Incorporate the latest bugfixes from the script

[mariusbarth]

These are the commits that we need to check if they are already implemented in the package. Some of these are probably now redundant or need a little discussion. For example, I think warnings and messages should be included in the output object, not in a separate file. I also added "MB" for those commits that I will take a look at asap.

• LOG_FILE option via sink(..)
• new functions to check input: data, EQN_FILE (MB)
• script should now work correctly for data sets with more than two levels (MB)
• add seed argument to MPTinR script
• write all meassages AND warnings to logfile
• set random seed (only in script)
• deactivate test settings (MB)
• updated results for fixed random seed
• PM data Smith et al., 2011 (MB)

[danheck]

set random seed (only in script) fixed in: 6914af9

note: by setting a random seed via the following option, it is not necessary to carry around an additional argument for the seed:
parallel::clusterSetRNGStream(cl, iseed = sample.int(.Machine$integer.max, 1))