vpcmodel.Rd
Perform visual predictive check for NLME models
vpcmodel(
model,
vpcParams,
params,
hostPlatform = NULL,
runInBackground = FALSE,
...
)
PK/PD model class object.
VPC argument setup. See NlmeVpcParams
.
If missing
, default values generated by NlmeVpcParams() are used.
Engine argument setup. See engineParams
. The following
arguments are the subject of interest: sort, ODE, rtolODE, atolODE, maxStepsODE.
If missing
, default values generated by engineParams(model) are used.
Host definition for model execution. See hostParams
.
If missing
, simple local host is used.
Set to TRUE
to run in background and return prompt.
Additional class initializer arguments for NlmeVpcParams
or
hostParams
, or arguments available inside engineParams
functions.
If engineParams
arguments are supplied through both params
argument
and additional argument (i.e., ellipsis), then the arguments in params
will be ignored
and only the additional arguments will be used with warning.
If hostParams
arguments are supplied through both hostPlatform
argument and additional argument, then its values will be overridden by additional arguments.
In addition, if NlmeVpcParams
arguments are supplied through both
vpcParams
argument and additional argument,
then its slots will be overridden by additional arguments.
if runInBackground is TRUE
, it returns job properties.
Otherwise,
If the function is called in an interactive mode, the resulting simulated tables and summary statistics tables will be loaded and presented as a list;
If the function is called in a non-interactive mode, it returns the full paths of the tables generated
if (FALSE) {
job <- fitmodel(model)
# View estimation results
print(job)
finalModelVPC <- copyModel(model, acceptAllEffects = TRUE, modelName = "model_VPC")
# View the model
print(finalModelVPC)
# Set up VPC arguments to have PRED outputted to simulation output dataset "predout.csv"
vpcSetup <- NlmeVpcParams(outputPRED = TRUE)
# Run VPC using the default host, default values for the relevant NLME engine arguments
finalVPCJob <- vpcmodel(model = finalModelVPC, vpcParams = vpcSetup)
# the same as:
finalVPCJob <- vpcmodel(model = finalModelVPC, outputPRED = TRUE)
# Observed dataset predcheck0.csv
dt_ObsData <- finalVPCJob$predcheck0
# Simulation output dataset predout.csv
dt_SimData <- finalVPCJob$predout
# Add PRED from REPLICATE = 0 of simulation output dataset to observed input dataset
dt_ObsData$PRED <- dt_SimData[REPLICATE == 0]$PRED
# tidyvpc package VPC example:
library(magrittr)
library(tidyvpc)
# Create a regular VPC plot with binning method set to be "jenks"
binned_VPC <- observed(dt_ObsData, x = IVAR, yobs = DV) %>%
simulated(dt_SimData, ysim = DV) %>%
binning(bin = "jenks") %>%
vpcstats()
plot_binned_VPC <- plot(binned_VPC)
# Create a pcVPC plot with binning method set to be "jenks"
binned_pcVPC <- observed(dt_ObsData, x = IVAR, yobs = DV) %>%
simulated(dt_SimData, ysim = DV) %>%
binning(bin = "jenks") %>%
predcorrect(pred = PRED) %>%
vpcstats()
plot_binned_pcVPC <- plot(binned_pcVPC)
}