lst • hyperion

library(hyperion)
#> 
#> 
#> ── pharos configuration ────────────────────────────────────────────────────────
#> ✖ pharos CLI not found on PATH
#> ✔ pharos.toml found: /tmp/Rtmp30uAYm/temp_libpath8e164f9cde4d/hyperion/pharos.toml
#>     └ hyperion.config_dir : (unset)
#> ── hyperion options ────────────────────────────────────────────────────────────
#> ✔ hyperion.significant_number_display : 4
#> ── hyperion nonmem object options ──────────────────────────────────────────────
#> ✔ hyperion.nonmem_model.show_included_columns : FALSE
#> ✔ hyperion.nonmem_summary.rse_threshold : 50
#> ✔ hyperion.nonmem_summary.shrinkage_threshold : 30

Parse lst

get_run_info(
    read_model( 
        file.path("models", "onecmt", "run001.mod")
    )
)
#> $run_details
#>                                      problem number_data_records
#> 1 Base one-compartment oral absorption model                 240
#>   number_subjects number_obs postprocess_time function_evaluations
#> 1              30        210             0.04                  123
#>   significant_digits only_sim
#> 1                4.5    FALSE
#>                                     estimation_method estimation_time
#> 1 First Order Conditional Estimation with Interaction            0.18
#>   covariance_time
#> 1            0.14
#> 
#> $run_heuristics
#>              heuristic_name value
#> 1   covariance_step_aborted FALSE
#> 2         eigenvalue_issues FALSE
#> 3   parameter_near_boundary FALSE
#> 4             hessian_reset FALSE
#> 5   minimization_terminated FALSE
#> 6 program_terminated_by_obj FALSE

get_run_info(
    read_model( 
        file.path("models", "onecmt", "run003b1.mod")
    )
)
#> $run_details
#>                                                                                                  problem
#> 1 Base one-compartment oral absorption model created from pharos see run003b1_metadata.json for details.
#>   number_data_records number_subjects number_obs postprocess_time
#> 1                 240              30        210             0.04
#>   function_evaluations significant_digits only_sim
#> 1                  297                3.2    FALSE
#>                                     estimation_method estimation_time
#> 1 First Order Conditional Estimation with Interaction            0.39
#>   covariance_time
#> 1              NA
#> 
#> $run_heuristics
#>              heuristic_name value
#> 1   covariance_step_aborted    NA
#> 2         eigenvalue_issues    NA
#> 3   parameter_near_boundary  TRUE
#> 4             hessian_reset FALSE
#> 5   minimization_terminated FALSE
#> 6 program_terminated_by_obj FALSE

mod_sum <- summary(
    read_model(
        file.path("models", "onecmt", "run002.mod")
    )
)

mod_sum

Model Summary: run002

Problem: Base one-compartment oral absorption model

Records: 240 | Observations: 210 | Subjects: 30

Final OFV: -103.5

Estimation Methods

First Order Conditional Estimation with Interaction
- Condition Number: 29.63

Heuristic Checks

[OK] Minimization Successful

[OK] No Objective Function Failure

[OK] Covariance Step Successful

[OK] No Eigenvalue Issues

[OK] No Parameters Near Boundary

[OK] No Hessian Resets

Theta Parameters

Parameter	Estimate	SE	RSE (%)	Fixed
TVCL	1.247	0.1288	10.33	No
TVV	40.85	3.027	7.411	No
TVKA	1.244	0.1134	9.117	No

Omega Parameters

Parameter	Random Effect	Estimate	SE	RSE (%)	Shrinkage (%)	Fixed
OM1 (TVCL)	ETA1	0.1304	0.06019	46.15	18.06	No
OM2 (TVV)	ETA2	0.1363	0.03971	29.13	4.986	No
OM3 (TVKA)	ETA3	0.1144	0.06144	53.71	27.19	No

Sigma Parameters

Parameter	Random Effect	Estimate	SE	RSE (%)	Shrinkage (%)	Fixed
SIGMA(1,1)	EPS1	0.03723	0.0116	31.16	15.44	No
SIGMA(2,2)	EPS2	0.006607	0.02792	422.6	15.44	No

mod_sum <- summary(
    read_model(
        file.path("models", "onecmt", "run003b1.mod")
    )
)

mod_sum

Model Summary: run003b1

Problem: Base one-compartment oral absorption model created from pharos see run003b1_metadata.json for details.

Records: 240 | Observations: 210 | Subjects: 30

Final OFV: -108.9