Package 'n2kupdate' reference manual

Title:	Auxiliary Functions to Update the n2kresult Database
Description:	The functions are useful to store the results from https:// github.com/inbo/n2kanalysis into a PostgreSQL database created with https:// github.com/inbo/n2kresult.
Authors:	Thierry Onkelinx [aut, cre] , Instituut voor Natuur en Bosonderzoek (INBO) [cph]
Maintainer:	Thierry Onkelinx <[email protected]>
License:	GPL-3
Version:	0.1.1
Built:	2024-10-04 15:19:58 UTC
Source:	https://github.com/inbo/n2kupdate

Convert all factors in a data.frame to characters

Description

Convert all factors in a data.frame to characters

Usage

character_df(x, ...)
character_df(x, ...)

Arguments

`x`	object to be coerced or tested.
`...`	further arguments passed to or from other methods.

connect to the unit test database

Description

connect to the unit test database

Usage

connect_ut_db(host = "localhost", dbname = "n2kunittest",
  user = "unittest_analysis", password = "unittest", port = 5432)
connect_ut_db(host = "localhost", dbname = "n2kunittest",
  user = "unittest_analysis", password = "unittest", port = 5432)

Arguments

`host`	the hostname of the database. Defaults to "localhost".
`dbname`	the name of the unit test database. Defaults to "n2kunittest".
`user`	the name of the unit test user. Defaults to "unittest_analysis".
`password`	the password for the user. Defaults to "unittest".
`port`	The port of host. Defaults to 5432.

The n2kAnalysisVersion class

Description

The n2kAnalysisVersion class

store source species in the database

Description

store source species in the database

Usage

store_analysis(analysis, model_set, analysis_version, analysis_relation,
  conn, hash, clean = TRUE)
store_analysis(analysis, model_set, analysis_version, analysis_relation,
  conn, hash, clean = TRUE)

Arguments

`analysis`	a data.frame with file_fingerprint, model_set_local_id, location_group, species_group, last_year, seed, analysis_version, analysis_date, status and status_fingerprint.
`model_set`	a data.frame with the model sets. Must have variables "local_id", "description", "first_year", "last_year" and "duration". The variable "long_description" is optional.
`analysis_version`	an n2kAnalysisVersion object. See `get_analysis_version`
`analysis_relation`	an optional data.frame with analysis and source_analysis. analysis contains the file_fingerprint of the current analysis. source_analysis contains the file_fingerprint of the parent analysis
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store analysis and dataset in the database

Description

store analysis and dataset in the database

Usage

store_analysis_dataset(analysis, model_set, analysis_version, dataset,
  analysis_dataset, clean = TRUE, hash, conn)
store_analysis_dataset(analysis, model_set, analysis_version, dataset,
  analysis_dataset, clean = TRUE, hash, conn)

Arguments

`analysis`	a data.frame with file_fingerprint, model_set_local_id, location_group, species_group, last_year, seed, analysis_version, analysis_date, status and status_fingerprint.
`model_set`	a data.frame with the model sets. Must have variables "local_id", "description", "first_year", "last_year" and "duration". The variable "long_description" is optional.
`analysis_version`	an n2kAnalysisVersion object. See `get_analysis_version`
`dataset`	a data.frame with names fingerprint, filename, datasource and import_date
`analysis_dataset`	A `data.frame` linking the `file_fingerprint` from `analysis` to the `fingerprint` from `dataset`.
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`hash`	the hash of the update session
`conn`	a DBIconnection

Store the analysis version in the database

Description

Store the analysis version in the database

Usage

store_analysis_version(analysis_version, hash, clean = TRUE, conn)
store_analysis_version(analysis_version, hash, clean = TRUE, conn)

Arguments

`analysis_version`	an n2kAnalysisVersion object. See `get_analysis_version`
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`conn`	a DBIconnection

Store anomaly

Description

Store anomaly

Usage

store_anomaly(anomaly, anomaly_type, parameter, hash, conn, clean = TRUE)
store_anomaly(anomaly, anomaly_type, parameter, hash, conn, clean = TRUE)

Arguments

`anomaly`	a data.frame with variables "anomaly_type_local_id", "datafield", "analyis" and "parameter_local_id".
`anomaly_type`	a data.frame with variables "local_id", "description" and "long_description". "long_description" is optional
`parameter`	a data.frame with parameters. Must contains the variables "description", "local_id", and "parent_parameter_local_id". Other variables are ignored.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store anomaly types

