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using yaps to access stansummary command

Open sreedta8 opened this issue 4 years ago • 14 comments

Hi

I learned about yaps for the first time today and I could install yaps (with its dependencies) and cmdstan and successfully run the example model of the coin toss. In addition to examining the parameter theta, I want to execute the stansummary command on the output.csv created by cmdstan which summarizes all the parameters. Please see the desired output I get from cmdstan

(base) sz-HP15-Nb:~/cmdstan$ bin/stansummary output.csv
Input file: output.csv
Inference for Stan model: bernoulli_model
1 chains: each with iter=(1000); warmup=(0); thin=(1); 1000 iterations saved.

Warmup took 0.0070 seconds
Sampling took 0.013 seconds

                Mean     MCSE   StdDev     5%   50%   95%    N_Eff  N_Eff/s    R_hat

lp__            -7.3  4.6e-02     0.72   -8.7  -7.0  -6.8      243    18684      1.0
accept_stat__   0.94  2.6e-03  8.3e-02   0.77  0.98   1.0  1.0e+03  7.7e+04  1.0e+00
stepsize__      0.86      nan  4.3e-15   0.86  0.86  0.86      nan      nan      nan
treedepth__      1.5  1.9e-02  6.0e-01    1.0   1.0   3.0  9.9e+02  7.6e+04  1.0e+00
n_leapfrog__     3.2  6.1e-02  1.9e+00    1.0   3.0   7.0  1.0e+03  7.8e+04  1.0e+00
divergent__     0.00      nan  0.0e+00   0.00  0.00  0.00      nan      nan      nan
energy__         7.8  6.2e-02  1.0e+00    6.8   7.5   9.7  2.6e+02  2.0e+04  1.0e+00

theta           0.24  5.6e-03     0.12  0.074  0.22  0.45      434    33358      1.0

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 
convergence, R_hat=1).

sreedta8 avatar Nov 25 '20 04:11 sreedta8