Changed from wilcox_test (coin) to wilcox.test (stats).
Added a summary line to results tables.
Minor changes.
Fixed minor error in processing that was altering AUC values.
Added summary line to printed results tables.
Changed from wilcox_test (coin) to wilcox.test (stats).
Added summary lines.
Other minor changes.
added explanation of data restrictions
minor comment fixed
Fixed a minor mistake that resulted in synonymous changes not being processed correcctly.
Noticed a couple more changes that are anomalous.  I'm trusting this study less and less.  There are 2 changes that appear synonymous after reconciling with the sequence data.
Made several changes to begin to accomodate old studies in Yampolsky & Stoltzfus, 2005.

Removed "fitness" binary column

Added extra co_type column to assign measure types (continuous or ordinal).  Filled in the corresponding values.

Added extra effect_type column to assign "fitness", "activity", "binding" etc.  Filled in corresonding values.

Added extra column bigger_is_better so that we know the measured value correlates positively or negatively with fitness.  Filled in corresponding values.

Added rows for the studies in Yampolsky & Stoltzfus, 2005.  These data need to be double-checked.
fixed comment at bottom
The main changes here are

1.  add function to remove or flatten the lower tail of distribution, so as to allow tests for biases and noise in the tail; invoke this function in titv and power_binary

2. weight AUC grand means by study size (instead of unweighted) .

There were some other minor changes.
added Rhistory
This commit is focused on computing a new version of exchangeability, EX2.

It adds a new Rmd file that computes EX2, a new R file with some functions for this, and several files representing the output of this, in the data/aa_matrices directory.
added gitignore
removing index file from tracked files, as it is auto-generated
added more about processing and dependencies
This file is actually the correct version of Table S2, with the main results of Deng, et al.  Due to mixed-up links on the publisher's web site, previously I was using a file with a different type of data, based on an alignment of related proteins rather than based on the experiments in Deng, et al.

This should have been checked in earlier with changes to process_deng.Rmd.