In this directory:
-
data/
- Where the raw data goes. -
medicago_data_setup.html
- some initial summaries of the data -
medicago_data_setup.Rmd
- the code that produced those summaries -
run_on_medicago.R
- computes local PC coordinates and MDS coordinates. -
reports/
- Summary reports showing the results of running the algorithm with different parameter combinations (e.g., window choice; number of PCs) on the data. -
summarize_run.Rmd
- templated report used to produce these. -
compare-parameter-runs.R
- postprocessing to compare different parameter combinations.
First-round analyses (without using the R package):
- plots
- Medicago_distance_all_chr.R
- Medicago_MDS.R
- Medicago_PCA_win104.R
- Medicago_recode_and_cov.R