NEWS

---

smoppix 1.2.3

• Switch to mgcv::scasm for monotonically decreasing p-splines

smoppix 1.2.2

• Adapt code for negative hypergeometric from the orphaned extraDistr package and take it in-house

smoppix 1.2.1

• Anticipate coming changes to lme4

smoppix 1.1.10

• Allow addition of scale bars in plotExplore and plotCells

smoppix 1.1.9

• Added citation file to refer to the preprint directly
• Make sure vignettes are build upon installation and mentioned in readme

smoppix 1.1.8

• Export some convenience functions for other packages

smoppix 1.1.7

• Remove memory intensive looping over features in data preparation for mixed-effect modelling
• Depend on Rfast package for fast rowsorting
• Include tikzpicture as schematic overview in readme

smoppix 1.1.6

• Removing functionality related to Moran’s I
• Speed up and reduce memory requirements of linear (mixed) model fitting by preparing design matrices only once
• Correct bug in weighting for cell-wise nn distributions

smoppix 1.1.5

• Export loadBalanceBplappy for use in other packages
• Mention Bioconductor installer in README

smoppix 1.1.4

• Optimize addWeightFunction

smoppix 1.1.3

• Some speedups in the buildDataFrame function
• With reference to bioRxiv preprint

smoppix 1.1.2

• Calculate nnPair PIs only between desired features

smoppix 1.1.1

• Allow to pass own colours to plotExplore

smoppix 0.99.44

• Limit number of features to avoid windows timeout

smoppix 0.99.43

• Fixed bug on windows using bpnworkers()

smoppix 0.99.42

• Reviewed all manpages, clarifying user options

smoppix 0.99.41

• Clean up manpages for functions sharing the same example set

smoppix 0.99.40

• Use DOIs in URLs following winbuilder
• Use makeCluster() on windows in the examples too

smoppix 0.99.39

• Further round of reducing documentation and test time by pooling examples
• Test windows on a single core

smoppix 0.99.36

• Simplify documentation and reducing example runtimes by pooling manpages using the rdname commend

smoppix 0.99.30

• Reduce computation time of tests and vignettes in view of BioConductor server warnings
• Automate choice of parallel backend for different operating systems in vignette

smoppix 0.99.26

• Version bump with serial processing to find bug occurring only on server

smoppix 0.99.25

• ggplot2 objects are now returned for user customization
• Repeated return() calls are omitted
• NEWS file was updated to reflect all changes

smoppix 0.99.24

• Nuclei can be plotted using plotExplore()

smoppix 0.99.23

• Added addNuclei() function for adding nuclei as spatstat::owin

smoppix 0.99.21

• Bugfix in buildDataFrame

smoppix 0.99.20

• Reducing running times of examples to pass R CMD CHECK

smoppix 0.99.19

• Shorter example times

smoppix 0.99.17

• Bugfix in calcnnPi

smoppix 0.99.10

• Reducing computation time of the examples

smoppix 0.99.9

• Prediction of cell types

• Bugfixes in hyperframe building

smoppix 0.99.4

• Prediction of cell types

smoppix 0.99.0

• Submission to BioConductor

smoppix 0.1.1

• Use regular rather than squared distances to calculate nearest neighbour PIs

smoppix 0.1.0

• Published on github