plot_scm: Visualize PsN SCM output.

In pmxTools: Pharmacometric and Pharmacokinetic Toolkit

Visualize PsN SCM output.

Description

plot_scm returns a visualization of a Perl-speaks-NONMEM (PsN, https://uupharmacometrics.github.io/PsN/) SCM (stepwise covariate modeling) procedure. It depends on the presence of scmlog.txt and short_scmlog.txt files in the specified directory.

Usage

plot_scm(
  dir,
  startPhase = "forward",
  fwdSuccessCol = "#66C2A5",
  fwdFailCol = "black",
  bwdSuccessCol = "#FC8D62",
  bwdFailCol = "black",
  defCol = "black",
  fwdSuccessFillCol = "#B3E2CD",
  fwdFailFillCol = "white",
  bwdSuccessFillCol = "#FDCDAC",
  bwdFailFillCol = "white",
  defFillCol = "white",
  fwdSuccessFontCol = "black",
  fwdFailFontCol = "black",
  bwdSuccessFontCol = "black",
  bwdFailFontCol = "black",
  defFontCol = "black",
  fullFwdCol = "#8DA0CB",
  finalCol = "#E78AC3",
  fullFwdFillCol = "#CBD5E8",
  finalFillCol = "#F4CAE4",
  fullFwdFontCol = "black",
  finalFontCol = "black",
  fullFwdWidth = "2px",
  finalWidth = "2px",
  defWidth = "1px",
  nodeStyle = "filled,rounded",
  nodeShape = "box",
  fontname = "helvetica",
  rankdir = "TB",
  layout = "dot",
  lookupDF = NULL,
  ...
)

Arguments

dir	A PsN SCM folder (containing scmlog.txt and short_scmlog.txt).
startPhase	Where to start collating the output; can be "forward" (the default) or "backward".
fwdSuccessCol	Node outline color for a model fit matching the forward inclusion criterion.
fwdFailCol	Node outline color for a model fit not matching the forward inclusion criterion.
bwdSuccessCol	Node outline color for a model fit matching the backward elimination criterion.
bwdFailCol	Node outline color for a model fit not matching the backward elimination criterion.
defCol	Default node outline color.
fwdSuccessFillCol	Node fill color for a model fit matching the forward inclusion criterion.
fwdFailFillCol	Node fill color for a model fit not matching the forward inclusion criterion.
bwdSuccessFillCol	Node fill color for a model fit matching the backward elimination criterion.
bwdFailFillCol	Node fill color for a model fit not matching the backward elimination criterion.
defFillCol	Default node fill color.
fwdSuccessFontCol	Node font color for a model fit matching the forward inclusion criterion.
fwdFailFontCol	Node font color for a model fit not matching the forward inclusion criterion.
bwdSuccessFontCol	Node font color for a model fit matching the backward elimination criterion.
bwdFailFontCol	Node font color for a model fit not matching the backward elimination criterion.
defFontCol	Default node font color.
fullFwdCol	Node outline color for the full forward model (i.e. the final model before the backward elimination procedure in SCM).
finalCol	Node outline color for the final reduced model (i.e. the final model reached after the backward elimination procedure in SCM).
fullFwdFillCol	Node fill color for the full forward model (i.e. the final model before the backward elimination procedure in SCM).
finalFillCol	Node fill color for the final reduced model (i.e. the final model reached after the backward elimination procedure in SCM).
fullFwdFontCol	Node font color for the full forward model (i.e. the final model before the backward elimination procedure in SCM).
finalFontCol	Node font color for the final reduced model (i.e. the final model reached after the backward elimination procedure in SCM).
fullFwdWidth	Node outline width for the full forward model (i.e. the final model before the backward elimination procedure in SCM).
finalWidth	Node outline width for the final reduced model (i.e. the final model reached after the backward elimination procedure in SCM).
defWidth	Default node outline width.
nodeStyle	Node style. A string containing a comma-separated list of options (which include "filled", "striped", "wedged", "diagonals" and "rounded"). See the GraphViz documentation for further details.
nodeShape	Node shape. Options include "box" (the default), "oval", "diamond", "egg", "plaintext", "point", "square", "triangle" and many more. See the GraphViz documentation for further details.
fontname	Font for nodes. Options depend heavily on the local system - see the GraphViz documentation for further details.
rankdir	Direction of graph layout. Possible values are "TB" (the default), "LR", "BT", "RL", corresponding to directed graphs drawn from top to bottom, from left to right, from bottom to top, and from right to left, respectively.
layout	Graph layout. Possible values are "dot" (the default), "neato", "twopi", and "circo". Note that of these, "dot" is the easiest to interpret and the others may produce odd results.
lookupDF	A data frame containing a lookup table for node labels. By default, plot_scm will use the PSN model names. If a lookup table containing the fields 'Model' and 'Alias' is provided, model names in 'Model' will be replaced in the output plots by mtaching labels in 'Alias'.
...	Additional parameters passed to the underlying SetNodeStyle and SetEdgeStyle functions, which in turn rely on DiagrammeR.

Details

This function parses PsN SCM output and displays it as a GraphViz graph (effectively, an HTML widget). It is built on plot.Node - please refer to doucmentation for this function for a more detailed overview of what is possible (a lot). For more specific details, see http://rich-iannone.github.io/DiagrammeR/docs.html.

Value

A grViz object.

Author(s)

Justin Wilkins, [e-mail]

See Also

NONMEM (https://www.iconplc.com/innovation/nonmem/)

GraphViz (https://graphviz.org/Documentation.php)

Lindbom L, Ribbing J & Jonsson EN (2004). Perl-speaks-NONMEM (PsN) - A Perl module for NONMEM related programming. Computer Methods and Programs in Biomedicine, 75(2), 85-94. doi: 10.1016/j.cmpb.2003.11.003

Lindbom L, Pihlgren P & Jonsson N (2005). PsN-Toolkit - A collection of computer intensive statistical methods for non-linear mixed effect modeling using NONMEM. Computer Methods and Programs in Biomedicine, 79(3), 241-257. doi: 10.1016/j.cmpb.2005.04.005

Other NONMEM reading: read_nm_all(), read_nm_multi_table(), read_nmcov(), read_nmext(), read_nmtables(), read_nm(), read_scm()

Examples

## Not run: 
scm <- plot_scm("E:/DrugX/ModelDevelopment/scm310")

## End(Not run)

pmxTools documentation built on March 7, 2023, 7:58 p.m.