README.md in flex-station-data-0.2.0 vs README.md in flex-station-data-0.3.0

@@ -1,10 +1,10 @@
 # FlexStationData
 
-Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/flex_station_data`. To experiment with that code, run `bin/console` for an interactive prompt.
+Tools for reading and analyzing data from the FlexStation microplate reader.
 
-TODO: Delete this and the text above, and describe your gem
+Currently this is somewhere between alpha and beta.
 
 ## Installation
 
 Add this line to your application's Gemfile:
 
@@ -18,18 +18,53 @@
 
 Or install it yourself as:
 
     $ gem install flex-station-data
 
+## Updating
+
+To update your installation, use:
+
+    $ gem update flex-station-data
+
 ## Usage
 
-TODO: Write usage instructions here
+### Viewing the sample data
 
-## Development
+To view the sample results from a set of plate readings, use the following
+command:
 
-After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+    $ flex-station sample-data <source file> [--threshold=<threshold>]
 
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+Where `source file` is the file that you got from the reader. You can specify
+multiple source files. The `threshold` setting is optional. If provided,
+samples with values that are below the `threshold` value will be skipped.
+`threshold` must be a number.
+
+The output is in CSV format. You'll probably want to save it to a file. You
+can do that by piping the output to a file:
+
+    $ flex-station sample-data source-data.csv --threshold=300 > sample-data.csv
+
+### Performing linear regression analysis on the sample data
+
+To perform a linear regression analysis on the sample data, use the following
+command:
+
+    $ flex-station-data liinear-regression <source file> [--threshold=<threshold>] [--verbose] [--min-r-squared=<mininmum R²>]
+
+Note that the `source file` and `threshold` options are the same as for the
+`sample-data` command above. If a `--min-r-squared` value is given, samples
+with a R² value that falls below the threshold will be flagged as "poor fits."
+If no `--min-r-squared` is specified, a default of 0.75 will be used.
+
+By default the linear regression tool will produce a summary report giving the
+slope, intercept, and R² values for each sample. However if `--verbose` is
+specified, it will also include the sample data and regressions for each well.
+
+As with the sample data tool, you will probably want to pipe the output to a file:
+
+    $ flex-station linear-regression source-data.csv --threshold=300 > linear-regression.csv
 
 ## Contributing
 
 Bug reports and pull requests are welcome on GitHub at https://github.com/johncarney/flex-station-data. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.