Create a list of inputs to EMLassemblyline functions (primarily for internal use only)

Source: R/template_arguments.R

Initialize the full list of possible inputs to EMLassemblyline functions (i.e. function arguments, metadata templates, and data objects). This enables bridging of upstream metadata and data sources (e.g. metabases, databases, Excel files, web forms, etc.).

template_arguments(
  path = NULL,
  data.path = NULL,
  data.table = NULL,
  other.entity = NULL,
  sep = NULL,
  empty = FALSE
)

Arguments

path

(character) Path to the directory containing EMLassemblyline metadata templates.

data.path

(character) Path to the directory containing data.table and other.entity data objects.

data.table

(character) File names of data tables. If more than one, then supply as a vector (e.g. data.table = c('decomp.csv', 'nitrogen.csv')).

other.entity

(character) File names of other entity data objects. If more than one, then supply as a vector (e.g. other.entity = c('ancillary_data.zip', 'processing_and_analysis.R')).

sep

(character) Data table field delimiter. Use this if this function fails to read your data.table.

empty

(logical) Initialize the output with a set of empty metadata templates? This option is useful when wanting to transfer metadata directly into the template files without having to call the templating functions.

Value

(named list) A list of all EMLassemblyline arguments, specified metadata templates and data objects.

Details

Character encoding in tabular metadata templates is converted to UTF-8 via enc2utf8(). Characters in TextType metadata templates are not yet converted. Note: This may lead to an inaccuracy and disconnect between values in the data objects and what is reported in the EML (e.g. a categorical variable listed in the EML may not be the same as it's corresponding value in the data object). To reduce the chance of this, warnings are issued if the input data object from which the metadata was extracted is not UTF-8 encoded.

Examples

# Output arguments and empty versions of metadata templates

r <- template_arguments(empty = TRUE)

# Output arguments, completed versions of metadata templates, and data objects

mydir <- file.copy(
  system.file('/examples/pkg_260', package = 'EMLassemblyline'), 
  tempdir(),
  recursive = TRUE)

setwd(paste0(tempdir(), "/pkg_260"))

r <- template_arguments(
  path = "./metadata_templates",
  data.path = "./data_objects",
  data.table = c("decomp.csv", "nitrogen.csv"),
  other.entity = c("ancillary_data.zip", "processing_and_analysis.R"))