inst/ubinc/scripts/analysis_multiple_file.r

In john-harrold/ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

#clearing the workspace
rm(list=ls())
graphics.off()
options(show.error.locations = TRUE)

# If we are in a stand alone ubiquity distribution we run 
# from there otherwise we try to load the package
if(file.exists(file.path('library', 'r_general', 'ubiquity.R'))){
  source(file.path('library', 'r_general', 'ubiquity.R'))
} else { 
  library(ubiquity) }

# Rebuilding the system (R scripts and compiling C code)
cfg = build_system(output_directory     = file.path(".", "output"),
                   temporary_directory  = file.path(".", "transient"))

# set name   | Description
# -------------------------------------------------------
# default    | mAb in Humans
# Selecting the default paraemter set
cfg = system_select_set(cfg, 'default')

# Fetching the parameter values
parameters = system_fetch_parameters(cfg)

# To overwrite the default dosing uncomment
cfg = system_zero_inputs(cfg)
cfg = system_set_bolus(cfg, state = "At",
                           times  = c(  0.0,  14.0,  28.0),
                           values = c(400.0, 400.0, 400.0))


# The following applies to both individual and stochastic simulations:
# Define the solver to use
cfg=system_set_option(cfg,group   = "simulation",
                          option  = "solver",
                          value   = "lsoda")

# Specify the output times 
cfg=system_set_option(cfg, group  = "simulation",
                           option = "output_times",
                           value  = seq(0,80,.1))
# -------------------------------------------------------------------------
# # Stochastic Simulation:
cfg=system_set_option(cfg, group  = "stochastic",
                           option = "nsub",
                           value  =  400)
                           
# Loading dataset with subjects
cfg = system_load_data(cfg, dsname     = "SUBS", 
                            data_file  = "mab_pk_subjects.csv")

# Linking the subjects dataset with the simulation routines
cfg=system_set_option(cfg, group  = "stochastic",
                           option = "sub_file",
                           value  = "SUBS")


cfg=system_set_option(cfg, group  = "stochastic",
                           option = "sub_file_sample",
                           value  = "with replacement")


# Uncomment the following to parallelize the simulations
# library(doParallel)
# 
# cfg=system_set_option(cfg, group  = "simulation",
#                            option = "parallel",    
#                            value  = "multicore")
# 
# cfg=system_set_option(cfg, group  = "simulation",
#                            option = "compute_cores", 
#                            value  = detectCores() - 1)


# This strips the output collected down to only the output C_ng_ml
# cfg = system_set_option(cfg, group="stochastic", option="ssp",     value=list())
# cfg = system_set_option(cfg, group="stochastic", option="states",  value=list())
# cfg = system_set_option(cfg, group="stochastic", option="outputs", value=c("C_ng_ml"))

som  = simulate_subjects(parameters, cfg)
# 
# graphics.off()
# library(ggplot2)
# myfig = ggplot(som$tcsummary, aes(x=ts.days, y=o.C_ng_ml.mean)) +
#                geom_ribbon(aes(ymin=o.C_ng_ml.lb_ci, 
#                                ymax=o.C_ng_ml.ub_ci), 
#                                fill="lightblue", 
#                                alpha=0.6) +
#                geom_line(linetype="solid", size=0.7, color="blue")  +
#                geom_line(aes(x=ts.days, y=o.C_ng_ml.ub_ci), linetype="dashed", size=0.2, color="blue")  +
#                geom_line(aes(x=ts.days, y=o.C_ng_ml.lb_ci), linetype="dashed", size=0.2, color="blue")  +
#                xlab("Time (days)")+
#                ylab("C (ng/ml) (units)")+
#                #scale_y_log10(limits=c(100, 200000)) +
#                guides(fill=FALSE) 
# 
# 
# myfig = gg_log10_yaxis(myfig, ylim_min=1e3, ylim_max=3e5)
# myfig = prepare_figure("print", myfig)
# print(myfig)
# 
# 
# ggsave(sprintf('output%smultiple.png', .Platform$file.sep), width=8, height=3.4, plot=myfig)

# sdf = som_to_df(cfg, som)
# -------------------------------------------------------------------------