Description

Store anomaly types

Usage

store_anomaly_type(anomaly_type, hash, conn, clean = TRUE)
store_anomaly_type(anomaly_type, hash, conn, clean = TRUE)

Arguments

`anomaly_type`	a data.frame with variables "local_id", "description" and "long_description". "long_description" is optional
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store a datafield in the database

Description

store a datafield in the database

Usage

store_datafield(datafield, conn, hash, clean = TRUE)
store_datafield(datafield, conn, hash, clean = TRUE)

Arguments

`datafield`	a data.frame with datafield metadata. Must contain the variables local_id, datasource, table_name, primary_key and datafield_type. Other variables are ignored.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store a vector of datafield types

Description

Store a vector of datafield types

Usage

store_datafield_type(datafield_type, hash, conn, clean = TRUE)
store_datafield_type(datafield_type, hash, conn, clean = TRUE)

Arguments

`datafield_type`	the vector with datafield types.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store a dataset is the database

Description

Store a dataset is the database

Usage

store_dataset(dataset, conn, clean = TRUE, hash)
store_dataset(dataset, conn, clean = TRUE, hash)

Arguments

`dataset`	a data.frame with names fingerprint, filename, datasource and import_date
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`hash`	the hash of the update session

store a datasource in the database

Description

store a datasource in the database

Usage

store_datasource(datasource, conn, clean = TRUE, hash)
store_datasource(datasource, conn, clean = TRUE, hash)

Arguments

`datasource`	a data.frame with datasource metadata
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`hash`	the hash of the update session

Details

datasource must contain at least the variables description, datasource_type and connect_method.

Store a vector of datasource parameters

Description

Store a vector of datasource parameters

Usage

store_datasource_parameter(datasource_parameter, hash, conn,
  clean = TRUE)
store_datasource_parameter(datasource_parameter, hash, conn,
  clean = TRUE)

Arguments

`datasource_parameter`	the vector with datasource parameters.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store a vector of datasource types

Description

Store a vector of datasource types

Usage

store_datasource_type(datasource_type, hash, conn, clean = TRUE)
store_datasource_type(datasource_type, hash, conn, clean = TRUE)

Arguments

`datasource_type`	the vector with datasource types.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store language

Description

Store language

Usage

store_language(language, hash, conn, clean = TRUE)
store_language(language, hash, conn, clean = TRUE)

Arguments

`language`	the data.frame with language Must contains code and description. Other variables are ignored. code and description must have unique values.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store locations in the database

Description

store locations in the database

Usage

store_location(location, datafield, conn, hash, clean = TRUE)
store_location(location, datafield, conn, hash, clean = TRUE)

Arguments

`location`	a data.frame with location metadata. Must contain the following columns: local_id, description, parent_local_id, datafield_local_id and external_code. Other columns are ignored.
`datafield`	a data.frame with datafield metadata. Must contain the variables local_id, datasource, table_name, primary_key and datafield_type. Other variables are ignored.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Details

location must have variables local_id, description, parent_local_id, datafield_local_id and extranal_code. Other variables are ignored
datafield must have variables local_id, datasource, table_name, primary_key and datafield_type
all local_id variables must be unique within their data.frame
all values in location$datafield_local_id must exist in datafield$local_id
all values in location$parent_location must be either NA or exist in location$local_id

Store location groups

Description

Store location groups

Usage

store_location_group(location_group, hash, conn, clean = TRUE)
store_location_group(location_group, hash, conn, clean = TRUE)

Arguments

`location_group`	the data.frame with location groups. Must contains local_id, description and scheme. Other variables are ignored. local_id must have unique values.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store the link between locations and location groups in the database

Description

store the link between locations and location groups in the database

Usage

store_location_group_location(location_group_location, location_group,
  location, datafield, conn, hash, clean = TRUE)
store_location_group_location(location_group_location, location_group,
  location, datafield, conn, hash, clean = TRUE)

Arguments

`location_group_location`	a data.frame with the locations per location group. Must contain location_group_local_id and location_local_id. Other columns are ignored.
`location_group`	the data.frame with location groups. Must contains local_id, description and scheme. Other variables are ignored. local_id must have unique values.
`location`	a data.frame with location metadata. Must contain the following columns: local_id, description, parent_local_id, datafield_local_id and external_code. Other columns are ignored.
`datafield`	a data.frame with datafield metadata. Must contain the variables local_id, datasource, table_name, primary_key and datafield_type. Other variables are ignored.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Details

location_group_location must have variables location_local_id and location_group_local_id.
location_group must have variables local_id, description and scheme
location must have variables local_id, description, parent_local_id, datafield_local_id and extranal_code. Other variables are ignored
datafield must have variables local_id, datasource, table_name, primary_key and datafield_type
all local_id variables must be unique within their data.frame
all values in location$datafield_local_id must exist in datafield$local_id
all values in location$parent_location must be either NA or exist in location$local_id
all values in location_group_location$location_local_id must exist in location$local_id
all values in location_group_location$location_group_local_id must exist in location_group$local_id

