NAIR 1.0.2

Minor Changes and Bug Fixes

NAIR 1.0.1

Breaking Changes

New Features

This section covers general new features. Other new features are grouped by subject in the following few sections.

Unified Primary Argument Across Functions

Several changes and additions have been made in favor of using the list of network objects returned by buildRepSeqNetwork() as a unified primary input and output across the core NAIR functions. Adopting this convention offers several benefits: It greatly simplifies usage, since users no longer need to know which components of the list to input to which function (or what each function returns); it eliminates the task of manually updating the list of network objects; it results in the core functions working with the pipe operator; and most importantly, it improves functionality within and between functions, since functions can read and modify anything in the network list. For instance, addPlots() can use the coordinate layout of any existing plots to ensure a consistent layout across plots (which is no longer guaranteed otherwise), while addClusterStats() can add cluster membership values to the node metadata and record in details that the cluster properties correspond to these membership values (and not the values from a different instance of clustering using a different algorithm).

The following changes encompass the move toward using the network list as a primary input/output:

See the new “Supplementary Functions” vignette for examples.

Multiple Instances of Clustering

The following changes and additions have been made to facilitate multiple instances of clustering on the same network using different clustering algorithms. See the new “Cluster Analysis” vignette for examples.

It may also be of interest in the future to add functionality allowing the network list to contain multiple sets of cluster properties corresponding to different instances of clustering.

Plots and Graph Layout

Plotting functions no longer fix the random seed when generating the coordinate layout for a plot. In order to facilitate a consistent layout across multiple plots of the same network graph, the following changes have been made.

Essentially, generating new plots with addPlots() will ensure a consistent layout with the initial plots. Fixing a random seed before calling buildRepSeqNetwork() (or before the first call to addPlots(), if buildRepSeqNetwork() is called with plots = FALSE) allows the same layout to be reproduced across multiple executions of the same code in which the initial plots are generated.

Improved File Input Functionality

Lifecycle Changes

Minor Changes and Bug Fixes

NAIR 0.0.9044

Breaking Changes

New Features

Minor Changes and Bug Fixes

Lifecycle Changes

Documentation Changes

Backend Package Changes

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Package Webpage

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Package Metadata



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Bug Fixes


Vignettes and Documentation

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