Author Information

Description

Author Information

Usage

FSKAuthor(
  title = NULL,
  familyName = NULL,
  givenName = NULL,
  email = NULL,
  telephone = NULL,
  streetAddress = NULL,
  country = NULL,
  zipCode = NULL,
  region = NULL,
  timeZone = NULL,
  gender = NULL,
  note = NULL,
  organization = NULL
)

FSKCreator(
  title = NULL,
  familyName = NULL,
  givenName = NULL,
  email = NULL,
  telephone = NULL,
  streetAddress = NULL,
  country = NULL,
  zipCode = NULL,
  region = NULL,
  timeZone = NULL,
  gender = NULL,
  note = NULL,
  organization = NULL
)

Arguments

Data Background Section

Description

Data Background Section

Usage

FSKDataBackground(
  study = NULL,
  studySample = NULL,
  dietaryAssessmentMethod = NULL,
  laboratory = NULL,
  assay = NULL
)

Arguments

General Information Section

Description

General Information Section

Usage

FSKGeneralInformation(
  name = NULL,
  source = NULL,
  identifier = NULL,
  author = NULL,
  creator = NULL,
  creationDate = NULL,
  modificationDate = NULL,
  rights = NULL,
  availability = NULL,
  url = NULL,
  format = NULL,
  reference = NULL,
  language = NULL,
  software = NULL,
  languageWrittenIn = NULL,
  modelCategory = NULL,
  status = NULL,
  objective = NULL,
  description = NULL
)

Arguments

FSK Metadata Classes

Description

S3 classes for FSK metadata based on the FSKX JSON schema specification. These classes ensure proper JSON serialization with correct array/scalar types.

Usage

FSKMetadata(
  modelType = "genericModel",
  generalInformation = NULL,
  scope = NULL,
  dataBackground = NULL,
  modelMath = NULL
)

Arguments

Model Category Information

Description

Model Category Information

Usage

FSKModelCategory(
  modelClass = NULL,
  modelSubClass = NULL,
  modelClassComment = NULL,
  basicProcess = NULL
)

Arguments

Model Math Section

Description

Model Math Section

Usage

FSKModelMath(
  parameter = NULL,
  qualityMeasures = NULL,
  modelEquation = NULL,
  fittingProcedure = NULL,
  exposure = NULL,
  event = NULL
)

Arguments

Parameter Information

Description

Parameter Information

Usage

FSKParameter(
  id = NULL,
  classification = NULL,
  name = NULL,
  description = NULL,
  unit = NULL,
  unitCategory = NULL,
  dataType = NULL,
  source = NULL,
  subject = NULL,
  distribution = NULL,
  value = NULL,
  reference = NULL,
  variabilitySubject = NULL,
  minValue = NULL,
  maxValue = NULL,
  error = NULL
)

Arguments

Reference Information

Description

Reference Information

Usage

FSKReference(
  isReferenceDescription = NULL,
  title = NULL,
  doi = NULL,
  publicationType = NULL,
  date = NULL,
  pmid = NULL,
  authorList = NULL,
  abstract = NULL,
  journal = NULL,
  volume = NULL,
  issue = NULL,
  status = NULL,
  website = NULL,
  comment = NULL
)

Arguments

Scope Section

Description

Scope Section

Usage

FSKScope(
  product = NULL,
  hazard = NULL,
  populationGroup = NULL,
  generalComment = NULL,
  temporalInformation = NULL,
  spatialInformation = NULL
)

Arguments

Startup FSK runner

Description

Starts FSK runner within RStudio.

Usage

FSK_runner()

Value

None

Checks that the files defined in the manifest exist

Description

Checks that the files defined in the manifest exist

Usage

check_manifest_files(my_manifest, file_dir)

Arguments

Recursively clean object by removing empty values

Description

Recursively clean object by removing empty values

Usage

clean_empty_values(obj)

Arguments

Value

Cleaned object with empty values removed

Clean empty values from JSON string

Description

Clean empty values from JSON string

Usage

clean_json_string(json_string)

Arguments

Value

Cleaned JSON string with empty arrays and null values removed

Fix the metadat so that it is lists

Description

Fix the metadat so that it is lists

Usage

convert_metadata_to_lists(my_metadata)

Arguments

Creates an FSK model from an existing R script

Description

The model includes the R model. If provided as arguments, it also includes the visualization script and the README. Besides, it generates a typical model_metadata, as well as a simulation (without parameters). The manifest is left empty.

Usage

create_fsk(
  r_model,
  r_visualization = NULL,
  readme = NULL,
  other_files = NULL,
  pckg_frame = NULL
)

Arguments

Value

An instance of FSK2R.

Examples

 model_path <- system.file("extdata", "model.r", package = "FSK2R")
 visualization_path <- system.file("extdata", "visualization.r", package = "FSK2R")
 FSK_from_R <- create_fsk(model_path, visualization_path)

Converts a dataframe to a list

Description

This function is needed to convert the output format of rjson to the one used by FSK2R.

