariance matrix of the predicted and observed data is returned, where m is the number of observations in the prediction data. If newdata is provided and cov_type is "obs.pred", the n \times m covariance matrix of the observed and prediction data is returned. If newdata is provided and cov_type is "pred.pred", the m \times m covariance matrix of the prediction data is returned.

...

Other arguments. Not used (needed for generic consistency).

Value

A covariance matrix (see cov_type).

Examples

# Copy the mf04p .ssn data to a local directory and read it into R
# When modeling with your .ssn object, you will load it using the relevant
# path to the .ssn data on your machine
copy_lsn_to_temp()
temp_path <- paste0(tempdir(), "/MiddleFork04.ssn")
mf04p <- ssn_import(temp_path, predpts = "CapeHorn", overwrite = TRUE)

ssn_mod <- ssn_lm(
  formula = Summer_mn ~ ELEV_DEM,
  ssn.object = mf04p,
  tailup_type = "exponential",
  additive = "afvArea"
)
covmatrix(ssn_mod)
covmatrix(ssn_mod, "CapeHorn")