NEWS.md

In xnet: Two-Step Kernel Ridge Regression for Network Predictions

xnet 0.1.11

Bug fixes

• unnecessary mentions of dots argument removed from some help pages.
• linear_filter() takes floating point errors into account when checking whether the alpha values sum to 1.

xnet 0.1.10

Breaking changes

• get_kernel is renamed get_kernelmatrix. the function get_kernel is deprecated.
• tskrrHomogenous and dependent classes are now called tskrrHomogeneous. The same correction is done for tskrrHeterogenous to tskrrHeterogeneous. This might affect code that uses get_loo_fun based on the class name.
• tskrrHomogeneousImpute and tskrrHeterogeneousImpute were renamed to tskrrImputeHomogeneous and tskrrImputeHeterogeneous to follow the naming convention for the classes.

New features

• the permtest class now has getters that allow to extract the information from the test.
• For LOO-CV, you can use the alternatives "edges" and "vertices" for the settings "interaction" and "both" respectively. These give the same results, and make it more clear what actually happens. This is adapted in functions loo(), get_loo_fun(), tune() and those dependent on it.

Bug fixes and minor improvements

• All help pages are checked and corrected where necessary.

xnet 0.1.9

Breaking changes

• For consistency, the g matrix in predict() now expects the new nodes to be on the rows.

New features

• the permtest function is added.

Bug fixes and minor improvements

xnet 0.1.8

Breaking changes

• For consistency, the arguments K and G for the function predict() have been renamed k and g (lower case).
• loo now adds the labels to the output (except for linear filters)

New features

• tune now allows for a one-dimensional grid search for heterogenous networks. Set onedim = TRUE to avoid a full grid search.
• has_onedim tells whether the grid search was one dimensional or not. This is a getter for the appropriate slote in the tskrrTune class.
• plot_grid allows you to plot the loss in function of the searched grid after tuning a model. It deals with both 1D and 2D grids and can be used for quick evaluation of the optimal lambda values.
• residuals allows you to calculate the residuals based on the predictions or on the loo values of choice.
• There's a plot method available now for tskrr objects. It allows to plot fitted values, residuals, original response and the results of different loo settings, together with dendrograms based on the kernel matrices.

Bug fixes and minor improvements

• predict didn't give correct output when only g was passed. fixed.
• colnames didn't get the correct labels for homogenous networks

xnet 0.1.7

Breaking changes

• Preliminary function impute_loo is removed from the package.
• eigen2hat, eigen2map and eigen2matrix had the second argument renamed from vec to val. The old name implied that the second argument took the vectors, which it doesn't!

New features

• A tskrrImpute virtual class is added to represent imputed models.

bug fixes and minor improvements

• is_symmetric didn't take absolute values to compare. Fixed.
• show methods for objects are cleaned up.
• predict gave nonsensical output. Fixed.

xnet 0.1.6

Breaking changes

• valid_labels now requires the K and G matrices to have the same ordering of row and column names. Otherwise the matrix wouldn't be symmetric and can't be used.
• linear_filter now forces the alphas to sum up to 1.
• tune now returns an object of class tskrrTuneHomogenous or tskrrTuneHeterogenous.

New features

• the class tskrrTune provides a more complete object with all information of tuning. It is a superclass with two real subclasses, tskrrTuneHeterogenous and tskrrTuneHomogenous.
• the function tune now allows to pass the matrices directly so you don't have to create a model with tskrr first.

bug fixes and minor improvements

• linear_filter gave totally wrong predictions due to a code error: fixed.
• linear_filter returned a matrix when NAs were present: fixed.
• fitted now has an argument labels which allows to add the labels to the returned object.
• tskrr now returns an error if the Y matrix is not symmetric or skewed when fitting a homogenous network.

• labels now produces more informative errors and warnings.

• In the testing procedures

  • testing skewed homogenous networks added.
  • testing validations added
  • testing symmetric calculations
  • testing processing of labels
  • testing shortcuts
  • testing update function

• input testing for tskrr moved to its own function and is also used by impute_tskrr now.

xnet 0.1.5

Breaking changes

• class tskrr, tskrrHeterogenous and tskrrHomogenous:

  • the slot has.orig has been removed as it doesn't make sense to keep the original kernel matrices. It is replaced by a slot has.hat allowing to store the hat matrices.
  • the slots k.orig and g.orig have been replaced by the slots Hk and Hg to store the hat matrices. These are more needed for fitting etc.

• The function has_original has been removed and replaced by has_hat

• The argument keep of the function tskrr now stores the hat matrices instead of the original kernel matrices.
• The function tskrr has lost its argument homogenous. It didn't make sense to set that by hand.

New features

• classes tskrrHeterogenousImpute and tskrrHomogenousImpute are added to allow for storing models with imputed predictions.

bug fixes and minor improvements

xnet 0.1.4

breaking changes

• get_loo_fun() :

  • argument homogenous removed in favor of x. This allows for extension of the function based on either an object or the class of that object.
  • x becomes the first argument.

New features

• There's a new function linear_filter that fits a linear filter over an adjacency matrix. This function comes with a class linearFilter.
• tune() has a new argument fun that allows to specify a function for optimization.
• functions loss_mse() and loss_auc() are provided for tuning.
• update() allows to retrain the model with new lambdas.

bug fixes and minor improvements

• predictions were calculated wrongly in tune(): fixed.
• MSE was calculated wrongly in the previous version of tune(): fixed.

xnet documentation built on Feb. 4, 2020, 9:10 a.m.