Usage

dataframe_to_list(this_frame)

Arguments

Functions for exporting the R model of an FSK2R object

Description

Functions for exporting the R model of an FSK2R object

Usage

export_R_model(fsk_object, out_path, check = FALSE)

Arguments

Exports an object of FSK class as an .fskx file

Description

Exports an object of FSK class as an .fskx file

Usage

export_fsk(fsk_object, out_path, check = TRUE)

Arguments

Value

None

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 class(my_fsk)
 export_fsk(my_fsk, out_path=file.path(tempdir(), "out.fskx"))

Functions for exporting the manifest of an FSK2R object

Description

Functions for exporting the manifest of an FSK2R object

Usage

export_manifest(fsk_object, out_path, check = FALSE)

Arguments

Function for exporting the metadata of an FSK2R object

Description

Function for exporting the metadata of an FSK2R object

Usage

export_metadata(fsk_object, out_path, check = FALSE)

Arguments

Functions for exporting the model metadata of an FSK2R object

Description

Functions for exporting the model metadata of an FSK2R object

Usage

export_modelmetadata(fsk_object, out_path, check = FALSE)

Arguments

Export other files

Description

Export other files

Usage

export_otherfiles(fsk_object, out_path, check = FALSE)

Arguments

Functions for exporting the packages of an FSK2R object

Description

Functions for exporting the packages of an FSK2R object

Usage

export_packages(fsk_object, out_path, check = FALSE)

Arguments

Functions for exporting the README of an FSK2R object

Description

Functions for exporting the README of an FSK2R object

Usage

export_readme(fsk_object, out_path, check = FALSE)

Arguments

Export the model.sbml

Description

Export the model.sbml

Usage

export_sbmlModel(fsk_object, out_path, check = FALSE)

Arguments

Export the sim.sedml

Description

Export the sim.sedml

Usage

export_simulation(fsk_object, out_path, check = FALSE)

Arguments

Functions for exporting the visualization script of an FSK2R object

Description

Functions for exporting the visualization script of an FSK2R object

Usage

export_visualization(fsk_object, out_path, check = FALSE)

Arguments

Functions for exporting the workspace of an FSK2R object

Description

Exports simulation environment variables as workspace.r file and workspace.RData for easy loading in R sessions.

Usage

export_workspace(fsk_object, out_path, check = FALSE, simulation_env = NULL)

Arguments

Extract script filenames from RDF metadata

Description

This function parses the metadata.rdf to find the actual filenames for model scripts and visualization scripts, rather than assuming standard names.

Usage

extract_script_filenames_from_rdf(rdf_metadata)

Arguments

Value

A list with modelScript and visualizationScript filenames

Finds where packages are stored

Description

Finds where packages are stored

Usage

find_packages(pckgs)

Arguments

Value

A list of packages locations. If one is not present, a character(0).

Returns the background of an FSK object

Description

Returns the background of an FSK object

Usage

get_background(fsk_obj)

Arguments

Value

A nested list with the following entries:

• studyTitle

• studyDescription

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 get_background(my_fsk)

Returns the general info of an FSK object

Description

Returns the general info of an FSK object

Usage

get_general_info(fsk_obj)

Arguments

Value

A nested list with the following entries:

• name

• source

• identifier

• creationDate

• rights

• language

• software

• creators

• reference

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 get_general_info(my_fsk)

Returns the model math of an FSK object

Description

Returns the model math of an FSK object

Usage

get_modelmath(fsk_obj)

Arguments

Value

A nested list with the following entries:

• parameter

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 get_modelmath(my_fsk)

Readme of an FSK object

Description

Readme of an FSK object

Usage

get_readme(fsk_obj)

Arguments

Value

A character vector with the text in the README file.

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 get_readme(my_fsk)

Returns the scope of an FSK object

Description

Returns the scope of an FSK object

Usage

get_scope(fsk_obj)

Arguments

Value

A nested list with the following entries:

• product

• hazard

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 get_scope(my_fsk)

Extract session information

Description

Extract session information

Usage

get_session_info()

Value

A list with 3 elements: r_version, platform and pckgs. The latter is a data.frame with two columns: package and version.

Returns a summary of the simulations of an FSK object

Description

Returns a summary of the simulations of an FSK object

Usage

get_simulations(fsk_obj)

Arguments

Value

A list of simulations, each with its parameters.

Import an FSK model into R

Description

Importst the file in file_path and transforms it into a list of class FSK2R.

Usage

import_fsk(file_path, check = FALSE)

Arguments

Value

An instance of FSK2R.

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 get_general_info(my_fsk)

Import of FSK with join node

Description

Join nodes are not yet supported by FSK2R. It just gives an error message when called.

Usage

import_fsk_join(file_path, check = TRUE)

Arguments

Is it an instance of FSK2R?

Description

Is it an instance of FSK2R?

Usage

is.FSK2R(object)

Arguments

Value

A logical vector

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 is.FSK2R(my_fsk)

Does the object have an R model?

Description

Does the object have an R model?

Usage

is_fsk_with_r(fsk_obj)

Arguments

Value

A logical vector.

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 is_fsk_with_r(my_fsk)

Map for the contents of the metadata

Description

Maps the location (range) of different pieces of data within the Excel/Google Sheets template. It also includes the names of the sheets.

