Description Usage Arguments Value Author(s) Examples
View source: R/as.ESS.object.R
The as.ESS.object
function compiles the main information
relating to a previous run of R2GUESS
and compiles them into
an ESS
object to be further analyzed. Main parameters (e.g. nsweep, burn.in
) are read from the
'feature
' file automatically generated at the end of every
R2GUESS
run. Main outputs are also included in the object to
enable post-processing and further analyses.
1 2 3 4 |
dataY |
a character vector (such as
' |
dataX |
is a character vector (such as
' |
path.input |
path linking to the directory containing the data
( |
path.output |
path indicating the directory in which output files are saved. |
root.file.output |
name specifying the file stem of the
different output files in the |
label.X |
a character vector specifying the name of the
predictors. If not specified (=NULL), the variables are labelled
by their position in the matrix. Predictors name and information
can be given in the |
label.Y |
a character vector specifying the name of
the outcomes. If not specified (=NULL), the outcomes are
labelled by Y1,..Yq where q is the dimension of the
response matrix, or will be the name of the argument
|
path.par |
path to the directory containing the
parameter file (argument |
path.init |
path to the directory containing the |
file.par |
name of the parameter file containing all the
user-specified parameters used to set up the run and the features
of the moves. This file is located in |
file.init |
name of the file specifying which variable have been included at the iteration of the MCMC run. |
file.log |
name of the log file. This file compiles in real time
summary information describing the initial parameters, the
computational time and state of the run. This file will also
contains information about moves sampled at each sweep. By default
(= |
MAP.file |
is either a one element character vector or a data
frame. If a character vector is used, it specifies, assuming that data are in the
|
command |
Boolean specifying whether the automatically generated C++ command line is saved in the object or not. |
An object of class ESS
which compiles the following
information:
|
a character vector defining the location of the response matrix, assuming that data are in the |
|
a character vector defining the location of the predictor matrix, assuming that data are in the |
|
path linking to the directory containing the data ( |
|
path indicating the directory in which output files were saved. |
|
path indicating the directory in which to find the parameter file used for the run. |
|
path indicating the location of file
describing the initial guess of the MCMC procedure. If no
|
|
Boolean value indicating if a file recording the
time each sweep took has been created and saved in |
|
name of the parameter file containing all the user-specified parameters used to set up the run and the features of the moves. |
|
name of the file specifying which variables
were arbitrarily included at the iteration of the MCMC run. If no |
|
location of the log file. |
|
file name specifying the file stem used
to write the output files in the directory specified by |
|
integer specifying the number of sweeps of the MCMC run (including the burn-in). |
|
the number of top models that are reported in the output. |
|
A list describing the best model
visited, with respect to the fields listed in the |
|
a character vector specifying the name of the predictors. If not specified (=NULL), the variables are labelled by their position in the matrix from 1 to p. |
|
a character vector specifying the name of the outcomes. If not specified (=NULL), the outcomes are labelled by Y1,..Yq, where q is the dimension of the outcome matrix. |
|
the number of predictors in the X matrix. |
|
the number of outcomes in the response matrix. |
|
the number of observations. |
|
the number of chains in the evolutionary algorithm. |
|
integer specifying the number of sweeps which were discarded to account for burn-in. |
|
a character vector defining the location of the file compiling observed values for the confounders of interest. |
|
a boolean value indicating if linear algebra operations have been re-routed towards the GPU. |
|
a priori average model size. |
|
a priori standard deviation of the model size. |
|
a character vector specifying the location of
the predictor annotation file, assuming that data are in
|
|
a character vector describing the |
|
the random seed used to initialise the pseudo-random number generator. |
|
a Boolean value indicating if the run terminated, or was interrupted before reaching the user-defined time limit. |
Benoit Liquet, b.liquet@uq.edu.au,
Marc Chadeau-Hyam m.chadeau@imperial.ac.uk,
Leonardo Bottolo l.bottolo@imperial.ac.uk,
Gianluca Campanella g.campanella11@imperial.ac.uk
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | dataX <- "data-X-C-CODE.txt"
dataY <- "data-Y-ALL-C-CODE.txt"
path.input <- system.file("Input", package="R2GUESS")
path.output <- tempdir()
file.copy(system.file("Output", package="R2GUESS"), path.output, recursive = TRUE)
path.output <- file.path(path.output, "Output")
path.par <- system.file("extdata", package="R2GUESS")
file.par <- "Par_file_example_Hopx.xml"
root.file.output <- "Example-GUESS-Y-Hopx"
label.Y <- c("ADR","Fat","Heart","Kidney")
my.env <- new.env()
data(MAP.file,envir=my.env)
MAP.file <- my.env$MAP.file
modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
path.output=path.output,root.file.output=root.file.output,label.X=NULL,
label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
print(modelY_Hopx)
class(modelY_Hopx)
|
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