mrgsolve_package: mrgsolve: Simulate from ODE-Based Models

In mrgsolve: Simulate from ODE-Based Models

mrgsolve: Simulate from ODE-Based Models

Description

mrgsolve is an R package maintained under the auspices of Metrum Research Group that facilitates simulation from models based on systems of ordinary differential equations (ODE) that are typically employed for understanding pharmacokinetics, pharmacodynamics, and systems biology and pharmacology. mrgsolve consists of computer code written in the R and C++ languages, providing an interface to a C++ translation of the lsoda differential equation solver. See aboutsolver for more information.

Resources

• Main mrgsolve resource page: https://mrgsolve.org

• User guide: https://mrgsolve.org/user_guide/

• Package documentation and vignettes: https://mrgsolve.org/docs/

Package-wide options

• mrgolve.project: sets the default project director (mread())

• mrgsolve.soloc: sets the default package build directory (mread())

• mrgsolve_mread_quiet: don't print messages during mread()

• mrgsolve.update.strict: this option has been deprecated; use the strict argument to update() instead

Author(s)

Maintainer: Kyle T Baron [e-mail] (ORCID)

Other contributors:

• Bill Gillespie [contributor]

• Charles Margossian [contributor]

• Devin Pastoor [contributor]

• Bill Denney (ORCID) [contributor]

• Dilawar Singh [contributor]

• Felicien Le Louedec (ORCID) [contributor]

• Timothy Waterhouse (ORCID) [contributor]

• Kyle Meyer [contributor]

• Metrum Research Group [copyright holder]

See Also

Useful links:

• https://mrgsolve.org/docs/

• https://github.com/metrumresearchgroup/mrgsolve

• Report bugs at https://github.com/metrumresearchgroup/mrgsolve/issues

Examples

## example("mrgsolve")

mod <- mrgsolve::house(delta=0.1)  %>% param(CL=0.5)

events <-  ev(amt=1000, cmt=1, addl=5, ii=24)

events

mod

see(mod)

## Not run: 
stime(mod)

## End(Not run)
param(mod)

init(mod)

out <- mod %>% ev(events) %>% mrgsim(end=168)

head(out)
tail(out)
dim(out)

plot(out, GUT+CP~.)

sims <- as.data.frame(out)

t72 <- dplyr::filter(sims, time==72)

str(t72)

idata <- data.frame(ID=c(1,2,3), CL=c(0.5,1,2),VC=12)
out <- mod %>% ev(events) %>% mrgsim(end=168, idata=idata, req="")
plot(out)

out <- mod %>% ev(events) %>% mrgsim(carry_out="amt,evid,cmt,CL")
head(out)

ev1 <- ev(amt=500, cmt=2,rate=10)
ev2 <- ev(amt=100, cmt=1, time=54, ii=8, addl=10)
events <- c(ev1+ev2)
events

out <- mod %>% ev(events) %>% mrgsim(end=180, req="")
plot(out)


## "Condensed" data set
data(extran1)
extran1

out <- mod %>% data_set(extran1) %>% mrgsim(end=200)

plot(out,CP~time|factor(ID))


## idata
data(exidata)

out <- 
  mod %>% 
  ev(amt=1000, cmt=1) %>% 
  idata_set(exidata) %>%  
  mrgsim(end=72)

plot(out, CP~., as="log10")


# Internal model library
## Not run: 
mod <- mread("irm1", modlib())

mod

x <- mod %>% ev(amt=300, ii=12, addl=3) %>% mrgsim


## End(Not run)

mrgsolve documentation built on Oct. 18, 2024, 5:12 p.m.