## ----------------------------------------------------------------------------- # install.packages("FSK2R") ## ----------------------------------------------------------------------------- library(FSK2R) ## ----------------------------------------------------------------------------- path_example <- system.file("extdata", "ToyModelv4.fskx", package = "FSK2R") print(path_example) ## ----------------------------------------------------------------------------- my_fsk <- import_fsk(path_example) ## ----------------------------------------------------------------------------- class(my_fsk) ## ----------------------------------------------------------------------------- is.FSK2R(my_fsk) ## ----------------------------------------------------------------------------- names(my_fsk) ## ----------------------------------------------------------------------------- my_fsk$manifest ## ----------------------------------------------------------------------------- my_fsk$model ## ----------------------------------------------------------------------------- my_fsk$packages ## ----------------------------------------------------------------------------- my_fsk$readme ## ----------------------------------------------------------------------------- cat(my_fsk$R_model) ## ----------------------------------------------------------------------------- cat(my_fsk$visualization) ## ----------------------------------------------------------------------------- model_path <- system.file("extdata", "model.r", package = "FSK2R") print(model_path) ## ----------------------------------------------------------------------------- visualization_path <- system.file("extdata", "visualization.r", package = "FSK2R") print(visualization_path) ## ----------------------------------------------------------------------------- FSK_from_R <- create_fsk(model_path, visualization_path) ## ----------------------------------------------------------------------------- class(FSK_from_R) ## ----------------------------------------------------------------------------- names(FSK_from_R) ## ----------------------------------------------------------------------------- FSK_from_R$model_metadata ## ----------------------------------------------------------------------------- is_fsk_with_r(FSK_from_R) ## ----------------------------------------------------------------------------- n_simuls_fsk(FSK_from_R) ## ----------------------------------------------------------------------------- run_simulation(FSK_from_R, 1) ## ----------------------------------------------------------------------------- run_simulation(FSK_from_R, 1, TRUE) ## ----------------------------------------------------------------------------- new_model <- set_new_simulation(my_fsk, "new", list(r = 0.09, Dose_matrix = "as.matrix(read.table(file =\"Dose_matrix.csv\",sep=\",\", header = TRUE, row.names=1))", alpha = 0.05, beta = 0.045, eta = 0.003 ) ) ## ----------------------------------------------------------------------------- n_simuls_fsk(new_model) ## ----------------------------------------------------------------------------- readme_text <- "This is an FSK-ML compliant model generated based on an existing R script" FSK_from_R <- set_readme(FSK_from_R, readme_text) ## ----------------------------------------------------------------------------- get_readme(FSK_from_R) ## ----------------------------------------------------------------------------- # get_simulations(my_fsk) ## ----------------------------------------------------------------------------- get_general_info(my_fsk) ## ----------------------------------------------------------------------------- get_scope(my_fsk) ## ----------------------------------------------------------------------------- get_background(my_fsk) ## ----------------------------------------------------------------------------- get_modelmath(my_fsk) ## ----------------------------------------------------------------------------- template_path <- system.file("extdata", "example_template.xlsx", package = "FSK2R") print(template_path) ## ----------------------------------------------------------------------------- FSK_from_R <- read_fsk_metadata_excel(FSK_from_R, template_path) ## ----------------------------------------------------------------------------- export_fsk(my_fsk, out_path=file.path(tempdir(), "out.fskx")) ## ----------------------------------------------------------------------------- imported_model <- import_fsk(file.path(tempdir(), "out.fskx"))