NumericalCheck: The numerical predictive checks

In nlmeVPC: Visual Model Checking for Nonlinear Mixed Effect Model

The numerical predictive checks

Description

This function calculates the numerical predictive checks for each prediction level. For a given level of prediction, the predicted interval is calculated using the simulated data, and the number of observed data below the predicted interval is counted. The expected number of points below the predicted interval is also calculated and compared to the observed number.

Usage

NumericalCheck(orig_data,
               sim_data,
               N_xbin = NULL,
               pred.level = c(0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9),
               conf.level = 0.95,
               X_name = "TIME",
               Y_name = "DV",
               MissingDV = NULL,
               Kmethod = "cluster",                
               maxK = NULL,
               beta = 0.2,
               lambda = 0.3,
               R = 4,
               C1 = 2.5,
               C2 = 7.8, ...)

Arguments

orig_data	A data frame of original data with X and Y variable.
sim_data	A matrix of simulated data with only Y values collected.
N_xbin	Number of bins in X variable. If NULL, optimal number of bins are automatically calcuated using optK function.
pred.level	Numeric vector of probabilities.
conf.level	Confidence level of the interval.
X_name	Name of X variable in orig_data (usually "TIME" in pharmacokinetic data).
Y_name	Name of Y variable in orig_data (usually "DV" in pharmacokinetic data).
MissingDV	Name of missing indicator variable in orig_data, which have value 1 if missing, value 0 otherwise. (usually "MDV" in pharmacokinetic data).
Kmethod	The way to calculate the penalty in automatic binning."cluster" or "kernel".
maxK	The maximum number of bins.
beta	Additional parameter for automatic binning, used in optK function.
lambda	Additional parameter for automatic binning, used in optK function.
R	Additional parameter for automatic binning, used in optK function.
C1	Additional parameter for automatic binning, used in optK function.
C2	Additional parameter for automatic binning, used in optK function.
...	Arguments to be passed to methods.

Value

The result of numerical predictive check

References

Holford N, & Karlsson M. (2008). "A tutorial on visual predictive checks, abstr 1434." Annual Meeting of the Populations Approach Group in Europe. www.page-meeting.org. 2008.

Harling, Uekcert, K. 2018. VPC and NPC User Guide. ICON plc.

https://github.com/UUPharmacometrics/PsN/releases/download/4.9.0/vpc_npc_userguide.pdf.

Examples

data(origdata)
data(simdata)
NumericalCheck(origdata,simdata,N_xbin=8)$NPC

nlmeVPC documentation built on Dec. 28, 2022, 2:49 a.m.