predict.pk {invivoPKfit}R Documentation

Get predictions

Description

Extract predictions from a fitted 'pk' object.

Usage

## S3 method for class 'pk'
predict(
  object,
  newdata = NULL,
  model = NULL,
  method = NULL,
  type = "conc",
  exclude = TRUE,
  use_scale_conc = FALSE,
  suppress.messages = NULL,
  include_NAs = FALSE,
  ...
)

Arguments

object

A [pk] object.

newdata

Optional: A 'data.frame' with new data for which to make predictions. If NULL (the default), then predictions will be made for the data in 'object$data'. 'newdata' is required to contain at least the following variables: 'Time', 'Time.Units', 'Dose', 'Route', and 'Media'.

model

Optional: Specify one or more of the fitted models for which to make predictions. If NULL (the default), predictions will be returned for all of the models in 'object$stat_model'.

method

Optional: Specify one or more of the [optimx::optimx()] methods for which to make predictions. If NULL (the default), predictions will be returned for all of the models in 'object$settings_optimx$method'.

type

Either '"conc"' (the default) or '"auc"'. 'type = "conc"' predicts concentrations; 'type = "auc"' predicts area under the concentration-time curve (AUC).

exclude

Logical: 'TRUE' to return 'NA_real_' for any observations in the data marked for exclusion (if there is a variable 'exclude' in the data, an observation is marked for exclusion when 'exclude 'FALSE' to return the prediction for each observation, regardless of exclusion. Default 'TRUE'.

use_scale_conc

Possible values: 'TRUE', 'FALSE', or a named list with elements 'dose_norm' and 'log10_trans' which themselves should be either 'TRUE' or 'FALSE'. If 'use_scale_conc = TRUE', then the concentration scaling/transformations in 'object' will be applied to both predicted and observed concentrations before the log-likelihood is computed. If 'use_scale_conc = FALSE' (the default for this function), then no concentration scaling or transformation will be applied before the log-likelihood is computed. If 'use_scale_conc = list(dose_norm = ..., log10_trans = ...)', then the specified dose normalization and/or log10-transformation will be applied.

suppress.messages

Logical: whether to suppress message printing. If NULL (default), uses the setting in 'object$settings_preprocess$suppress.messages'

include_NAs

Logical: 'FALSE' by default. Determines whether to include aborted fits which have NAs as coefficients.

...

Additional arguments.

Value

A data.frame with one row for each 'data_group', 'model' and 'method'. Includes variable 'Conc_est' that contains the predicted concentration or AUC at that timepoint given the TK parameters for that 'model' and 'method' specified in [coefs()]. If 'use_scale_conc un-transformed concentrations in the same units as 'object$data$Conc.Units'. If 'use_scale_conc concentrations in the same units as 'object$data$Conc_trans.Units'.

Author(s)

Caroline Ring, Gilberto Padilla Mercado

See Also

Other methods for fitted pk objects: AAFE.pk(), AFE.pk(), AIC.pk(), BIC.pk(), coef.pk(), coef_sd.pk(), eval_tkstats.pk(), get_fit.pk(), get_hessian.pk(), get_tkstats.pk(), logLik.pk(), residuals.pk(), rmse.pk(), rsq.pk()


[Package invivoPKfit version 2.0.1 Index]