Nothing
#clearing the workspace
rm(list=ls())
graphics.off()
options(show.error.locations = TRUE)
# If we cannot load the ubiquity package we try the stand alone distribution
if("ubiquity" %in% rownames(installed.packages())){require(ubiquity)} else
{source(file.path("library", "r_general", "ubiquity.R")) }
# -------------------------------------------------------------------------
# Use system_new(system_file="empty") to create a minimal system file
# Build the system
cfg = build_system(system_file="system.txt",
output_directory = file.path(".", "output"),
temporary_directory = file.path(".", "transient"))
# -------------------------------------------------------------------------
# Loading Datasets
#
# From Excel sheet
# cfg = system_load_data(cfg, dsname = "DSNAME",
# data_file = "DS.xls",
# data_sheet = "SHEET")
#
# From csv
# cfg = system_load_data(cfg, dsname = "DSNAME",
# data_file = "DS.csv")
#
# From tab
# cfg = system_load_data(cfg, dsname = "DSNAME",
# data_file = "DS.tab")
#
# To see default PKNCA options use the following command:
# def_NCA_opts = PKNCA.options()
# Use this to overwrite specific values:
# my_NCA_opts = list(max.aucinf.pext = 10,
# min.hl.r.squared = .9)
# Replace the NULL value of NCA_options below with my_NCA_opts
# to overwrite the PKCNA defaults.
# Performing NCA
# cfg = system_nca_run(cfg,
# dsname = "DSNAME",
# dscale = 1,
# NCA_options = NULL,
# NCA_min = 4,
# analysis_name = "analysis",
# dsfilter = NULL,
# dsmap = list(TIME = "TIME",
# NTIME = "NTIME",
# CONC = "DV",
# DOSE = "AMT",
# ROUTE = "ROUTE",
# ID = "ID",
# DOSENUM = NULL),
# digits = 3)
#-------------------------------------------------------
# Writing the results to a PowerPoint report
# # Creating an empty report
# cfg = system_rpt_read_template(cfg, template="PowerPoint")
# # Giving the report a title slide
# cfg = system_rpt_add_slide(cfg,
# template = "title_slide",
# elements = list( title= list(content = "NCA Single Dose PK", type = "text")))
# # Appending the NCA results to the report
# cfg = system_rpt_nca(cfg=cfg, analysis_name="analysis")
# # Writing the results to a PowerPoint file
# system_rpt_save_report(cfg=cfg, output_file=file.path("output","analysis-report.pptx"))
#-------------------------------------------------------
# Writing the results to a Word report
# # Creating an empty report
# cfg = system_rpt_read_template(cfg, template="Word")
# # Appending the NCA results to the report
# cfg = system_rpt_nca(cfg=cfg, analysis_name="analysis")
# # Writing the results to a Word file
# system_rpt_save_report(cfg=cfg, output_file=file.path("output","analysis-report.docx"))
#-------------------------------------------------------
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