diff --git a/src/cmdstan-guide/stansummary.Rmd b/src/cmdstan-guide/stansummary.Rmd index 389acf91e..ffc016a0a 100644 --- a/src/cmdstan-guide/stansummary.Rmd +++ b/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 `- `; long option names can be specified either as `--