plot_scm: Visualize PsN SCM output.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plot_scm.R

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

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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, justin.wilkins@occams.com

See Also

NONMEM (http://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. https://doi.org/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. https://doi.org/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

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

## End(Not run)

pmxTools documentation built on Aug. 27, 2020, 1:10 a.m.