Store model sets in the database

Description

Store model sets in the database

Usage

store_model_set(model_set, hash, clean = TRUE, conn)
store_model_set(model_set, hash, clean = TRUE, conn)

Arguments

`model_set`	a data.frame with the model sets. Must have variables "local_id", "description", "first_year", "last_year" and "duration". The variable "long_description" is optional.
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`conn`	a DBIconnection

Store model type in the database

Description

Store model type in the database

Usage

store_model_type(model_type, hash, clean = TRUE, conn)
store_model_type(model_type, hash, clean = TRUE, conn)

Arguments

`model_type`	a data.frame with the modeltypes. Must have a variable "description". The variable "long_description" is optional.
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`conn`	a DBIconnection

store an n2kImport object into the database

Description

store an n2kImport object into the database

Usage

store_n2kImport(object, conn, hash, clean = TRUE)
store_n2kImport(object, conn, hash, clean = TRUE)

Arguments

`object`	a `n2kImport-class` object
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store all models from an n2kManifest

Description

store all models from an n2kManifest

Usage

store_n2kManifest(manifest, base, project, conn, status = "converged",
  hash, clean = TRUE)
store_n2kManifest(manifest, base, project, conn, status = "converged",
  hash, clean = TRUE)

Arguments

`manifest`	a `n2kManifest-class`
`base`	the base location to read the model
`project`	will be a relative path within the base location
`conn`	a DBIconnection
`status`	the status of the objects to be imported
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

extract the results from an n2kModel and stored them

Description

extract the results from an n2kModel and stored them

Usage

store_n2kModel(x, conn, hash, clean = TRUE)
store_n2kModel(x, conn, hash, clean = TRUE)

Arguments

`x`	the n2kModel object
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store an n2kResult object into the database

Description

store an n2kResult object into the database

Usage

store_n2kResult(object, conn, hash, clean = TRUE)
store_n2kResult(object, conn, hash, clean = TRUE)

Arguments

`object`	a `n2kResult-class` object
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store a datafield in the database

Description

store a datafield in the database

Usage

store_observation(datafield, observation, location, parameter, conn, hash,
  clean = TRUE)
store_observation(datafield, observation, location, parameter, conn, hash,
  clean = TRUE)

Arguments

`datafield`	a data.frame with datafield metadata. Must contain the variables local_id, datasource, table_name, primary_key and datafield_type. Other variables are ignored.
`observation`	a data.frame with observation metadata. Must contain the variables local_id, datafield_local_id, external_code, location_local_id, year and parameter_local_id. Other variables are ignored. datafield_local_id, external_code and parameter_local_id can be missing.
`location`	a data.frame with location metadata. Must contain the following columns: local_id, description, parent_local_id, datafield_local_id and external_code. Other columns are ignored.
`parameter`	a data.frame with parameters. Must contains the variables "description", "local_id", and "parent_parameter_local_id". Other variables are ignored.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store parameters

Description

Store parameters

Usage

store_parameter(parameter, hash, conn, clean = TRUE)
store_parameter(parameter, hash, conn, clean = TRUE)

Arguments

`parameter`	a data.frame with parameters. Must contains the variables "description", "local_id", and "parent_parameter_local_id". Other variables are ignored.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store a vector of schemes

Description

Store a vector of schemes

Usage

store_scheme(scheme, hash, conn, clean = TRUE)
store_scheme(scheme, hash, conn, clean = TRUE)

Arguments

`scheme`	the vector with scheme descriptions.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store source species in the database

Description

store source species in the database

Usage

store_source_species(source_species, datafield, conn, hash, clean = TRUE)
store_source_species(source_species, datafield, conn, hash, clean = TRUE)

Arguments

`source_species`	a data.frame with source species metadata. Must contain local_id, description, datafield_local_id and extrenal_code. Other variables are ignored.
`datafield`	a data.frame with datafield metadata. Must contain variables local_id, datasource, table_name, primary_key and datafield_type.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store source species in the database

Description

store source species in the database

Usage

store_source_species_species(species, language, source_species,
  source_species_species, datafield, conn, hash, clean = TRUE)
store_source_species_species(species, language, source_species,
  source_species_species, datafield, conn, hash, clean = TRUE)

