Merge pull request #669 from stan-dev/feature/stansummary-improvements

Update stansummary documentation

src/cmdstan-guide/stansummary.Rmd

@@ -32,7 +32,7 @@ chapter of the Stan Reference Manual which describes both the theory and practic
 estimation techniques.
 The summary statistics and the algorithms used to compute them are described in sections
 [Notation for samples](https://mc-stan.org/docs/reference-manual/notation-for-samples-chains-and-draws.html)
-and 
+and
 [Effective Sample Size](https://mc-stan.org/docs/reference-manual/effective-sample-size.html).
 
 ## Building the stansummary command
@@ -95,7 +95,7 @@ tau               7.2     0.26     5.2    1.5   5.9    17    401     1657      1
 
 Samples were drawn using hmc with nuts.
 For each parameter, N_Eff is a crude measure of effective sample size,
-and R_hat is the potential scale reduction factor on split chains (at 
+and R_hat is the potential scale reduction factor on split chains (at
 convergence, R_hat=1).
 ```
 
@@ -159,15 +159,22 @@ Options:
   -c, --csv_filename [file]   Write statistics to a CSV file.
   -h, --help                  Produce help message, then exit.
   -p, --percentiles [values]  Percentiles to report as ordered set of
-                              comma-separated integers from (1,99), inclusive.
+                              comma-separated numbers from (0.1,99.9), inclusive.
                               Default is 5,50,95.
   -s, --sig_figs [n]          Significant figures reported. Default is 2.
                               Must be an integer from (1, 18), inclusive.
+  -i, --include_param [name]  Include the named parameter in the summary output.
+                              By default, all parameters in the file are summarized,
+                              passing this argument one or more times will filter
+                              the output down to just the requested arguments.
 ```
 
 Both short an long option names are allowed.  Short names are specified as `-<o> <value>`;
 long option names can be specified either as `--<option>=<value>` or `--<option> <value>`.
 
+The `--percentiles` argument can also be passed an empty string `""`, which
+results in no percentiles being displayed in the output of the command.
+
 The amount of precision
 in the sampler output limits the amount of real precision in the summary report.
 CmdStan's command line interface also has output argument `sig_figs`.