Usage

map_FSK_metadata(type_of_model = "generic", fsk_version = "1.04")

Arguments

Value

A list with two components: the 'range' where each piece of information is stored and 'ws_name' with the name of the relevant sheet in the GoogleSheet template.

Map between the names used in the template and the xml

Description

Returns a map of the names used within the sheets of the Excel/GoogleSheets template and the ones in metadata.json.

Usage

map_metadata_xml_template()

From read_fsk_metadata_XX to FSK2R format

Description

Converts the contents of the Excel/Google Sheets template into a list with the format of the FSK2R object.

Usage

metadata_list_to_fsk(my_metadata, fsk_version = "1.0.5")

Arguments

Number of simulations in the FSK2R object

Description

Number of simulations in the FSK2R object

Usage

n_simuls_fsk(fsk_obj)

Arguments

Value

An integer vector of length one.

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 n_simuls_fsk(my_fsk)

Reads the R model in an FSK model

Description

Reads the R model in an FSK model

Usage

read_R_model(file_dir, check = FALSE, filename = "model.R")

Arguments

Value

A character string with the contents of the R file.

Read the metadata.json file

Description

Read the metadata.json file

Usage

read_fsk_json_metadata(file_dir, check = FALSE, filename = "metaData.json")

Arguments

Value

A list with the contents of the metadata file.

Read the manifest of an FSK file and convert it to a data.frame

Description

Read the manifest of an FSK file and convert it to a data.frame

Usage

read_fsk_manifest(file_dir, check = FALSE, filename = "manifest.xml")

Arguments

Value

A data.frame with the contents of the xlm file.

FSK metadata from local Excel file

Description

FSK metadata from local Excel file

Usage

read_fsk_metadata_excel(
  fsk_object,
  path,
  type_of_model = "generic",
  fsk_version = "1.0.5"
)

Arguments

Value

A list with the information in the Excel file as generated by metadata_list_to_fsk.

Read the model.sbml

Description

Read the model.sbml

Usage

read_fsk_model(file_dir, check = FALSE, filename = "model.sbml")

Arguments

Value

A list with the contents of the .xml file.

Read the packages.json

Description

Read the packages.json

Usage

read_fsk_packages(file_dir, check = FALSE, filename = "packages.json")

Arguments

Value

A list with the contents of the JSON file.

Read the metadata.rdf

Description

Read the metadata.rdf

Usage

read_fsk_rdf_metadata(file_dir, check = FALSE, filename = "metadata.rdf")

Arguments

Value

A list with the contents of the .xml file.

Read the README file

Description

Read the README file

Usage

read_fsk_readme(file_dir, check = FALSE, filename = "README.txt")

Arguments

Value

A character string with the content of the README file.

Read the sim.sedml file

Description

Read the sim.sedml file

Usage

read_fsk_sim(file_dir, check = FALSE, filename = "sim.sedml")

Arguments

Value

A list with the content of the xml file.

Read "other files"

Description

The R models may require further files that we can not predict. This functions just reads all the "unrecognized" files included in the manifest and copies them to the working directory.

Usage

read_other_files(my_tempdir, my_manifest, check = FALSE, rdf_metadata = NULL)

Arguments

Reads the visualization script in an FSK model

Description

Reads the visualization script in an FSK model

Usage

read_visualization(file_dir, check = FALSE, filename = "visualization.R")

Arguments

Value

A character string with the contents of the R file.

Run every simulation in an FSK object

Description

Runs every simulation defined in the FSK object. This includes the ones originally included in the FSK container, as well as the ones added using set_new_simulation().

Usage

run_all_simulations(
  fsk_object,
  run_visualization = FALSE,
  copy_workspace = FALSE,
  workspace_mode = "all",
  inject_to_global = FALSE
)

Arguments

Value

A named list with the results of all simulations

Run one simulation in an FSK object

Description

Runs the simulation corresponding to index. If defined, it also calls any visualization script. Returns all user-created variables from the simulation environment, supporting various data types including scalars, vectors, data frames, lists, and matrices.

Usage

run_simulation(
  fsk_object,
  index,
  run_visualization = FALSE,
  copy_workspace = FALSE,
  workspace_mode = "all",
  inject_to_global = FALSE
)

Arguments

Value

A named list containing all variables created by the simulation model. Each element preserves the original data type (numbers, strings, data frames, lists, matrices, etc.). Returns an empty list if no variables are created. When inject_to_global=TRUE, variables are also available in the global environment.

Define a new simulation in an FSK2R object

Description

Sets a new simulation using the parameters defined in simulation_pars. The method updates all the relevant methods.

Usage

set_new_simulation(fsk_object, simulation_id, parameters)

Arguments

Value

An instance of FSK2R with the additional simulation data.

Readme of an FSK object

Description

Readme of an FSK object

Usage

set_readme(fsk_object, readme_text)

Arguments

Value

An instance of FSK2R.

Examples

 path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R")
 my_fsk <- import_fsk(path_example)
 set_readme(my_fsk, "This is the README.")

Updates the manifest file

Description

Updates the manifest file

Usage

update_manifest(fsk_object)

Arguments