For the full project please see, "DahnYoung_Dong_Final" markdown and the knitted html/pdf (pdf document not formatted well so I recommend look at html or knit the final md yourself). Markdown link is here https://github.com/Dahn-YoungDong/finalproject/blob/master/DahnYoung_Dong_Final.Rmd
Dec 10th Final Project write-up is done. Noted for the caveat in data interpretation due to small sample size.
Dec 9th Start write the results and discussion based on comparing different K values.
Dec 8th FinalProject Markdown finished. Deleted all intermediary files.
Dec 7th Consolidating and finalizing all script into the finalproject markdown. When all transfer is done, the step-wise markdowns will be removed
Dec 1st Look at "1.prep"" to make sense the data prepping code
Nov 30th Finished prelim analysis. Produced an ancestry proportion graph, and a comparative plot of both spatially interpolated ancestry coefficients and population location mapped on elevation.
I will no longer consider TreeMix for this project.
Nov 24th: still figuring out the structure for minimal viability analysis.
For population mapping- Closely following https://github.com/jdalapicolla/LanGen_pipeline_version2/blob/master/1.3_MAPS.R
And I decontructed the steps into three markdowns 1. filter , 2. structure, and 3. mapping
For TreeMix, I am still figuring out how to make it run over cluster with the large dataset. But since I switched to pilot dataset, I might try again with my laptop.