SpecimenInfo — SpecimenInfo • pmotoolsr

Information on specimen info.

Auto-generated R6 class from JSON Schema.

Format

An R6::R6Class() generator object.

Constructor

new(...) supports the following arguments.

alternate_identifiers: A list of alternative names.
blood_meal: Whether host specimen has had a recent blood meal.
collection_country: The name of country collected in, would be the same as admin level 0.
collection_date: The date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD.
drug_usage: Any drug used by subject and the frequency of usage; can include multiple drugs used.
env_broad_scale: The broad environment from which the specimen was collected, e.g. highlands, lowlands, mountainous region.
env_local_scale: The local environment from which the specimen was collected, e.g. jungle, urban, rural.
env_medium: The environment medium from which the specimen was collected from.
geo_admin1: Geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0).
geo_admin2: Geographical admin level 2, the third large demarcation of a nation (nation = admin level 0).
geo_admin3: Geographical admin level 3, the third large demarcation of a nation (nation = admin level 0).
gravid: Whether host specimen is currently pregnant.
gravidity: The gravidity of the specimen host (number of previous pregnancies).
has_travel_out_six_month: Has travelled out from local region in the last six months.
host_age: If specimen is from a person, the age in years of the person, can be float value so for 3 month old put 0.25.
host_sex: If specimen is collected from a host with a sex, the sex listed for that host.
host_subject_name: An identifier for the individual/person/patient a specimen was collected from.
host_taxon_id: The NCBI taxonomy number of the host that the specimen was collected from.
lat_lon: The latitude and longitude of a specific site.
parasite_density_info: One or more parasite densities in microliters for this specimen.
project_id: The index into the project_info list.
specimen_accession: If specimen is deposited in a database, what accession is it associated with.
specimen_collect_device: The way the specimen was collected, e.g. whole blood, dried blood spot.
specimen_comments: Any additional comments about the specimen.
specimen_name: An identifier for the specimen, should be unique within this sample set.
specimen_store_loc: The specimen store site, address or facility name.
specimen_taxon_id: The NCBI taxonomy number of the organism(s) in the specimen, can list multiple if a mixed sample.
specimen_type: What type of specimen this is, e.g. negative_control, positive_control, field_sample.
storage_plate_info: Plate location of where specimen is stored if stored in a plate.
travel_out_six_month: Specification of the countries travelled in the last six months; can include multiple travels.
treatment_status: If person has been treated with drugs, what was the treatment outcome.
extras: Additional properties not explicitly defined in the schema.

Methods

See inline method documentation for initialize(), validate(), to_list(), to_json_list(), and to_json().

Public fields

alternate_identifiers: A list of alternative names.
blood_meal: Whether host specimen has had a recent blood meal.
collection_country: The name of country collected in, would be the same as admin level 0.
collection_date: The date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD.
drug_usage: Any drug used by subject and the frequency of usage; can include multiple drugs used.
env_broad_scale: The broad environment from which the specimen was collected, e.g. highlands, lowlands, mountainous region.
env_local_scale: The local environment from which the specimen was collected, e.g. jungle, urban, rural.
env_medium: The environment medium from which the specimen was collected from.
geo_admin1: Geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0).
geo_admin2: Geographical admin level 2, the third large demarcation of a nation (nation = admin level 0).
geo_admin3: Geographical admin level 3, the third large demarcation of a nation (nation = admin level 0).
gravid: Whether host specimen is currently pregnant.
gravidity: The gravidity of the specimen host (number of previous pregnancies).
has_travel_out_six_month: Has travelled out from local region in the last six months.
host_age: If specimen is from a person, the age in years of the person, can be float value so for 3 month old put 0.25.
host_sex: If specimen is collected from a host with a sex, the sex listed for that host.
host_subject_name: An identifier for the individual/person/patient a specimen was collected from.
host_taxon_id: The NCBI taxonomy number of the host that the specimen was collected from.
lat_lon: The latitude and longitude of a specific site.
parasite_density_info: One or more parasite densities in microliters for this specimen.
project_id: The index into the project_info list.
specimen_accession: If specimen is deposited in a database, what accession is it associated with.
specimen_collect_device: The way the specimen was collected, e.g. whole blood, dried blood spot.
specimen_comments: Any additional comments about the specimen.
specimen_name: An identifier for the specimen, should be unique within this sample set.
specimen_store_loc: The specimen store site, address or facility name.
specimen_taxon_id: The NCBI taxonomy number of the organism(s) in the specimen, can list multiple if a mixed sample.
specimen_type: What type of specimen this is, e.g. negative_control, positive_control, field_sample.
storage_plate_info: Plate location of where specimen is stored if stored in a plate.
travel_out_six_month: Specification of the countries travelled in the last six months; can include multiple travels.
treatment_status: If person has been treated with drugs, what was the treatment outcome.
extras: Additional properties not explicitly defined in the schema.

