Missing R package `aod`

[terhorstd]

When running the down-scaled version things break with a non-explaning error message:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-5-4ee3a90d4926> in <module>
----> 1 M = MultiAreaModel(network_params, simulation=True,
      2                    sim_spec=sim_params,
      3                    theory=True,
      4                    theory_spec=theory_params)
      5 p, r = M.theory.integrate_siegert()

~/multi-area-model/multiarea_model/multiarea_model.py in __init__(self, network_spec, theory, simulation, analysis, *args, **keywords)
    104                 json.dump(self.custom_params, f)
    105             # Execute Data script
--> 106             compute_Model_params(out_label=str(rand_data_label),
    107                                  mode='custom')
    108         else:

~/multi-area-model/multiarea_model/data_multiarea/Model.py in compute_Model_params(out_label, mode)
     59         print("Replacing base path with: %s" % basepath)
     60     # Load and process raw data
---> 61     process_raw_data()
     62     raw_fn = os.path.join(basepath, 'viscortex_raw_data.json')
     63     proc_fn = os.path.join(basepath, 'viscortex_processed_data.json')

~/multi-area-model/multiarea_model/data_multiarea/VisualCortex_Data.py in process_raw_data()
   1324                                 stdout=subprocess.PIPE)
   1325         out = proc.communicate()[0].decode('utf-8')
-> 1326         R_fit = [float(out.split('\n')[1].split(' ')[1]),
   1327                      float(out.split('\n')[1].split(' ')[3])]
   1328     except OSError:

IndexError: list index out of range

I've tracked this down to the call to Rscript SLN_logdensities.R returning an error which is not caught. Running the command manually on the command line reveals

$ Rscript SLN_logdensities.R .
Error in library("aod") : there is no package called ‘aod’
Execution halted

Problem found, but seems to be not easily to solve for non-R people:

$ R
> install.packages("oad")
[...]
Warning message:
package ‘oad’ is not available (for R version 3.6.0)

Unfortunately changing the version of R itself is not easily possible for me. How can I continue the workflow?

[jarsi]

Thanks for reporting this. Just to be sure, did you try to install aod or oad? Your comment hints at a typo.

[terhorstd]

:smile: good catch! :dart: Indeed, installing aod works much better! My apologies for bothering you with such stupidity...