Parameter key requirements

Source: R/param-key.R

The parameter key used in the pmparams functions can either be a yaml or data frame. It must contain the following:

name or yaml variable= THETA, OMEGA, SIGMA. See examples below.

abb = abbreviation you want to appear in the parameter table (use latex coding)

desc = description you want to appear in the parameter table

panel = indicate which panel each parameter should appear under.

Current options include:

  • panel=="struct" ~ "Structural model parameters"

  • panel=="cov" ~ "Covariate effect parameters"

  • panel=="IIV" ~ "Interindividual covariance parameters" (off-diagonals << function takes care of this)

  • panel=="IIV" ~ "Interindividual variance parameters" (diagonals << function takes care of this)

  • panel=="IOV" ~ "Interoccasion variance parameters"

  • panel=="RV" ~ "Residual variance"

trans = define how the parameter will be transformed. Current options include:

  • "none" - untransformed parameters, e.g. THETAs or off-diagonals

  • "logTrans" - THETAs estimated in the log domain

  • "logitTrans" - THETAs estimated using a logit transform

  • "lognormalOm"- for log-normal omegas e.g. CL = THETA(1) * exp(ETA(1)) - returns est.+CV%

  • "OmSD" - for omegas where you want to return SD only - returns estimate & SD; use this for additive omegas e.g. CL = THETA(1) + ETA(1)

  • "logitOmSD" - for omegas using logit transform - returns estimate & SD (calculated with logitnorm package); this option requires you provide the associated THETA separated with a "~"; e.g. "logitOmSD ~ THETA3"

  • "addErr" - for additive error terms (coded using THETA or SIGMA in $ERROR) - returns est.+ SD

  • "propErr" - for proportional error terms (coded using THETA or SIGMA in $ERROR) - returns est.+CV%

  • "addErrLogDV" - for an additive error term on log-transformed data (coded using THETA or SIGMA in $ERROR) - returns est.+CV%

YAML Example

Example of YAML syntax for parameter key file

THETA1
  abb: "KA (1/h)"
  desc: "First order absorption rate constant"
  panel: struct
  trans: logTrans

THETA2
  abb: "V2/F (L)"
  desc: "Apparent central volume"
  panel: struct
  trans: logTrans

Examples


# Example of parameter key data frame:
# It must contain parameter names, abb, desc, panel, and trans columns.

paramKey = dplyr::tribble(
  ~name, ~abb, ~desc, ~panel, ~trans,
  "THETA1",  "KA (1/h)", "First order absorption rate constant",   "struct", "logTrans",
  "THETA2", "V2/F (L)",  "Apparent central volume",                "struct", "logTrans"
)
paramKey
#> # A tibble: 2 × 5
#>   name   abb      desc                                 panel  trans   
#>   <chr>  <chr>    <chr>                                <chr>  <chr>   
#> 1 THETA1 KA (1/h) First order absorption rate constant struct logTrans
#> 2 THETA2 V2/F (L) Apparent central volume              struct logTrans