iso_get_all_data: Aggregate all isofiles data

In isoreader: Read Stable Isotope Data Files

Description

This function aggregates all isofiles data and returns it in a large data frame with nested columns for each type of information (file_info, raw_data, etc.). For targeted retrieval of specific data iso_get_raw_data, iso_get_file_info, iso_get_vendor_data_table, etc. are much faster and easier to work with. This function is primarily useful for downstream processing pipelines that want to carry all information along. To unnest any of the specific data types (e.g. raw_data), make sure to filter first for the files that have this data type available (e.g. filter(has_raw_data)). Exclude specific types of information by setting its include... parameter to NULL (Note: for historical reasons, setting it to FALSE will also include the information).

Usage

iso_get_all_data(
  iso_files,
  include_file_info = everything(),
  include_raw_data = everything(),
  include_standards = everything(),
  include_resistors = everything(),
  include_vendor_data_table = everything(),
  include_problems = NULL,
  gather = FALSE,
  with_explicit_units = with_units,
  with_units = FALSE,
  with_ratios = NULL,
  quiet = default(quiet)
)

Arguments

iso_files	collection of iso_file objects
include_file_info	which file information to include (see iso_get_file_info). Use c(...) to select multiple, supports all select syntax including renaming columns.
include_raw_data	which columns from the raw data to include. Use c(...) to select multiple columns, supports all select syntax including renaming columns. Includes all columns by default. Set to NULL to include no raw data.
include_standards	which columns from the standards info to include. Use c(...) to select multiple columns, supports all select syntax including renaming columns. By default, everything is included (both standards and ratios). To omit the ratios, change to select = file_id:reference. Set to NULL to include no standards info.
include_resistors	which columns from the resistors info to include. Use c(...) to select multiple columns, supports all select syntax including renaming columns. Includes all columns by default. Set to NULL to include no resistors info.
include_vendor_data_table	which columns from the vendor data table to include. Use c(...) to select multiple columns, supports all select syntax including renaming columns. Includes all columns by default. Set parameter with_explicit_units = TRUE to make column units explicit (keep in mind that this will require specific include_vendor_data_table column selections to reflect the column names including the units). Set to NULL to include no vendor data table.
include_problems	which columns from problems to include. Use c(...) to select multiple columns, supports all select syntax including renaming columns. Includes none of the read problems by default. Set to include_problems = everything() to include all columns.
gather	whether to gather raw data into long format (e.g. for ease of use in plotting). Not that the select parameter applies to the data columns BEFORE gathering.
with_explicit_units	whether to include units in the column headers of the returned data frame instead of the column data types (see iso_double_with_units). Note that any select conditions have to refer to the column names including the full units.
with_units	this parameter has been DEPRECATED with the introduction of unit-data types (see iso_double_with_units) and will be removed in future versions of isoreader. Please use with_explicit_units instead if you really want columns to have units explicitly in the column name. Alternatively, consider working with the new implicit unit system and convert vendor data tables as needed with iso_make_units_explicit and iso_make_units_implicit.
with_ratios	deprecated, please use the select parameter to explicitly include or exclude ratio columns
quiet	whether to display (quiet=FALSE) or silence (quiet = TRUE) information messages. Set parameter to overwrite global defaults for this function or set global defaults with calls to iso_turn_info_messages_on and iso_turn_info_messages_off

Value

data_frame with file_ids, file_types and nested data frames for each data type (file_info, raw_data, vendor_data_table, etc.)

See Also

Other data retrieval functions: iso_get_bgrd_data(), iso_get_file_info(), iso_get_raw_data(), iso_get_resistors(), iso_get_standards(), iso_get_vendor_data_table()

isoreader documentation built on Nov. 19, 2021, 1:07 a.m.