inst/templates/run_EMLassemblyline.R

In EDIorg/EMLassemblyline: A tool kit for building EML metadata workflows

# This script executes an EMLassemblyline workflow.

# Initialize workspace --------------------------------------------------------

# Update EMLassemblyline and load

remotes::install_github("EDIorg/EMLassemblyline")
library(EMLassemblyline)

# Define paths for your metadata templates, data, and EML

path_templates <- ""
path_data <- ""
path_eml <- ""

# Create metadata templates ---------------------------------------------------

# Below is a list of boiler plate function calls for creating metadata templates.
# They are meant to be a reminder and save you a little time. Remove the 
# functions and arguments you don't need AND ... don't forget to read the docs! 
# E.g. ?template_core_metadata

# Create core templates (required for all data packages)

EMLassemblyline::template_core_metadata(
  path = path_templates,
  license = "",
  file.type = "")

# Create table attributes template (required when data tables are present)

EMLassemblyline::template_table_attributes(
  path = path_templates,
  data.path = path_data,
  data.table = c(""))

# Create categorical variables template (required when attributes templates
# contains variables with a "categorical" class)

EMLassemblyline::template_categorical_variables(
  path = path_templates, 
  data.path = path_data)

# Create geographic coverage (required when more than one geographic location
# is to be reported in the metadata).

EMLassemblyline::template_geographic_coverage(
  path = path_templates, 
  data.path = path_data, 
  data.table = "", 
  lat.col = "",
  lon.col = "",
  site.col = "")

# Create taxonomic coverage template (Not-required. Use this to report 
# taxonomic entities in the metadata)

remotes::install_github("EDIorg/taxonomyCleanr")
library(taxonomyCleanr)

taxonomyCleanr::view_taxa_authorities()

EMLassemblyline::template_taxonomic_coverage(
  path = path_templates, 
  data.path = path_data,
  taxa.table = "",
  taxa.col = "",
  taxa.name.type = "",
  taxa.authority = 3)

# Make EML from metadata templates --------------------------------------------

# Once all your metadata templates are complete call this function to create 
# the EML.

EMLassemblyline::make_eml(
  path = path_templates,
  data.path = path_data,
  eml.path = path_eml, 
  dataset.title = "", 
  temporal.coverage = c("YYYY-MM-DD", "YYYY-MM-DD"), 
  geographic.description = "", 
  geographic.coordinates = c("N", "E", "S", "W"), 
  maintenance.description = "", 
  data.table = c(""), 
  data.table.name = c(""),
  data.table.description = c(""),
  other.entity = c(""),
  other.entity.name = c(""),
  other.entity.description = c(""),
  user.id = "",
  user.domain = "", 
  package.id = "")