Methods

`SpecimenInfo$new()`

Create a new instance.

Usage

SpecimenInfo$new(
  alternate_identifiers = NULL,
  blood_meal = NULL,
  collection_country = NULL,
  collection_date = NULL,
  drug_usage = NULL,
  env_broad_scale = NULL,
  env_local_scale = NULL,
  env_medium = NULL,
  geo_admin1 = NULL,
  geo_admin2 = NULL,
  geo_admin3 = NULL,
  gravid = NULL,
  gravidity = NULL,
  has_travel_out_six_month = NULL,
  host_age = NULL,
  host_sex = NULL,
  host_subject_name = NULL,
  host_taxon_id = NULL,
  lat_lon = NULL,
  parasite_density_info = NULL,
  project_id = NULL,
  specimen_accession = NULL,
  specimen_collect_device = NULL,
  specimen_comments = NULL,
  specimen_name = NA_character_,
  specimen_store_loc = NULL,
  specimen_taxon_id = NULL,
  specimen_type = NULL,
  storage_plate_info = NULL,
  travel_out_six_month = NULL,
  treatment_status = NULL,
  extras = list()
)

Arguments

alternate_identifiers: A list of alternative names.
blood_meal: Whether host specimen has had a recent blood meal.
collection_country: The name of country collected in, would be the same as admin level 0.
collection_date: The date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD.
drug_usage: Any drug used by subject and the frequency of usage; can include multiple drugs used.
env_broad_scale: The broad environment from which the specimen was collected, e.g. highlands, lowlands, mountainous region.
env_local_scale: The local environment from which the specimen was collected, e.g. jungle, urban, rural.
env_medium: The environment medium from which the specimen was collected from.
geo_admin1: Geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0).
geo_admin2: Geographical admin level 2, the third large demarcation of a nation (nation = admin level 0).
geo_admin3: Geographical admin level 3, the third large demarcation of a nation (nation = admin level 0).
gravid: Whether host specimen is currently pregnant.
gravidity: The gravidity of the specimen host (number of previous pregnancies).
has_travel_out_six_month: Has travelled out from local region in the last six months.
host_age: If specimen is from a person, the age in years of the person, can be float value so for 3 month old put 0.25.
host_sex: If specimen is collected from a host with a sex, the sex listed for that host.
host_subject_name: An identifier for the individual/person/patient a specimen was collected from.
host_taxon_id: The NCBI taxonomy number of the host that the specimen was collected from.
lat_lon: The latitude and longitude of a specific site.
parasite_density_info: One or more parasite densities in microliters for this specimen.
project_id: The index into the project_info list.
specimen_accession: If specimen is deposited in a database, what accession is it associated with.
specimen_collect_device: The way the specimen was collected, e.g. whole blood, dried blood spot.
specimen_comments: Any additional comments about the specimen.
specimen_name: An identifier for the specimen, should be unique within this sample set.
specimen_store_loc: The specimen store site, address or facility name.
specimen_taxon_id: The NCBI taxonomy number of the organism(s) in the specimen, can list multiple if a mixed sample.
specimen_type: What type of specimen this is, e.g. negative_control, positive_control, field_sample.
storage_plate_info: Plate location of where specimen is stored if stored in a plate.
travel_out_six_month: Specification of the countries travelled in the last six months; can include multiple travels.
treatment_status: If person has been treated with drugs, what was the treatment outcome.
extras: Additional properties not explicitly defined in the schema.

`SpecimenInfo$validate()`

Validate the current instance against schema-derived constraints.

Usage

SpecimenInfo$validate()

`SpecimenInfo$to_list()`

Convert the object to a plain R list using in-memory values.

Usage

SpecimenInfo$to_list()

`SpecimenInfo$to_json_list()`

Convert the object to a JSON-ready R list.

Usage

SpecimenInfo$to_json_list()

`SpecimenInfo$to_json()`

Convert the object to a JSON string.

Usage

SpecimenInfo$to_json(pretty = FALSE, auto_unbox = TRUE, ...)

Arguments

pretty: Logical; pretty-print the JSON.
auto_unbox: Logical; passed to jsonlite::toJSON().
...: Additional arguments passed to jsonlite::toJSON().

`SpecimenInfo$clone()`

The objects of this class are cloneable with this method.

Usage

SpecimenInfo$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.