read_tables: Read data tables of a data package

In kzollove/hymetDP: Tools to Create, Use, and Convert hymetDP data

Read data tables of a data package

Description

Read data tables of a data package from the EML metadata.

Usage

read_tables(
  eml,
  strip.white = FALSE,
  na.strings = NULL,
  convert.missing.value = NULL,
  add.units = FALSE,
  table.names = NULL
)

Arguments

eml	(xml_document, xml_node) EML metadata returned from read_eml().
strip.white	(logical) Strips leading and trailing whitespaces of unquoted fields. Default if FALSE.
na.strings	(character) Strings to be interpreted as NA. Setting na.strings = "" converts "" to NA. By default, blank strings "" are read as is.
convert.missing.value	(logical) Converts all missing value codes specified in eml (e.g. "-99999", "NaN", "Not measured") to NA. Missing value codes vary across data packages and converting to a consistent form recognized by R makes downstream use simpler. However, care must be exercised when using this argument. The author of a dataset described by eml may have defined "missing value code" to mean something different than you expect (e.g. "below detection limit") therefore reviewing the authors missing value code definitions is a good idea. Default is FALSE.
add.units	(logical) If TRUE, a variable's unit of measurement will be added to the table in a separate column with a column name of the form: <unit>_<variable_name>. This argument is useful when gathering variables into a long (attribute-value) table.
table.names	(character) Character vector of one or more table names (<objectName> from EML) to selectively download tables.

Details

This function uses data.table::fread() and uses default argument values if the EML based values return an error.

Default settings preserve the form the data were originally published in.

Value

(list) List of named data frames

Examples

## Not run: 
eml <- read_metadata('knb-lter-mcm.9003.11')

tables <- read_tables(
  eml = eml,
  strip.white = TRUE,
  na.strings = "",
  convert.missing.value = TRUE,
  add.units = TRUE)


## End(Not run)

kzollove/hymetDP documentation built on Nov. 22, 2022, 10:41 p.m.