Starts documenting the program usage

docs/usage.md

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+# Usage
+This section describes how to use *pyRona*. It is not yet complete, and for now it is just a shallow copy of the help text.
+
+```
+How to get online help:
+ -h, --help show this help message and exit
+
+Input/Output options:
+ -pc PRESENT_COVARS_FILE
+ File with Present environmental data.
+ -fc FUTURE_COVARS_FILE
+ File with Future environmental data.
+ -pop POPNAMES_FILE File with population names.
+ -beta BAYPASS_SUMMARY_BETAI_FILE
+ Baypass summary betai file.
+ -pij BAYPASS_PIJ_FILE
+ Baypass pij file.
+ -out OUTFILE Path to where RONA plot should be saved. Supports PDF, SVG and PNG extensions.
+
+Program execution options:
+ -bf BAYES_FACTOR Bayes factor treshold for considering associations.
+ -covars NUM_COVARS Number of covars to calculate the RONA for.
+ -outliers {0,1,2} Number of outliers to remove. 0 does no outier removal, 1 removes **at most** 1 outlier and 2 removes **any** number of outliers that match the distance criteria.
+ -immutables IMMUTABLES [IMMUTABLES ...]
+ List of immutable covariates. These are not even parsed from the betai file. By default the first 3 covars are skipped. You can enter any other values here.
+ -ronatype {diff,absdiff,dist}
+ Type of RONA to calculate. Default is absolute difference as in Rellstab et al. 2016. Other options are 'difference' (not abs) and 'distance' (future vs. trendline).
+
+Miscellaneous options:
+ -no-plots Pass this option if you don't want individual regression plots to be drawn.
+ -no-weighted-means Pass this option if you don't want to useweighted means for RONA calculations.
+```
+
+Example run:
+
+```
+Coming soon
+```