Arguments

`species`	a data.frame with species metadata. Must contain at least 'local_id', 'scientific_name' and 'nbn_key'. Other variable names must match the values in 'language$code'.
`language`	the data.frame with language Must contains code and description. Other variables are ignored. code and description must have unique values.
`source_species`	a data.frame with source species metadata. Must contain local_id, description, datafield_local_id and extrenal_code. Other variables are ignored.
`source_species_species`	as data.frame linking the local species id to the local source_species id. Must contain species_local_id and source_species_local_id. Other variables are ignored.
`datafield`	a data.frame with datafield metadata. Must contain variables local_id, datasource, table_name, primary_key and datafield_type.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store species in the database

Description

store species in the database

Usage

store_species(species, language, conn, hash, clean = TRUE)
store_species(species, language, conn, hash, clean = TRUE)

Arguments

`species`	a data.frame with species metadata. Must contain at least 'local_id', 'scientific_name' and 'nbn_key'. Other variable names must match the values in 'language$code'.
`language`	the data.frame with language Must contains code and description. Other variables are ignored. code and description must have unique values.
`conn`	a DBIconnection
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store species groups

Description

Store species groups

Usage

store_species_group(species_group, hash, conn, clean = TRUE)
store_species_group(species_group, hash, conn, clean = TRUE)

Arguments

`species_group`	the data.frame with species groups. Must contains local_id, description and scheme. Other variables are ignored. local_id must have unique values.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

store all species related information in the database

Description

store all species related information in the database

Usage

store_species_group_species(species, language, source_species,
  source_species_species, datafield, species_group, species_group_species,
  hash, conn, clean = TRUE)
store_species_group_species(species, language, source_species,
  source_species_species, datafield, species_group, species_group_species,
  hash, conn, clean = TRUE)

Arguments

`species`	a data.frame with species metadata. Must contain at least 'local_id', 'scientific_name' and 'nbn_key'. Other variable names must match the values in 'language$code'.
`language`	the data.frame with language Must contains code and description. Other variables are ignored. code and description must have unique values.
`source_species`	a data.frame with source species metadata. Must contain local_id, description, datafield_local_id and extrenal_code. Other variables are ignored.
`source_species_species`	as data.frame linking the local species id to the local source_species id. Must contain species_local_id and source_species_local_id. Other variables are ignored.
`datafield`	a data.frame with datafield metadata. Must contain variables local_id, datasource, table_name, primary_key and datafield_type.
`species_group`	the data.frame with species groups. Must contains local_id, description and scheme. Other variables are ignored. local_id must have unique values.
`species_group_species`	as data.frame linking the local species group id to the local species id. Must contain variables species_local_id and species_group_local_id. Other variables are ignored.
`hash`	the hash of the update session
`conn`	a DBIconnection
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.

Store status levels in the database

Description

Store status levels in the database

Usage

store_status(status, hash, clean = TRUE, conn)
store_status(status, hash, clean = TRUE, conn)

Arguments

`status`	a character vector with statuses
`hash`	the hash of the update session
`clean`	perform all database operations within a transaction and clean up the staging tables. Defaults to TRUE.
`conn`	a DBIconnection

Truncate all tables in the public schema: USE WITH CATION

Description

Truncate all tables in the public schema: USE WITH CATION

Usage

truncate_public(conn)
truncate_public(conn)

Arguments

conn

a DBIconnection

Package 'n2kupdate'

Help Index

Convert all factors in a data.frame to characters

Description

Usage

Arguments

connect to the unit test database

Description

Usage

Arguments

The n2kAnalysisVersion class

Description

store source species in the database

Description

Usage

Arguments

store analysis and dataset in the database

Description

Usage

Arguments

Store the analysis version in the database

Description

Usage

Arguments

Store anomaly

Description

Usage

Arguments

Store anomaly types

Description

Usage

Arguments

store a datafield in the database

Description

Usage

Arguments

Store a vector of datafield types

Description

Usage

Arguments

Store a dataset is the database

Description

Usage

Arguments

store a datasource in the database

Description

Usage

Arguments

Details

Store a vector of datasource parameters

Description

Usage

Arguments

Store a vector of datasource types

Description

Usage

Arguments

Store language

Description

Usage

Arguments

store locations in the database

Description

Usage

Arguments

Details

Store location groups

Description

Usage

Arguments

store the link between locations and location groups in the database

Description

Usage

Arguments

Details

Store model sets in the database

Description

Usage

Arguments

Store model type in the database