Displays information (dosing, simulation options, covariates, etc) about the system.
Arguments
- cfg
ubiquity system object
- field
string indicating the aspect of the system to display
- verbose
Boolean variable that when set to true will echo the information to the screen
Value
sequence of strings with system in formation (one line per element)
The field
"all"will show all information about the system"parameters"summary of parameter information"bolus"currently set bolus dosing"rate"infusion rate dosing"covariate"covariates"iiv"variance/covariance information"datasets"loaded datasets"simulation"simulation options"estimation"estimation options"nca"non-compartmental analyses that have been performed
Examples
# To log and display the current system information:
# \donttest{
# Creating a system file from the mab_pk example
fr = system_new(file_name = "system.txt",
system_file = "mab_pk",
overwrite = TRUE,
output_directory = tempdir())
# Building the system
cfg = build_system(system_file = file.path(tempdir(), "system.txt"),
output_directory = file.path(tempdir(), "output"),
temporary_directory = tempdir())
#>
#> ── Building the system: /var/folders/l9/6pm7xq5j1hn6l00zrs22j6mc0000gn/T//RtmpoL
#> → ubiquity: https://r.ubiquity.tools
#> → Distribution: package (2.0.4)
#> → Compiling C version of system
#> → Loading the shared C library
#> ✔ System built
#> ℹ To fetch a new analysis template use `system_fetch_template`
#> ℹ For example:
#> ℹ fr = system_fetch_template(cfg, template = "Simulation")
#> ℹ fr = system_fetch_template(cfg, template = "Estimation")
msgs = system_view(cfg, verbose=TRUE)
#> Warning: one argument not used by format ' %s, %s(%s)'
#> Warning: one argument not used by format ' %s, %s(%s)'
#> Warning: one argument not used by format ' %s, %s(%s)'
#> Warning: one argument not used by format ' %s, %s(%s)'
#> Warning: one argument not used by format ' %s, %s(%s)'
#> Warning: one argument not used by format ' '
#> → Parameter Information
#> → Parameter set selected:
#> → Short Name: default
#> → Description: mAb in Humans
#> → Default parameters for current set:
#> → name | value | units
#> → ----------------------------------------------------
#> → F1 | 0.7440 | ---
#> → ka | 0.2820 | 1/day
#> → CL | 0.2000 | L/day
#> → Vc | 3.6100 | L
#> → Vp | 2.7500 | L
#> → Q | 0.7470 | L/day
#> → MW | 140.0000 | kD
#> → prop_err | 0.1000 | --
#> → add_err | 0.1000 | ng/ml
#> → ----------------------------------------------------
#> →
#> → Bolus dosing details
#> → field | values | scaling | units
#> → --------------------------------------------------
#> → times | 0 7 14 | 1 | days
#> → At | 400 0 0 | 1e3/MW | mg
#> → Cc | 0 0 0 | 1e3/MW/Vc | mg
#> → --------------------------------------------------
#> → Infusion rate details
#> → Rate | field | values | scaling | units
#> → -----------------------------------------------------------------
#> → Dinf | time | 0 30 | 1/60/24 | min
#> → | levels | 0 0 | 60*24*1e3/MW | mg/min
#> → -----------------------------------------------------------------
#> →
#> → Covariate details
#> → Covariate | field | values | units
#> → --------------------------------------------------
#> → DOSE | time | 0 | day
#> → (step) | levels | 400 | mg
#> → WT | time | 0 | day
#> → (step) | levels | 60 | kg
#> → --------------------------------------------------
#> →
#> → IIV details
#> → IIV/Parameter set:
#> → Short Name: default
#> → Variance/covariance matrix
#> →
#> → ETAka ETACL ETAVc ETAVp ETAQ
#> → ETAka 0.4160 0 0 0 0
#> → ETACL 0 0.0988 0.0786 0.0619 0
#> → ETAVc 0 0.0786 0.1160 0.0377 0
#> → ETAVp 0 0.0619 0.0377 0.0789 0
#> → ETAQ 0 0 0 0 0.6990
#> →
#> → On parameters
#> → Vp, ETAVp(LN)
#> → Q, ETAQ(LN)
#> → Vc, ETAVc(LN)
#> → ka, ETAka(LN)
#> → CL, ETACL(LN)
#> →
#> → integrate_with c-file
#> → output_times min = 0; max = 10.0; length = 101
#> → No datasets loaded
#> →
#> → Estimation details
#> → Parameter set: default
#> → Parameters estimated: F1, ka, CL, Vc, Vp, Q, MW, prop_err, add_err
#> → objective_type ml
#> → observation_function system_od_general
#> → No cohort information found
#> → No NCA has been performed
# }