Post date: Dec 18, 2014 12:31:30 AM
The R code for these analyses and the results are scattered all over the place and are a bit disorganized. Hopefully this will help:
Some notes are in black notebook: 13v13, 14v13, 16Dec14, 17Dec14
Rcode_CS_env_data_17dec14.txt: This file has the mantel tests with distances from mapping project and mean pairwise GST; also has the PCAs of environmental variables and the PC scores used to make distance matrices for the partial mantel tests. #How to summarize all this PCA stuff in the paper?!
EcalcFST_17dec14.R: This file has the partial mantel test (PC1 only) for Eurycea.
*Rwsp is on USU cluster in eurycea/
highFSTloci_17dec14.R: This file has the partial mantel tests (PC1 and PC2 made sense for these datasets) for Heterelmis and Stygobromus datasets.
*Rwsp is on USU cluster in heterelemis/ and stygobromus/
SpcalcFst_source_stygoparnus_17dec14.R: This file has the partial mantel test (PC1 only) for Stygoparnus.
*No Rasp. Need to upload 6 pairwise FST files (e.g., pairwidefst_1_2); found on my laptop GST/stygoparnus_pairwiseFST_loci/
There are some summary notes in draft of ms, CS_ms_17xii14.doc.