Nothing
## ----setup, include=FALSE, message=FALSE, eval=TRUE---------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE, eval=FALSE)
require(ubiquity)
require(deSolve)
require(ggplot2)
require(foreach)
require(doParallel)
require(rhandsontable)
## ---- message=FALSE-----------------------------------------------------------
# library(ubiquity)
# fr = workshop_fetch(section="Simulation", overwrite=TRUE)
## ----results="hide", echo=FALSE----------------------------------------------
# library(ubiquity)
# system_new(file_name="system.txt", system_file="mab_pk", overwrite = TRUE)
## ----results="hide"-----------------------------------------------------------
# cfg = build_system(system_file = "system.txt")
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# cfg_orig = cfg
# save(cfg_orig, file="Simulation_cfg_orig.RData")
## ----echo=FALSE, eval=TRUE----------------------------------------------------
load(file="Simulation_cfg_orig.RData")
## ----results="hide"-----------------------------------------------------------
# system_fetch_template(cfg, template="Simulation")
## ----results="hide", warning=FALSE--------------------------------------------
# cfg = build_system(system_file = "system.txt")
# parameters = system_fetch_parameters(cfg)
## ----results="hide"-----------------------------------------------------------
# cfg = system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,3*4*7,1))
## ----results="hide"-----------------------------------------------------------
# cfg = system_zero_inputs(cfg)
# cfg = system_set_bolus(cfg, state = "At",
# times = c( 0, 14, 28, 42 ), # day
# values = c(200, 200, 200, 200 )) # mg
## ----results="hide", warning=FALSE--------------------------------------------
# som = run_simulation_ubiquity(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# save(som, file="Simulation_som_single.RData")
## ----echo=FALSE, eval=TRUE----------------------------------------------------
load("Simulation_som_single.RData")
rhandsontable(som$simout, width=600, height=300)
## ----warning=FALSE, fig.width=7, fig.height=3, eval=TRUE----------------------
p = ggplot() +
geom_line(data=som$simout, aes(x=ts.days, y=C_ng_ml), color="blue") +
xlab("Time (days)")+
ylab("C (ng/ml) (units)")
p = gg_log10_yaxis(p, ylim_min=1e3, ylim_max=3e5)
p = prepare_figure("print", p)
print(p)
## ----warning=FALSE, comment='', message=TRUE, echo=FALSE, eval=TRUE-----------
message(paste(system_view(cfg_orig, 'iiv'), collapse="\n"))
## ----warning=FALSE, results=FALSE---------------------------------------------
# cfg=system_set_option(cfg, group = "stochastic",
# option = "nsub",
# value = 20)
#
# som = simulate_subjects(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # Creating a reduced form of the simulation output to save it and use less disk space
# tmpsom = som
# som = list()
# som$tcsummary = data.frame(o.C_ng_ml.mean = tmpsom$tcsummary$o.C_ng_ml.mean,
# o.C_ng_ml.ub_ci = tmpsom$tcsummary$o.C_ng_ml.ub_ci,
# o.C_ng_ml.lb_ci = tmpsom$tcsummary$o.C_ng_ml.lb_ci,
# ts.days = tmpsom$tcsummary$ts.days)
# save(som, file="Simulation_som_multiple.RData")
## ----echo=FALSE, eval=TRUE----------------------------------------------------
load("Simulation_som_multiple.RData")
## ----warning=FALSE, fig.width=7, fig.height=3, eval=TRUE----------------------
p = 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)")+
guides(fill="none")
p = gg_log10_yaxis(p , ylim_min=1e3, ylim_max=3e5)
p = prepare_figure("print", p )
print(p)
## ----echo=TRUE, warning=FALSE-------------------------------------------------
# cfg = system_load_data(cfg,
# dsname = "SUBS",
# data_file = system.file("ubinc", "csv", "mab_pk_subjects.csv",
# package = "ubiquity"))
## ----echo=FALSE, eval=TRUE----------------------------------------------------
SUBSCSV= read.csv(system.file("ubinc", "csv", "mab_pk_subjects.csv", package = "ubiquity"))
rhandsontable( SUBSCSV, width=800, height=300)
## ----results=FALSE------------------------------------------------------------
# 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")
## ----results=FALSE, warning=FALSE, eval=FALSE---------------------------------
# som = simulate_subjects(parameters, cfg)
## ----echo=TRUE, eval=FALSE----------------------------------------------------
# cfg=system_set_option(cfg, group = "simulation",
# option = "parallel",
# value = "multicore")
#
# cfg=system_set_option(cfg, group = "simulation",
# option = "compute_cores",
# value = detectCores() - 1)
#
## ----echo=FALSE, comment='', message=TRUE, eval=TRUE--------------------------
cat(readLines(system.file("ubinc", "systems","system-mab_pk.txt", package="ubiquity")), sep="\n")
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