Output table/data.frame options

Usage

tableControl(
  npde = NULL,
  cwres = NULL,
  nsim = 300,
  ties = TRUE,
  censMethod = c("truncated-normal", "cdf", "ipred", "pred", "epred", "omit"),
  seed = 1009,
  cholSEtol = (.Machine$double.eps)^(1/3),
  state = TRUE,
  lhs = TRUE,
  eta = TRUE,
  covariates = TRUE,
  addDosing = FALSE,
  subsetNonmem = TRUE,
  cores = NULL,
  keep = NULL,
  drop = NULL
)

Arguments

npde

When TRUE, request npde regardless of the algorithm used.

cwres

When TRUE, request CWRES and FOCEi likelihood regardless of the algorithm used.

nsim

represents the number of simulations. For rxode2, if you supply single subject event tables (created with [eventTable()])

ties

When `TRUE` jitter prediction-discrepancy points to discourage ties in cdf.

censMethod

Handle censoring method:

- `"truncated-normal"` Simulates from a truncated normal distribution under the assumption of the model and censoring.

- `"cdf"` Impute censored observations with NPDE (below) and use the imputed values as the DV of the other residuals (`cwres` etc).

- `"omit"` omit the residuals for censoring

- `"ipred"`, `"pred"` and `"epred"` replace a censored DV with the IPRED, PRED or EPRED in the residuals.

For NPDE, every method but `"omit"` replaces each censored observation by a draw from the subject's simulated predictive distribution (a Gaussian copula of the simulations), conditional on its measured observations and truncated to its censoring interval; `"omit"` gives censored observations no NPDE and leaves them out of the decorrelation.

The NPDE that `"omit"` keeps are not expected to be N(0,1) under censoring, even for a true model: only the quantified observations are kept, while the simulations they are compared with are not censored. Below a lower limit the kept observations are the high ones, so their mean drifts upward as more is censored (downward above an upper limit). This holds for any NPDE restricted to the uncensored rows; to check a model's fit with censored data, use a method that keeps the censored rows, such as `"truncated-normal"`.

seed

an object specifying if and how the random number generator should be initialized; when given, it takes precedence over an active rxSetSeed() stream for this solve, and the caller's .Random.seed is restored afterwards. rxControl() only stores it; the seed is applied when the control is used by a solve. Re-solving a result by assignment (eg s$params <- p) reapplies its seed, while update() uses only a seed it is given

cholSEtol

The tolerance for the `rxode2::choleSE` function

state

is a Boolean indicating if `state` values will be included (default `TRUE`)

lhs

is a Boolean indicating if remaining `lhs` values will be included (default `TRUE`)

eta

is a Boolean indicating if `eta` values will be included (default `TRUE`)

covariates

is a Boolean indicating if covariates will be included (default `TRUE`)

addDosing

Boolean indicating if the solve should add rxode2 EVID and related columns. This will also include dosing information and estimates at the doses. Be default, rxode2 only includes estimates at the observations. (default FALSE). When addDosing is NULL, only include EVID=0 on solve and exclude any model-times or EVID=2. If addDosing is NA the classic rxode2 EVID events are returned. When addDosing is TRUE add the event information in NONMEM-style format; If subsetNonmem=FALSE rxode2 will also include extra event types (EVID) for ending infusion and modeled times:

EVID=-1 when the modeled rate infusions are turned off (matches rate=-1)
EVID=-2 When the modeled duration infusions are turned off (matches rate=-2)
EVID=-10 When the specified rate infusions are turned off (matches rate>0)
EVID=-20 When the specified dur infusions are turned off (matches dur>0)
EVID=101,102,103,... Modeled time where 101 is the first model time, 102 is the second etc.

subsetNonmem

subset to NONMEM compatible EVIDs only. By default TRUE.

cores

Number of cores used in parallel ODE solving. This is equivalent to calling setRxThreads()

keep

is the keep sent to the table

drop

is the dropped variables sent to the table

Value

A list of table options for nlmixr2

Details

Use addCwres to add CWRES/FOCEi objective function, or addNpde to add NPDE/EPRED columns.

Author

Matthew L. Fidler