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FSK2R

R package for reading/writing FSK-ML models.

FSK2R is an R package that enables users to work with FSK-ML models and data in R. Some of its features are:

  • Model import and export
  • Model creation
  • Model edition
  • Running simulations
  • Visualizing results

FSK2R has been initiated and provided by the Federal Institute for Risk Assessment, BfR (Berlin, Germany), and Universidad Politécnica de Cartagena, UPCT (Cartagena, Spain). It is in beta status. Before using the software you have to read and accept the license and disclaimer. If you do not agree, do not use this software.

Development version

The development version can be installed with devtools from GitLab.

# install.packages("devtools")
devtools::install_gitlab('miguelalba/fsk2r')

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Version

Install

install.packages('FSK2R')

Monthly Downloads

227

Version

0.1.3

License

GPL-3

Maintainer

Alberto Garre

Last Published

February 25th, 2022

Functions in FSK2R (0.1.3)

get_general_info

Returns the general info of an FSK object
get_modelmath

Returns the model math of an FSK object
is_fsk_with_r

Does the object have an R model?
is.FSK2R

Is it an instance of FSK2R?
export_readme

Functions for exporting the README of an FSK2R object
read_fsk_manifest

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

Map for the contents of the metadata
export_sbmlModel

Export the model.sbml
create_fsk

Creates an FSK model from an existing R script
map_metadata_xml_template

Map between the names used in the template and the xml
find_packages

Finds where packages are stored
export_otherfiles

Export other files
import_fsk

Import an FSK model into R
import_fsk_join

Import of FSK with join node
export_simulation

Export the sim.sedml
get_session_info

Extract session information
export_visualization

Functions for exporting the visualization script of an FSK2R object
metadata_list_to_fsk

From read_fsk_metadata_XX to FSK2R format
n_simuls_fsk

Number of simulations in the FSK2R object
get_simulations

Returns a summary of the simulations of an FSK object (NULL)
read_fsk_rdf_metadata

Read the metadata.rdf
export_packages

Functions for exporting the packages of an FSK2R object
read_R_model

Reads the R model in an FSK model
read_fsk_json_metadata

Read the metadata.json file
read_visualization

Reads the visualization script in an FSK model
read_fsk_metadata_excel

FSK metadata from local Excel file
read_fsk_sim

Read the sim.sedml file
read_fsk_readme

Read the README file
read_other_files

Read "other files"
update_manifest

Updates the manifest file
set_readme

Readme of an FSK object
run_all_simulations

Run every simulation in an FSK object
run_simulation

Run one simulation in an FSK object
read_fsk_packages

Read the packages.json
get_readme

Readme of an FSK object
read_fsk_model

Read the model.sbml
get_scope

Returns the scope of an FSK object
get_background

Returns the background of an FSK object
set_new_simulation

Define a new simulation in an FSK2R object
export_R_model

Functions for exporting the R model of an FSK2R object
FSK_runner

Startup FSK runner
export_fsk

Exports an object of FSK class as an .fskx file
export_metadata

Function for exporting the metadata of an FSK2R object
convert_metadata_to_lists

Fix the metadat so that it is lists
dataframe_to_list

Converts a dataframe to a list
check_manifest_files

Checks that the files defined in the manifest exist
export_modelmetadata

Functions for exporting the model metadata of an FSK2R object
export_manifest

Functions for exporting the manifest of an FSK2R object