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hib_fit_lme4: Fit an lme4 style mixed-effects model

Source: R/hib_fit_lme4.R
hib_fit_lme4.Rd

This function fits an lme4 model using the supplied database, formula and other function arguments tuning the model fitting process.

Usage

hib_fit_lme4(
  obj,
  form,
  family = stats::gaussian,
  REML = TRUE,
  calc_CIs = NULL,
  optimise_ranefs = FALSE,
  model_dredge = FALSE,
  model_average = FALSE,
  weight_specs = list(weights = NULL, weight_type = NULL),
  scale_specs = list(covars_to_scale = NULL, scale_func = NULL),
  relevel_specs = c(NULL),
  ...
)

Arguments

obj

A HibDatabase object, or a list of databases.

form

Model formula in the style of lme4 - including fixed and random effects.

family

A family function, e.g. gaussian, poisson - as allowed by lme4. Dafault is 'gaussian'.

REML

A logical - if using a gaussian family, should the model be fitted using restricted maximum likelihood (REML, T) or maximum likelihood (F) - as in lme4::lmer().

calc_CIs

An indication of whether fixed effect confidence intervals (95%) should be calculated or not, and if so how - one of NULL, "Wald", "profile", "boot".

optimise_ranefs

Not currently applicable - future dev

model_dredge

Not currently applicable - future dev

model_average

Not currently applicable - future dev

weight_specs

A named list containing "weights" and "weight_type".

  • weights: a numeric vector containing the relative weights to assign to each dataset/site, should sum to 1.

  • weight_type: a character, specifying either "dataset" or "site" - i.e. should the weights argument assign relative weights to whole datasets, or for sites in each dataset.

Only applicable if a list of HibDatabases are provided.
The length of 'weights' should be equal to the number of HibDatabases.

scale_specs

A named list containing "covars_to_scale" and "scale_func".

  • covars_to_scale is a character vector of numeric covariates that should be scaled prior to modelling.

  • scale_func is a function that will be used to scale the specified covariates - if NULL, base::scale() will be used.

relevel_specs

A vector where each item is: "<covar_to_relevel_name>" = "<base_level>".

...

Any other named arguments that can be passed to lme4::lmer()/lme4::glmer(), e.g., na.action

Value

HibModelLME4

Details

This function takes the supplied database object (and various other arguments), fits the specified model and returns a HibModelLME4 object.

References

  • Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48. doi:10.18637/jss.v067.i01.

See also

HibModelLME4 lmer glmer

Examples

if (FALSE) { # \dontrun{
  mod <- hib_fit_lme4(obj, y ~ x + ( 1 | a ), ...)
} # }