plotcim.explore
(Package: R2GUESS) :
Plots a cluster image mapping of correlations between
The plot.cim.explore function plots a cluster image mapping of correlations between outcomes and all the predictors.
● Data Source:
CranContrib
● Keywords:
● Alias: plotcim.explore
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1 images
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plot.ESS
(Package: R2GUESS) :
Provides diagnostic plots to assess the convergence of the MCMC
The plot.ESS function provides a set of four plots summarising the behaviour of all chains along the Evolutionary Monte Carlo run. These plots are used to assess the convergence of the algorithm and comprise: (i)- the history plot of the shrinkage factor g, (ii)- the history plot of the model size in each chain, (iii)- the history plot of the log posterior in each chain, and (iv)- the history plot of each chain's temperature (during the burn-in only, as temperatures are fixed at the end of the burn-in).
● Data Source:
CranContrib
● Keywords:
● Alias: plot.ESS
●
1 images
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pairwise.correlation
(Package: R2GUESS) :
Calculates and plots the pairwise correlation between outcomes
The pairwise.correlation function plots an image with the pairwise correlation between phenotypes and provides the corresponding source matrix.
● Data Source:
CranContrib
● Keywords:
● Alias: pairwise.correlation
●
1 images
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plotvariable
(Package: R2GUESS) :
Visualisation of the best models
The plotvariable function provides a plot indicating the variables included in each of the best models.
● Data Source:
CranContrib
● Keywords:
● Alias: plotvariable
●
1 images
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summarybest.model
(Package: R2GUESS) :
Internal function used for the summary.ESS function.
Internal function used for the summary.ESS function.
● Data Source:
CranContrib
● Keywords: internal
● Alias: summarybest.model
●
0 images
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get.best.models
(Package: R2GUESS) :
Internal function used to read in R the result of the best model
Internal function used to read in R the result of the best model
● Data Source:
CranContrib
● Keywords: internal
● Alias: get.best.models
●
0 images
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R2GUESS.perm
(Package: R2GUESS) :
Internal function used for the parallel computation on the permutation procedure for the calibration of the FDR threshold
Internal function used for the parallel computation on the permutation procedure for the calibration of the FDR threshold regarding the significance of the MPPI. This function run GUESS on permutation sample.
● Data Source:
CranContrib
● Keywords: internal
● Alias: R2GUESS.perm
●
0 images
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check.convergence
(Package: R2GUESS) :
Diagnostic plots for the evaluation of the convergence of the
The check.convergence function provides two plots (selectable by which) to investigate the convergence of the posterior distribution towards the target distribution at different stages of the algorithm.
● Data Source:
CranContrib
● Keywords:
● Alias: check.convergence
●
6 images
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R2GUESS
(Package: R2GUESS) :
Wrapper function that reads the input files and parameter values required by
The R2GUESS function reads and compiles data, input files and parameters that are required to run GUESS source code. It automatically runs GUESS (enabling or not the GPU capacity), saves the results and summary files in text files. For portability, R2GUESS generates an ESS object which compiles information about the input and parameters used to run GUESS, and outputs as detailed in as.ESS.object.
● Data Source:
CranContrib
● Keywords:
● Alias: R2GUESS
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0 images
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Analysis.permutation
(Package: R2GUESS) :
Computing the FDR-controlled level for the significance of the MPPI
Reads outputs from a preliminary set of permutation runs of GUESS mimicking the null hypothesis of no association (shuffling the responses). Results will subsequently be used to derive the cut-off values for the Marginal Posterior Probability Inclusion of (MPPI ) ensuring an empirical FDR control at a user-defined level. Several cut-off values will be investigated and, for each, the corresponding empirical FDR will be returned. The cut-off value providing the closest FDR estimate to the desired level will be retained. Exact match to the desired level will be achieved by linear interpolation. For flexibility, Analysis.permutation only performs the calculation of the FDR-controlled cut-off value based on a preliminary set of permuted runs of GUESS, while the function FDR.permutation - which is based on the same procedure - also includes the permutations.
● Data Source:
CranContrib
● Keywords:
● Alias: Analysis.permutation
●
0 images
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.