| NEWS | R Documentation |
New goftest() function, which may return a test of goodness of fit.
Improved sampling of parameter space in refine().
Several functions have a new argument 'cluster_args', passed to parallel::makeCluster(), for better control of the parallel computations. These functions' 'nb_cores' argument now acts as a shortcut for cluster_args$spec, in a backward-compatible way.
add_reftable() results can be more easily subsetted thanks to a new '[' method.
For better control of 1D profiles, plot1Dprof() gets new options for argument 'type', and new argument 'control'.
Refined use of function optimizers, which generally performs better than the previously used base optimizer (optim()).
plot.SLik_j(), plot1Dprof() and plot2Dprof() now re-run MSL(., eval_RMSEs=FALSE, CIs=FALSE) when they detect a new likelihood maximum, and discard pre-existing CI/RMSE information as these depend on the maximum. plot1Dprof() and plot2Dprof() now have a return value indicating whether MSL() was re-run.
New extractor get_from() to extract elements from summary-likelihood objects in a backward-compatible way.
Better control of verbosity in refine().
Tenfold larger default 'knotNbr' for ranger() projection method than previously.
New 'logLik' extractor.
'Rmixmod', which had disappeared from the dependencies in recent versions, is back in Suggested packages.
'nloptr' and 'minqa' now used for optimization.
'crayon' added in Suggests, with no visible effects yet in standard use.
Default model for Gaussian mixture modelling changed.
add_simulation() argument 'Simulate' can now be a function (rather than a name) and the return value's attr(.,"Simulate") is always the function rather than its name.
New Infusion.options "mixturing" (which replaces some previously undocumented options).
Slightly modified parameter sampling in refine(), so that all ensuing results will be slightly modified.
add_simulation() could fail to pass the definition of 'Simulate' to child processes in parallel computations.
project.default() could fail on one-dimensional statistics (a toy case).
Out-of-bag projections used whenever relevant in projections using random-forests methods (which definitely improves the results over "in-bag" projections).
New 'eval_RMSEs' argument of function refine.default().
New argument 'update_projectors' in refine.default(), effective only for the reference table method.
'ranger' package included in Suggests; random forest by 'ranger' is the new default projection 'method' in project.character().
infer_SLik_joint() can now (automatically) provide correct results when there is *one* probability mass in the distribution of the summary statistics.
infer_SLik_joint() can now handle 'using="mclust"' (but this will still provide incorrect results when there is a probability mass in the distribution of the summary statistics).
Objects of class 'SLik_j' using projection now retain a cumulative table of unprojected simulations, from which new projections can be generated.
Revised documentation including examples for the inference method based on reference tables.
Internal methods in infer_SLik_joint() are modified by default so that numerical results are slightly modified. See its new argument 'marginalize' to control this.
Defaults Infusion options 'projTrainingSize' and 'projKnotNbr' for projection by REML have been increased, because the called procedures are more efficiently implemented in versions of spaMM >= 2.7.0.
RMSE computation on SLik_j objects could fail following Rmixmod::mixmodCluster()'s failure to fit a bootstrap replicate.
Potential problems with figure rendering when Rstudio's graphic device was *not* used.
New 'nb_cores', 'packages' and 'env' arguments for more widely allowing parallel simulation in add_simulation() and refine().
New '...' (or 'control.Simulate') argument in add_simulation() for controlling the 'Simulate' arguments.
Dependencies changed for parallel computations; ”doSNOW' usage has been reinstated optionally (though only 'foreach' appears in the package dependencies). See help("Infusion.options") for details.
plot.SLik() failed for more than two parameters.
project() did not work on reference tables.
DESCRIPTION now Suggests 'Rmixmod' rather than Imports it. This means that, even if 'Rmixmod' were to be archived from CRAN (which has nearly occurred in March 2018), 'Infusion' could still be installed and run without 'Rmixmod', using 'mclust' as an alternative for model-based clustering. 'Rmixmod' is still the preferred method.
'mclust', 'caret' and 'ks' have been removed from DESCRIPTION (but can still be used without changes in user's code).
Imports package 'pbapply' to draw progress bars, including in parallel computations; no longer Suggests the package 'foreach' (and optionally 'doSNOW') for the same effect.
infer_SLik_joint() can now use procedures from the 'mclust' package (controlled by new argument 'using').
The calls to 'mclust' procedures in other Infusion functions have been revised to be comparable to calls to 'Rmixmod' procedures. This means in particular that the 'G' and 'modelNames' arguments of 'mclust' procedures are set to values equivalent to the corresponding arguments of calls to 'Rmixmod' procedures, and that Infusion uses AIC to select the number of gaussian clusters in both cases (although selection by AIC is implemented in neither of the clustering packages).
infer_logLs() can now analyze the input distributions in parallel. This is controlled by its new 'nb_cores' argument, and may make use of another new argument, 'packages'.
Infusion.options(<new values>) did not return old values.
New function infer_SLik_joint() to infer likelihood surfaces from a simulation table where each simulated data set is drawn for a distinct (vector-valued) parameter, as is usual for reference tables in Approximate Bayesian Computation.
'Infusion' now depends on package 'blackbox' for several functions moved there from package 'spaMM'.