Fetches Information from an rxode2 Object — fetch

This will provide information like parameter names, covriates, etc from an rxode2 object.

Usage

fetch_rxinfo(object)

Arguments

object: rxode2 model object An ID string that corresponds with the ID used to call the modules UI elements

Value

List with the following elements.

isgood: Boolean variable indicating if the model is good.
msgs: Any messages from parsing the model.
elements: List with names of simulation elements:
- covariates: Names of the covariates in the system.
- parameters: Names of the parameters (subject level) in the system.
- iiv: Names of the iiv parameters in the system.
- states: Names of the states/compartments in the system.
txt_info: Summary information in text format.
list_info: Summary information in list format used with onbrand reporting.
ht_info: Summary information in HTML formot.

Examples

library(formods)
library(ggplot2)

# For more information see the Clinical Trial Simulation vignette:
# https://ruminate.ubiquity.tools/articles/clinical_trial_simulation.html

# None of this will work if rxode2 isn't installed:
if(is_installed("rxode2")){
library(rxode2)
set.seed(8675309)
rxSetSeed(8675309)

my_model = function () 
{
    description <- "One compartment PK model with linear clearance using differential equations"
    ini({
        lka <- 0.45
        label("Absorption rate (Ka)")
        lcl <- 1
        label("Clearance (CL)")
        lvc <- 3.45
        label("Central volume of distribution (V)")
        propSd <- c(0, 0.5)
        label("Proportional residual error (fraction)")
        etalcl ~ 0.1
    })
    model({
        ka <- exp(lka)
        cl <- exp(lcl + etalcl)
        vc <- exp(lvc)
        kel <- cl/vc
        d/dt(depot) <- -ka * depot
        d/dt(central) <- ka * depot - kel * central
        Cc <- central/vc
        Cc ~ prop(propSd)
    })
}

# This creates an rxode2 object
object  = rxode(my_model)

# If you want details about the parameters, states, etc
# in the model you can use this:
rxdetails = fetch_rxinfo(object)

rxdetails$elements

# Next we will create subjects. To do that we need to 
# specify information about covariates:
nsub = 2
covs = list(
  WT         = list(type     = "continuous",
                    sampling = "log-normal",
                    values   = c(70, .15))
)

subs = mk_subjects(object = object,
                   nsub   = nsub,
                   covs   = covs)

head(subs$subjects)

rules = list(
  dose = list(
    condition = "TRUE",
    action    = list(
      type  = "dose",
      state     = "central", 
      values    = "c(1)",
      times     = "c(0)",
      durations = "c(0)")
    )
)

# We evaulate the rules for dosing at time 0
eval_times =  0

# Stop 2 months after the last dose
output_times = seq(0, 56, 1)

# This runs the rule-based simulations
simres = 
  simulate_rules(
    object        = object,
    subjects      = subs[["subjects"]],
    eval_times    = eval_times,
    output_times  = output_times, 
    rules         = rules)

# First subject data:
sub_1 = simres$simall[simres$simall$id == 1, ]

# First subjects events
evall = as.data.frame(simres$evall)
ev_sub_1 = evall[evall$id ==1, ]

# All of the simulation data
simall = simres$simall
simall$id = as.factor(simall$id)

# Timecourse
psim = 
  plot_sr_tc(
    sro    = simres,
    dvcols = "Cc")
psim$fig

# Events
pev = 
  plot_sr_ev(
    sro    = simres,
    ylog   = FALSE)
pev$fig

}
#> rxode2 2.1.3.9000 using 5 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`
#>  
#>  
#>  
#>  
#>  
#>  
#> Warning: multi-subject simulation without without 'omega'
#>  
#>  
#> Warning: multi-subject simulation without without 'omega'
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?