Check brmsfit objects save as RDS files

increase_iterations checks brmsfit objects save as RDS files.

increase_iterations(
  path = ".",
  fits = list.files(path = path, pattern = ".RDS$", ignore.case = TRUE, full.names =
    TRUE),
  cores = 1,
  pb = TRUE,
  check.rhat = FALSE,
  increase = "2x",
  chains = 4,
  robust = TRUE,
  html = FALSE,
  verbose = TRUE
)

Arguments

path

Directory in which to look for .rds files.

fits

Name of the .rds files to be read. Optional.

cores

Number of cores to use for parallelization. Default is 1 (no parallelization).

pb

Logical to control if a progress bar is used. Default is TRUE.

check.rhat

NOT YET IMPLEMENTED.

increase

NOT YET IMPLEMENTED.

chains

NOT YET IMPLEMENTED.

robust

Logical to control the type of central tendency measure as in summary.brmsfit). NOT YET IMPLEMENTED.

html

Logical to control whether results are returned in html format. Useful for creating Rmd or quarto html reports. Is FALSE (default) the table is return as a data frame object. NOT YET IMPLEMENTED.

verbose

Logical to control if messages are printed into the console. NOT YET IMPLEMENTED.

Value

Returns a data frame with a summary of fitted models. Can be used to make sure all models were run with the same parameters (e.g. before combining models). If html = FALSE the function will return a data frame, otherwise it will print the estimates in a table in html format. The summary includes: prior, formula, number of iterations, number of chain, thinning, warmup, number of parameters, number of divergent transitions, number of rhats higher than 1.05, tail and bulk effective sample sizes and seed.

Details

The function reads all fits saved as rds files in the supplied directory and generates a table listing the parameters used to fit models.

References

Araya-Salas (2022), brmsish: miscellaneous functions to customize brms bayesian regression models. R package version 1.0.0.Paul-Christian Buerkner (2017). brms: An R Package for Bayesian Multilevel Models Using Stan. Journal of Statistical Software, 80(1), 1-28. doi:10.18637/jss.v080.i01

See also

extended_summary, combine_rds_fits

Author

Marcelo Araya-Salas marcelo.araya@ucr.ac.cr)

Examples

{
# create directory
dir.create(file.path(tempdir(), "rdss"))
# run 2 models
md1 <- brm(Petal.Length ~ Petal.Width + Species, iris, chains = 1,
iter = 500, file = file.path(tempdir(), "rdss", "md1"))

md2 <- brm(Petal.Length ~ Species, iris, chains = 1,
iter = 500, file = file.path(tempdir(), "rdss", "md2"))

# check fits
increase_iterations(path = file.path(tempdir(), "rdss"))
}
#> Warning: '/tmp/RtmpbELMrV/rdss' already exists
#> Compiling Stan program...
#> Error in .fun(model_code = .x1): Boost not found; call install.packages('BH')