Adding some docs

doc/bayeswave-output.md

+BayesWave stores its output in `outputDir`, provided by the user. If using through condor on the LDG, the progress of the run can be monitored through `logs/BayesWave_*out` where you can find the current iteration. 
+
+Once the run is complete, the typical content of `outputDir` includes:
+
+1. A `chains/` directory where the full chains are stored.
+
+Depending on the settings of your run, you should have chains for each run mode (clean, glitch, signal, noise). Possible chains include
+
+* `*_model.dat.0`: general information about the run, such as the number of iterations, the likelihood, the number of wavelets used etc. The `0` refers to the coldest chain
+* `*_lorentz_IFO.dat.0`: parameters for the lorentzians used to fit the PSD in each IFO, where the `0` refers to the coldest chain. This is only present when running with `BayesLine`.
+* `*_spline_IFO.dat.0`: parameters for the splines used to fit the PSD in each IFO, where the `0` refers to the coldest chain. This is only present when running with `BayesLine`.
+* `signal_params_h0.dat.0`: parameters of the signal wavelets that fit power coherently across all detectors. The `h0` refers to the cross signal polarization, and the `0` refers to the coldest chain.
+* `glitch_params_IFO.dat.0`: parameters of the glitch wavelets that fit power incoherently per detector IFO. The `0` refers to the coldest chain.
+
+
+2. A `checkpoint/` directory that holds the last checkpointed state.
+
+You are most likely not interested in the contents
+
+3. A `post/` directory with the output of `BayesWavePost`.
+
+Each model has its own subdirectory here such as `signal/` and `glitch/` with more or less similar content that is usually helpfully named. For example, in the `signal/` subdirectory some of the most useful files are:
+
+* `fourier_domain_signal_median_residual_IFO.dat`: frequency bin, real, and imaginary part of the median residual (data after the median signal has been subtracted)
+* `signal_anderson_darling_IFO.dat`: Anderson darling statistic and corresponding p value that test how well the PSD has whitened the data. This is only present when running with `BayesLine`. Columns include the sampling rate up to which this is computed, the AD, and the p value.
+* Various median estimates characterizing the signal mode. These files in general are structured as
+
+`frequency/time, median, lower50, upper50, lower90, upper90`
+
+where (for example) upper 50 is the upper boundary of the 50th percentile.
+* Various files containing moments characterizing the signal reconstructions such as SNR, bandwidth, duration, overlap etc. Each files contains a header describing the moments included and then lists the moments per iterations. The are computed from both the whitened and the colored signal (option given in the file name).
+
+
+4. A `waveforms/` directory that is populated if you have run with the `gnuplot` flag with 200 draws from the posterior .
+
+It is probably not advisable to run with this flag on the LDG as it produces a lot of output.
+
+5. Various files printing PSDs and ASDs per IFO, such as `L1_burninpsd.dat` and `L1_fairdraw_psd.dat`. These are needed by `BayesWavePost`.
+
+6. `evidence.dat` contains the evidence (and standard deviation) per model, while files such as `model_evidence.dat` contain various pieces that go into the evidence calculations (such as temperatures and likelihoods per chain).
+
+7. A `plots/` directory that holds the output plots from `megaplot`. 
\ No newline at end of file

doc/build.sh

@@ -15,6 +15,7 @@ cat >> index.rst << EOF
    quickstart
    running
    examples
+   bayeswave-output
    releasing
 EOF