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Combine bootstrap estimates with parameter key

Source: R/define_boot_table.R
define_boot_table.Rd

Combines bootstrap estimates with information in parameter key and performs some additional formatting.

Usage

define_boot_table(
  .boot_estimates,
  .key,
  .ci = 95,
  .na.rm = TRUE,
  .nonboot_estimates = NULL
)

Arguments

.boot_estimates

One of the following:

  • Output from bbr::bootstrap_estimates() or a wide data frame denoting the parameter estimates for each run. See details.

  • A file path to a csv containing the above dataset.

.key

path to parameter key or data.frame of parameter key. Described in more detail in param_key

.ci

the confidence interval. A value from 1 to 100 denoting the percent confidence interval, or "iqr" (interquartile range). Default is 95.

.na.rm

logical (T/F). If TRUE, any NA and NaN's are removed before the quantiles are computed. Passed to stats::quantile().

.nonboot_estimates

Deprecated. Parameter estimates are now joined later in the workflow.

Details

Below is the expected format of .boot_estimates if a data frame is provided:

run   THETA1 THETA2 THETA3 THETA4 THETA5 THETA6   THETA7 THETA8
<chr>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>    <dbl>  <dbl>
001    0.494   4.19   1.20   4.20   1.24  0.488 -0.0615   0.377
002    0.405   4.07   1.14   4.23   1.32  0.536 -0.103    0.517
003    0.500   4.09   1.15   4.21   1.27  0.413 -0.0752   0.523
004    0.578   4.16   1.20   4.18   1.30  0.518 -0.0502   0.418
005    0.499   4.14   1.16   4.25   1.22  0.436 -0.0686   0.394

Notes:

  • Some parameter names may have punctuation (such as OMEGA(1,1)). A new name column is automatically added that specifies the name without punctuation (i.e. OMEGA11).

  • Parameter details from the parameter key are joined to the bootstrap parameter estimates. A dplyr::inner_join is used so that only parameters in the model output are kept in the table. This was done so that, if your base and final model used the same structural THETAs and random parameters, the same parameter key could be used for both.

    • This join adds the following columns: abb (abbreviation), desc (parameter description), panel, trans (transformation).

  • A final check is performed to determine whether parameters with special transformation rules were defined correctly. In addition, a series of TRUE/ FALSE columns are added that will be used downstream.

See also

param_key(), define_param_table(), format_boot_table()

Examples


model_dir <- system.file("model/nonmem", package = "pmparams")
paramKey <-  file.path(model_dir, "pk-parameter-key-new.yaml")

# Using a file path:
boot_path <- file.path(model_dir, "boot/data/boot-106.csv")
define_boot_table(
 .boot_estimates = boot_path,
 .key = paramKey
)
#> # A tibble: 15 × 23
#>    parameter_names   lower   value   upper ci_level name    abb      desc  panel
#>    <chr>             <dbl>   <dbl>   <dbl>    <dbl> <chr>   <chr>    <chr> <chr>
#>  1 THETA1           1.39    1.57    1.78         95 THETA1  KA (1/h) Firs… stru…
#>  2 THETA2          58.3    61.5    65.1          95 THETA2  V2/F (L) Appa… stru…
#>  3 THETA3           3.07    3.23    3.42         95 THETA3  CL/F (L… Appa… stru…
#>  4 THETA4          65.0    67.3    69.8          95 THETA4  V3/F (L) Appa… stru…
#>  5 THETA5           3.37    3.61    3.86         95 THETA5  Q/F (L/… Appa… stru…
#>  6 THETA6           0.408   0.484   0.558        95 THETA6  CL/F ~ … eGFR… cov  
#>  7 THETA7          -0.167  -0.0386  0.0878       95 THETA7  CL/F ~ … Age … cov  
#>  8 THETA8           0.294   0.420   0.587        95 THETA8  CL/F ~ … Seru… cov  
#>  9 OMEGA(1,1)       0.130   0.218   0.331        95 OMEGA11 IIV-KA   Vari… IIV  
#> 10 OMEGA(2,2)       0.0643  0.0821  0.101        95 OMEGA22 IIV-V2/F Vari… IIV  
#> 11 OMEGA(3,3)       0.0896  0.112   0.140        95 OMEGA33 IIV-CL/F Vari… IIV  
#> 12 OMEGA(2,1)       0.0328  0.0656  0.107        95 OMEGA21 V2/F-KA  Cova… IIV  
#> 13 OMEGA(3,1)       0.0805  0.121   0.173        95 OMEGA31 CL/F-KA  Cova… IIV  
#> 14 OMEGA(3,2)       0.0525  0.0696  0.0882       95 OMEGA32 CL/F-V2… Cova… IIV  
#> 15 SIGMA(1,1)       0.0376  0.0400  0.0424       95 SIGMA11 Proport… Vari… RV   
#> # ℹ 14 more variables: trans <chr>, transTHETA <lgl>, THETAERR <lgl>, TH <lgl>,
#> #   OM <lgl>, S <lgl>, LOG <lgl>, LOGIT <lgl>, lognormO <lgl>, Osd <lgl>,
#> #   logitOsd <lgl>, propErr <lgl>, addErr <lgl>, addErrLogDV <lgl>

# Using a `bbr` bootstrap model object:
if (FALSE) { # \dontrun{
boot_run <- bbr::read_model(file.path(model_dir, "106-boot"))
define_boot_table(
 .boot_estimates = bbr::bootstrap_estimates(boot_run),
 .key = paramKey
)
} # }