Nothing
#clearing the workspace
rm(list=ls())
graphics.off()
options(show.error.locations = TRUE)
# if we are in a stand alone 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))
# -------------------------------------------------------------------------
# Individual Simulation:
som = run_simulation_ubiquity(parameters, cfg)
library(ggplot2)
myfig = ggplot() +
geom_line(data=som$simout, aes(x=ts.days, y=C_ng_ml), color="red") +
xlab("Time (days)")+
ylab("C (ng/ml)")
myfig = gg_log10_yaxis(myfig, ylim_min=1e3, ylim_max=3e5)
myfig = prepare_figure("print", myfig)
print(myfig)
# -------------------------------------------------------------------------
ggsave(sprintf('output%ssingle.png', .Platform$file.sep), width=8, height=3.4, plot=myfig)
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