#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_all_sd.csv")
# Options can be passed to PKNCA
# Performing NCA
cfg = system_nca_run(cfg, dsname = "PKDATA",
dscale = 1e6,
analysis_name = "pk_single_dose",
extrap_C0 = FALSE,
dsmap = list(TIME = "TIME_HR",
NTIME = "TIME_HR",
CONC = "C_ng_ml",
DOSE = "DOSE",
ROUTE = "ROUTE",
ID = "ID"))
# You can access the results as a csv file in the output directory
# file.path("output", "pk_single_dose-nca_summary.csv")
# Or you can pull them out programmatically with the fetch function:
NCA_results = system_fetch_nca(cfg, analysis_name = "pk_single_dose")
NCA_sum = NCA_results["NCA_summary"]
# This will provide you metadata about all of the available
# columns in the NCA analysis
NCA_cols = system_fetch_nca_columns(cfg, analysis_name = "pk_single_dose")
# To print the available columns to the screen you can use the
# system_view command:
# system_view(cfg, "nca", verbose=TRUE)
# To summarize the results in a table use the system_nca_summary function.
# This will summarize the results for the subjects in the 30 mg dose group:
NCA_summary = system_nca_summary(cfg,
analysis_name = "pk_single_dose",
params_include = c( "ID", "cmax", "tmax", "half.life", "auclast"),
params_header = list(cmax = c( "<label>", "(ng/ml)")),
ds_wrangle = "NCA_sum = NCA_sum %>% dplyr::filter(Dose == 30)",
summary_stats = list("<MEAN> (<STD>)" = c("auclast", "half.life"),
"<MEDIAN>" = c("tmax")),
summary_labels = list(MEAN = "Mean",
STD = "Std Dev",
N = "N obs",
MEDIAN = "Median",
SE = "Std Err."),
summary_location = "ID")
#-------------------------------------------------------
# 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 Single Dose PK", type = "text")))
cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_single_dose")
system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_single_dose-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_single_dose")
system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_single_dose-report.docx"))
#-------------------------------------------------------
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