Fix more R warnings, update and fix initiation of sparse matrices, and update example plot in showcase.R

[bockthom]

Prerequisites

• [x] I adhere to the coding conventions (described here) in my code.
• [x] I have updated the copyright headers of the files I have modified.
• [x] I have written appropriate commit messages, i.e., I have recorded the goal, the need, the needed changes, and the location of my code modifications for each commit. This includes also, e.g., referencing to relevant issues.
• [x] I have put signed-off tags in all commits.
• [x] I have updated the changelog file NEWS.md appropriately.
• [x] I have checked whether I need to adjust the showcase file showcase.R with respect to my changes.
• [x] The pull request is opened against the branch dev.

Description

In this PR, some R warnings are fixed that are caused by vectorized is.na calls, the initiation of sparse matrices is updated (as the interface has changed in more recent versions of the Matrix package), bugs in handling sparse matrices are fixed, and the example plot generation in the showcase.R is adjusted to the behavior of current ggplot2 versions.

Changelog

• Prevent further R warnings in if conditions
• Adjust adjacency matrix to recent Matrix package versions and fix corresponding bugs
• Fix wrong bracket in logging statement
• Add empty bots list to empty test data
• Adjust ggsave call in showcase.R and update example plot