plot_eGOF: FUNCTION FOR PRODUCING GOF PLOTS

In jgrevel/BAST1-R-Library: BAST R function library.

Description

Function to generate GOF plots for NONMEM models Similar to the standard GOF plots in BAST1 library except: Colours are all grayscale or black Units can be added to axis labels, LOWESS smoothed lines can be removed (set fval=NA) DV, PRED, and IPRED can be set to display on log scale Mean residuals in bins can be used instead of LOWESS smooths (set bin limits using bins_PRED and bins_ind_var arguments) Alternative layout can be resquested for IWRES plots

Extensive examples of use are available in this location:

\\BAST_SERVER\BAST_Shared_Files\QA Documents\BAST Computer Systems Validation\final_documents\BAST_NONMEM_USERS_MANUAL\GOF_VPC_examples\enhanced_GOF\run100

Usage

plot_eGOF(data, type = "CWRES", ind_var = "TAD", log_ind_var = FALSE,
  bks = 30, fval = 0.66, bins_PRED = NA, bins_ind_var = NA,
  dv_units = "ug/L", dv_label = "DV", ind_var_units = "hour",
  loglog = FALSE, pt_col = "gray70", alt_plots = FALSE)

Arguments

data	Data frame containing output from NONMEM run
type	Defines type of plots to return: CWRES / IWRES / NPDE (default='CWRES')
ind_var	Name of the independent variable column (default='TAD')
log_ind_var	FALSE/TRUE for setting logarithmic x-axis in some of the plots (default=FALSE)
bks	Defines number of bins in histograms (default=30)
fval	Smoothing setting for LOWESS trend lines (larger values give smore smoothing, default=0.66). Set to NA to exclude trend lines.
bins_PRED	Defines bin limits for PRED/IPRED if binned residual display is required (default=NA)
bins_ind_var	Defines bin limits for ind_var if binned residual display is required (default=NA)
dv_units	Units of the observations for axis labelling (default='ug/L')
dv_label	Axis label for DV in plots (default='DV')
ind_var_units	Units of the independent variable for axis labelling (default='hour')
loglog	TRUE/FALSE. If TRUE then DV vs PRED and DV vs IPRED are presented on log-log scales, and CWRES/IWRES vs. PRED/IPRED has log x-axis (default=FALSE)
pt_col	Colour of points in all plots (default='gray70')
alt_plots	Specifies if alternative layout of IWRES plots should be returned FALSE/TRUE (default=FALSE)

Details

If alt_plots=FALSE then output will be: CWRES: DV VS. PRED, DV VS. IPRED, CWRES VS. PRED, CWRES VS. ind_var, QQ plot of CWRES, histogram of CWRES IWRES: IWRES VS. IPRED, IWRES VS. ind_var, |IWRES| VS. IPRED, |IWRES| VS. ind_var, QQ plot of IWRES, histogram of IWRES NPDE: NPDE VS. ind_var, NPDE VS. PRED, QQ plot of NPDE, histogram of NPDE

If alt_plots=TRUE then IWRES output will be changed to: IWRES: DV VS. PRED, DV VS. IPRED, IWRES VS. PRED, IWRES VS. ind_var, QQ plot of IWRES, histogram of IWRES

Value

Produces a panel of GOF plots

Author(s)

Rupert Austin

jgrevel/BAST1-R-Library documentation built on May 21, 2019, 10:11 a.m.