outline easy-mode workflow

[petrelharp]

Input data:

• data frame of spatial locations of samples and labels
• data frame of heterozygosities and diversities
• data frame of coordinates of corners of range polygon, counter-clockwise

Input parameters:

• epsilon
• mesh resolution
• regularization strengths (four of these?)
• filenames of the three input data files
• output directory basename

Steps:

0. (make the range polygon)
1. run the method
2. (do crossvalidation?)
3. tweak plots (?)

Output:

1. optimization diagnostics: history of parameter values and loss values, messages
2. optimal ellipse and vector fields:
   • images (png or pdf)
   • optimized equation (including mesh, function space, optimal values, etc) (if pickle-able??)
3. crossvalidation error (?)
   • plot
   • values in csv

Advanced parameters:

• scipy-minimize tolerances and other options

To do crossvalidation:

• command to make one crossvalidation subdirectory
• script/notebook to make bash script to run lots of crossvalidation things
• script/notebook to collate results from many subdirectories

How to get the range polygon?

• raster file -> gdal-contour -> polygon
• ellipse/rectangle etc with meshr -> ??
• should standardize coordinates, at least internally?
• "convex hull" can get counter-clockwise points