feemlist {albatross}

Create lists of FEEM objects

Description

Convert vectors of file names or objects from other packages (such as eemR or EEM) into flat named lists of feem objects.

Usage

  feemlist(x, ...)
  ## S3 method for class 'character'
feemlist(
    x, format, pattern = NULL, recursive = TRUE, ignore.case = FALSE,
    simplify.names = TRUE, progress = TRUE, ...
  )
  ## S3 method for class 'eemlist'
feemlist(x, ...)
  ## S3 method for class 'EEM'
feemlist(x, ...)

Arguments

x

A character vector containing names of files and directories to import using feem.

Alternatively, an eemlist object from the eemR package or an EEM object from the EEM package.

format

Corresponds to the format argument of feem. Currently, one format is assumed for all files to be imported.

Alternatively, can be a function that takes a path to a file and anything passed in ... and returns a feem object corresponding to the file. This is done to make it easier to import groups of files in formats not yet supported by feem itself.

pattern, recursive, ignore.case

These options are passed to list.files for directories encountered in x and can be used to e.g. only choose files with a given suffix in the name. Note the non-default value for the recursive option.

simplify.names

If TRUE (default), split resulting names by the path separator (/, also \ on Windows) and remove leading components that have the same value for all samples, but leave at least one component. See Details on how this is related to name generation.

progress

If true, show a text progress bar using txtProgressBar.

...

When importing files, remaining options are passed to feem or the import function passed in the format argument. Otherwise, no options are allowed.

Details

Names of x are preserved; if x is not named, names are assigned from the values of x itself, and so are empty names in partially-named x. Every directory in x is replaced with its contents (as returned by list.files), their names obtained by concatenating the name of the directory element with their paths inside the directory (with .Platform$file.sep as a separator). For example, when importing x = c('foo' = 'bar') with directory ‘bar’ containing ‘baz.txt’, resulting name would be ‘foo/baz.txt’.

When importing many files from the same directory, the simplify.names option is useful to avoid duplication in resulting names. For example, feemlist('.', simplify.names = FALSE) results in a list with all names starting with ./, while feemlist('foo/bar/baz', simplify.names = TRUE) (default) would shave off all three common path components and the separators.

Mixing files and directories in x will most likely not preserve the order of the elements.

Note: Please don't rely on the name generation behaving exactly as specified as it may be changed in the future versions.

When importing custom file formats, the format function should typically take the following form:

  function(filename, ...) {
    # read data from filename
    # take additional arguments passed from feemlist(...) if needed
    return(feem(data))
  }

Value

A flat named list of feem objects.

See Also

feem; the packages eemR and EEM.

Examples

  feemlist(
    system.file('extdata/pano2.txt', package = 'albatross'),
    'table', transpose = TRUE, na = 0
  )
  if (requireNamespace('eemR')) feemlist(eemR::eem_read(
    system.file('extdata/ho_aq.csv', package = 'albatross'),
    import_function='aqualog'
  ))
  if (requireNamespace('EEM')) feemlist(EEM::readEEM(
    system.file('extdata/ho_aq.dat', package = 'albatross')
  ))
  feemlist(
    system.file('extdata/custom.rds', package = 'albatross'),
    readRDS
  )