data matrix with experiments in the columns (binary or continious)
inference
search to use exhaustive enumeration, triples for triple-based inference, pairwise for the pairwise heuristic, ModuleNetwork for the module based inference, nem.greedy for greedy hillclimbing, nem.greedyMAP for alternating MAP optimization using log odds or log p-value densities
models
a list of adjacency matrices for model search. If NULL, an exhaustive enumeration of all possible models is performed.
control
list of parameters: see set.default.parameters
verbose
do you want to see progression statements? Default: TRUE
...
other arguments to pass to function nem or network.AIC
Details
nemModelSelection internally calls nem to infer a model with a given regularization constant. The comparison between models is based on the BIC or AIC criterion, depending on the parameters passed to network.AIC.
Value
nem object
Author(s)
Holger Froehlich
See Also
set.default.parameters, nem, network.AIC
Examples
data("BoutrosRNAi2002")
D <- BoutrosRNAiDiscrete[,9:16]
hyper = set.default.parameters(unique(colnames(D)), para=c(0.13, 0.05), Pm=diag(4))
res <- nemModelSelection(c(0.1,1,10), D, control=hyper)
plot.nem(res,main="highest scoring model")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(nem)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/nem/nemModelSelection.Rd_%03d_medium.png", width=480, height=480)
> ### Name: nemModelSelection
> ### Title: Model selection for nested effect models
> ### Aliases: nemModelSelection
> ### Keywords: graphs models
>
> ### ** Examples
>
> data("BoutrosRNAi2002")
> D <- BoutrosRNAiDiscrete[,9:16]
> hyper = set.default.parameters(unique(colnames(D)), para=c(0.13, 0.05), Pm=diag(4))
> res <- nemModelSelection(c(0.1,1,10), D, control=hyper)
Greedy hillclimber for 4 S-genes (lambda = 0.1 )...
Computing (marginal) likelihood for 1 models
--> Using regularization to incorporate prior knowledge
12 local models to test ...
Computing (marginal) likelihood for 12 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 20.75064 )
--> Edge added, removed or reversed
12 local models to test ...
Computing (marginal) likelihood for 12 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 1.486884 )
--> Edge added, removed or reversed
11 local models to test ...
Computing (marginal) likelihood for 11 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 0.4669048 )
--> Edge added, removed or reversed
10 local models to test ...
Computing (marginal) likelihood for 10 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 15.02184 )
--> Edge added, removed or reversed
5 local models to test ...
Computing (marginal) likelihood for 5 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 82.00684 )
log-likelihood of model = -288.0096
Greedy hillclimber for 4 S-genes (lambda = 1 )...
Computing (marginal) likelihood for 1 models
--> Using regularization to incorporate prior knowledge
12 local models to test ...
Computing (marginal) likelihood for 12 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 20.75064 )
--> Edge added, removed or reversed
12 local models to test ...
Computing (marginal) likelihood for 12 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 1.486884 )
--> Edge added, removed or reversed
11 local models to test ...
Computing (marginal) likelihood for 11 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 1.366905 )
--> Edge added, removed or reversed
10 local models to test ...
Computing (marginal) likelihood for 10 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 13.22184 )
--> Edge added, removed or reversed
5 local models to test ...
Computing (marginal) likelihood for 5 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 83.80684 )
log-likelihood of model = -255.6682
Greedy hillclimber for 4 S-genes (lambda = 10 )...
Computing (marginal) likelihood for 1 models
--> Using regularization to incorporate prior knowledge
12 local models to test ...
Computing (marginal) likelihood for 12 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 20.75064 )
--> Edge added, removed or reversed
12 local models to test ...
Computing (marginal) likelihood for 12 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 1.486884 )
--> Edge added, removed or reversed
11 local models to test ...
Computing (marginal) likelihood for 11 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 10.3669 )
--> Edge added, removed or reversed
10 local models to test ...
Computing (marginal) likelihood for 10 models
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
--> Using regularization to incorporate prior knowledge
((Marginal) posterior likelihood difference of best vs. second best model for rel key tak mkk4hep : 4.778158 )
log-likelihood of model = -259.0487
==> AIC ( lambda = ) = 487.532817873473 ( #param = 5 )===============
==> AIC ( lambda = ) = 487.532817873473 ( #param = 5 )===============
==> AIC ( lambda = ) = 509.543078495049 ( #param = 3 )===============
====> chosen best model with lambda = 0.1
>
> plot.nem(res,main="highest scoring model")
>
>
>
>
>
> dev.off()
null device
1
>