#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-mab_pk.txt",
output_directory = file.path(".", "output"),
temporary_directory = file.path(".", "transient"))
# -------------------------------------------------------------------------
# Loading Dataset
cfg = system_load_data(cfg, dsname = "PKDATA",
data_file = "pk_sparse_sd.csv")
# Performing NCA
cfg = system_nca_run(cfg, dsname = "PKDATA",
dscale = 1e6,
analysis_name = "pk_sparse",
sparse = TRUE,
dsmap = list(TIME = "TIME_HR",
NTIME = "TIME_HR",
CONC = "C_ng_ml",
DOSE = "DOSE",
ROUTE = "ROUTE",
ID = "ID",
SPARSEGROUP = "DOSE"),
dsinc = c("ROUTE"))
# You can access the results as a csv file in the output directory
# file.path("output", "pk_sparse-nca_summary.csv")
# Or you can pull them out programmatically with the fetch function:
NCA_results = system_fetch_nca(cfg, analysis_name = "pk_sparse")
#-------------------------------------------------------
# Writing the results to a PowerPoint report
cfg = system_rpt_read_template(cfg, template="PowerPoint")
cfg = system_rpt_add_slide(cfg,
template = "title_slide",
elements = list( title= list(content = "NCA of Sparsely Sampled PK", type = "text")))
cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_sparse")
system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_sparse-report.pptx"))
#-------------------------------------------------------
# Writing the results to a Word report
cfg = system_rpt_read_template(cfg, template="Word")
cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_sparse")
system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_sparse-report.docx"))
#-------------------------------------------------------
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