# Pm.sample result does not work with az.plot\_trace or other az functions

**URL:** <https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711>\
**Category:** v5\
**Created:** [June 22, 2022, 5:20am UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711 "2022-06-22T05:20:15Z")\
**Posts on this page:** 10\
**Page:** 1

<div class="post-metadata">

**Author:** ![Hyung](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/hyung/32/5316_2.png) [@Hyung](https://discourse.pymc.io/u/Hyung)\
**Post date:** [June 22, 2022, 5:20am UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/1 "2022-06-22T05:20:15Z")

</div>

I got the idata from pm.sample(), and tried to draw a trace plot using az. However, it shows the following error.

```auto
Can only convert xarray dataarray, xarray dataset, dict, netcdf filename, numpy array, pystan fit, pymc3 trace, emcee fit, pyro mcmc fit, numpyro mcmc fit, cmdstan fit csv filename, cmdstanpy fit to InferenceData, not tuple

```

when I check the data, it shows:  
(Inference data with groups:  
\> posterior  
\> log\_likelihood  
\> sample\_stats  
\> observed\_data,)

In addition, when do pm.plot\_posterior(idata), it shows the same error.

```auto
ValueError: Can only convert xarray dataarray, xarray dataset, dict, netcdf filename, numpy array, pystan fit, pymc3 trace, emcee fit, pyro mcmc fit, numpyro mcmc fit, cmdstan fit csv filename, cmdstanpy fit to InferenceData, not tuple

```

I am using pymc version 4.0.0.

Please advise!

---

<div class="post-metadata">

**Author:** ![ricardoV94](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/ricardov94/32/5775_2.png) [@ricardoV94](https://discourse.pymc.io/u/ricardoV94)\
**Post date:** [June 22, 2022, 5:53am UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/2 "2022-06-22T05:53:00Z")

</div>

You seem to have a basic error with passing a tuple instead of an InferenceData, can you share the code and /or a longer error message?

---

<div class="post-metadata">

**Author:** ![Hyung](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/hyung/32/5316_2.png) [@Hyung](https://discourse.pymc.io/u/Hyung)\
**Post date:** [June 22, 2022, 1:00pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/3 "2022-06-22T13:00:55Z")

</div>

```auto
print(pm. __version__ )
print(az. __version__ )
4.0.0
0.12.1

```

Here are the code and longer error message:

Code:

```auto
def fn(a,b,c,x):
      [...]
      return y

with pm.Model() as model:
    
    a = pm.TruncatedNormal('a', mu=1/50, sigma=1, lower=1/1000, upper=1, initval=1/50)
    b = pm.Normal('b', 0, 10, initval=0)
    c = pm.Normal('c', 0, 10, initval=0)
    ϵ = pm.HalfCauchy('ϵ', 100, initval=1)
    mu = fn(a, b, c, x)
    pm.Potential("negative_penalty", pm.math.switch(mu<0, -np.inf, 0))
    
    y_pred = pm.Gamma('y_pred', mu=mu, sigma=ϵ, observed=y_obs)

    idata = pm.sample(draws=1000, tune=500, chains=2, target_accept = 0.999))

```

Check the idata variable:

```auto
idata
(Inference data with groups:
 	> posterior
 	> log_likelihood
 	> sample_stats
 	> observed_data,)

```

Error message:

```auto
az.plot_trace(idata, var_names=["a", "b", "c"])

---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [107], in <cell line: 1>()
----> 1 az.plot_trace(idata, var_names=["a", "b"])

File /opt/anaconda3/envs/pymc/lib/python3.10/site-packages/arviz/plots/traceplot.py:194, in plot_trace(data, var_names, filter_vars, transform, coords, divergences, kind, figsize, rug, lines, circ_var_names, circ_var_units, compact, compact_prop, combined, chain_prop, legend, plot_kwargs, fill_kwargs, rug_kwargs, hist_kwargs, trace_kwargs, rank_kwargs, labeller, axes, backend, backend_config, backend_kwargs, show)
    191 else:
    192 divergence_data = False
--> 194 coords_data = get_coords(convert_to_dataset(data, group="posterior"), coords)
    196 if transform is not None:
    197 coords_data = transform(coords_data)

File /opt/anaconda3/envs/pymc/lib/python3.10/site-packages/arviz/data/converters.py:179, in convert_to_dataset(obj, group, coords, dims)
    140 def convert_to_dataset(obj, *, group="posterior", coords=None, dims=None):
    141 """Convert a supported object to an xarray dataset.
    142 
    143 This function is idempotent, in that it will return xarray.Dataset functions
   (...)
    177 xarray.Dataset
    178 """
--> 179 inference_data = convert_to_inference_data(obj, group=group, coords=coords, dims=dims)
    180 dataset = getattr(inference_data, group, None)
    181 if dataset is None:

File /opt/anaconda3/envs/pymc/lib/python3.10/site-packages/arviz/data/converters.py:131, in convert_to_inference_data(obj, group, coords, dims, **kwargs)
    116 else:
    117 allowable_types = (
    118 "xarray dataarray",
    119 "xarray dataset",
   (...)
    129 "cmdstanpy fit",
    130 )
--> 131 raise ValueError(
    132 "Can only convert {} to InferenceData, not {}".format(
    133 ", ".join(allowable_types), obj. __class__. __name__
    134 )
    135 )
    137 return InferenceData(**{group: dataset})

ValueError: Can only convert xarray dataarray, xarray dataset, dict, netcdf filename, numpy array, pystan fit, pymc3 trace, emcee fit, pyro mcmc fit, numpyro mcmc fit, cmdstan fit csv filename, cmdstanpy fit to InferenceData, not tuple

