run_checks: DDEPN function tests.

In ddepn: Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

Description

Perform function tests for the different inference types and prior models.

Usage

run_checks(outfile = NULL, plotresults = TRUE)

wrapddepn(dataset, phit, stimuli, debug=FALSE, plotresults=TRUE, ...)
 
cls()

Arguments

outfile	String. A file name giving the file where output plots should be stored. If NULL, the user is asked for a file name via CLI. Unused, if plotresults=FALSE.
plotresults	Boolean. If TRUE, result plots are generated for each test and stored in file outfile. If FALSE, plots are omitted.
dataset	A sample dataset, e.g. generated by makedata.
phit	A sample network adjacency matrix, e.g. generated by signalnetwork.
stimuli	A list with sample stimuli, e.g. generated by signalnetwork.
debug	Boolean. Debug mode switch.
...	Further arguments passed to the ddepn call.

Details

run_checks

Run a set of tests to check whether all ddepn functions are working. The following tests are performed:

[1]	"GA, BIC optimisation"
[2]	"GA, uniform prior"
[3]	"GA, laplaceinhib, two types, lambda fix"
[4]	"GA, laplaceinhib, two types, lambda integrated"
[5]	"GA, laplace, one type, lambda fix"
[6]	"GA, laplace, one type, lambda integrated"
[7]	"GA, scalefree"
[8]	"inhibMCMC, uniform prior"
[9]	"inhibMCMC, laplaceinhib, two types, lambda fix"
[10]	"inhibMCMC, laplaceinhib, two types, lambda integrated"
[11]	"inhibMCMC, laplace, one type, lambda fix"
[12]	"inhibMCMC, laplace, one type, lambda integrated"
[13]	"inhibMCMC, scalefree"
[14]	"inhibMCMC, laplaceinhib, two types, sample lambda"

wrapddepn

A simple ddepn wrap function defining a default call of ddepn for the checks.

cls

Function for clearing the R-console.

Value

Matrix with the test results, where the first column holds the test and the second the result (passed or failed).

Author(s)

Christian Bender

Examples

## Not run: 
library(ddepn)
tests <- run_checks(plotresults=FALSE)

## End(Not run)

ddepn documentation built on May 2, 2019, 4:42 p.m.