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OskarHansson / pcrsim

An R package for simulation of the forensic DNA process
https://sites.google.com/site/forensicapps/pcrsim
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A little feedback #2

Open petergreen5678 opened 4 years ago

petergreen5678 commented 4 years ago

Hello again Oskar,

I now have my simple mixture simulations working the way I want - I prefer the script approach, and wrote the two simple jobs attached below, broadly similar to the sample workflow on your https://sites.google.com/site/forensicapps/pcrsim page. If looking at these suggests I have missed something important, please tell me.

A few little bits of feedback that other users might appreciate:

  1. Simple scripts like these providing a complete example workflow could be generally useful.
  2. I didn't find very clear the role of the 'sim' column in the data frames, especially in the case of fixed non-random profiles. It wasn't clear to me for example how to make a mixture of different amounts of two or more fixed profiles, without using two separate calls to sinProfile and simSample.
  3. Contrary to the impression from the example in the simProfile help page, the 'Marker' variable needs to have character not factor values, or compact() fails.
  4. The generateEPG function seems to need at least one marker for each colour dye, or it fails with an obscure error message. This requirement isn't mentioned in the documentation.

Thanks again for providing this useful package! best regards, Peter Green

mixture 2 random contributors.R.txt mixture 2 fixed contributors.R.txt

OskarHansson commented 4 years ago

Thanks for the feedback and your observations!

With your permission I could put your code examples on the web page (of course with credits). The EPG generator lives within the strvalidator package and could use a face-lift. If I am not wrong it is (now) possible to have empty facets in ggplot2, so #4 could be fixed. I wished I could have spent more time improving and polishing pcrsim before finalising it (sadly no time to develop this package anymore). If you have specific suggestions for improving code or documentation you are more than welcome to make pull requests. And if you are interested to take pcrsim further, or learn of alternative software, there are some suggestions in my thesis that could greatly improve simulation speed.