```

---

<div class="post-metadata">

**Author:** ![cluhmann](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/cluhmann/32/3083_2.png) [@cluhmann](https://discourse.pymc.io/u/cluhmann)\
**Post date:** [June 22, 2022, 1:13pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/4 "2022-06-22T13:13:37Z")

</div>

Not sure how that happened as your code shouldn’t have produced such a result. Somehow your `idata` object is wrapped in a tuple (notice the parentheses around the result). When I run a simplified version of you model, this is what I get:

```python
In [3]: idata
Out[3]: 
Inference data with groups:
	> posterior
	> log_likelihood
	> sample_stats
	> observed_data

```

---

<div class="post-metadata">

**Author:** ![Hyung](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/hyung/32/5316_2.png) [@Hyung](https://discourse.pymc.io/u/Hyung)\
**Post date:** [June 22, 2022, 1:17pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/5 "2022-06-22T13:17:29Z")

</div>

Yes, this is very weird. Why my idata comes with tuple not the arviz.InferenceData? When I do

```auto
pm.plot_forest(idata)

```

It works, but no other pm.plot\_\* function.

I tried with pymc3 version, but the same issue is still there.  
Any other suggestion?

Thank you.

---

<div class="post-metadata">

**Author:** ![cluhmann](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/cluhmann/32/3083_2.png) [@cluhmann](https://discourse.pymc.io/u/cluhmann)\
**Post date:** [June 22, 2022, 1:28pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/6 "2022-06-22T13:28:03Z")

</div>

I would try to modify your model until you figure out what’s going on. Here’s the simplified version that I ran:

```python
import pymc as pm

with pm.Model() as model:
    
    a = pm.TruncatedNormal('a', mu=1/50, sigma=1, lower=1/1000, upper=1, initval=1/50)
    b = pm.Normal('b', 0, 10, initval=0)
    c = pm.Normal('c', 0, 10, initval=0)
    ϵ = pm.HalfCauchy('ϵ', 100, initval=1)
    #mu = fn(a, b, c, x)
    #pm.Potential("negative_penalty", pm.math.switch(mu<0, -np.inf, 0))
    mu = 1
    
    y_pred = pm.Gamma('y_pred', mu=mu, sigma=ϵ, observed=[1,2,3])

    idata = pm.sample()

```

---

<div class="post-metadata">

**Author:** ![OriolAbril](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/oriolabril/32/2497_2.png) [@OriolAbril](https://discourse.pymc.io/u/OriolAbril)\
**Post date:** [June 22, 2022, 2:37pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/7 "2022-06-22T14:37:35Z")

</div>

Make sure there is no comma after the `pm.sample` call because that would create a tuple:

```auto
In [1]: import arviz as az
idata = 
In [2]: idata = az.load_arviz_data("rugby"),

In [3]: idata
Out[3]: 
(Inference data with groups:
 	> posterior
 	> posterior_predictive
 	> sample_stats
 	> prior
 	> observed_data,)

```

Note the InferenceData text is inside some parenthesis. The comma after the `load_arviz_data` puts the InferenceData returned by the function inside a tuple. On the other hand:

```auto
In [4]: idata = az.load_arviz_data("rugby")

In [5]: idata
Out[5]: 
Inference data with groups:
	> posterior
	> posterior_predictive
	> sample_stats
	> prior
	> observed_data

```

Returns the inferencedata without wrapping it inside a tuple. I know I am not using `pm.sample` but I am using a function that returns an inferencedata object, so I am quite sure that for this specific issue both are interchangeable

---

<div class="post-metadata">

**Author:** ![Hyung](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/hyung/32/5316_2.png) [@Hyung](https://discourse.pymc.io/u/Hyung)\
**Post date:** [June 22, 2022, 2:45pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/8 "2022-06-22T14:45:40Z")

</div>

@OriolAbril You pinned it! I accidently put (,) after pm.sample().  
I should have put (,) after # when commented out other arguments.  
Thank you for time and help! (@ricardoV94 and @cluhmann as well!).

---

<div class="post-metadata">

**Author:** ![OriolAbril](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/oriolabril/32/2497_2.png) [@OriolAbril](https://discourse.pymc.io/u/OriolAbril)\
**Post date:** [June 22, 2022, 2:47pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/9 "2022-06-22T14:47:20Z")

</div>

Side note, `plot_forest` and `plot_density` will work in both cases because they both can take an inferencedata object or an iterable of inferencedata objects, and a tuple of length 1 with an inferencedata inside is an iterable of inferencedata objects.

---

<div class="post-metadata">

**Author:** ![Hyung](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/hyung/32/5316_2.png) [@Hyung](https://discourse.pymc.io/u/Hyung)\
**Post date:** [June 22, 2022, 2:49pm UTC](https://discourse.pymc.io/t/pm-sample-result-does-not-work-with-az-plot-trace-or-other-az-functions/9711/10 "2022-06-22T14:49:55Z")

</div>

Yes! I was about to ask this. Your explanation actually explains everything now.