Using custom Python versions

knitr::opts_chunk$set(echo = TRUE)

This vignette describes the three different ways to initialize the R session's connection to Python using the rMIDAS package as well as reticulate.

Option 1: Do nothing!

rMIDAS relies on Python 3.X to run the MIDAS imputation algorithm (note: Python 3.9 is not yet supported). For most users, the default settings in rMIDAS will be sufficient. Both train() and complete() check if Python has been initialized and, if not, run the required setup using the best Python 3 version available on your system (as determined by reticulate). The first time you run rMIDAS after installation, you may be prompted to install additional Python dependencies.

If a suitable Python version is not found on your system, you will be asked to manually set the path to a Python binary. You can do this using the next option.

Option 2:

If the automatic setup returns an error or you wish to use a specific Python binary on your system, you can use the set_python_env() function in rMIDAS, providing an exact path to your chosen Python binary:


set_python_env(python = "~/path/to/bin/python")

# Then proceed as normal...

With set_python_env() you can also set a virtualenv or condaenv environment:


set_python_env(python = "myenv", type = "virtualenv")

# or

set_python_env(python = "mycondaenv", type = "conda")

# Then proceed as normal...

rMIDAS will handle the rest of the initialization and setup.

Note: reticulate only allows you to set a Python binary once per R session, so if you wish to switch to a different Python binary, or have already run train() or convert(), you will need to restart R prior to using set_python_env().

Option 3:

If you desire more granular control of the R-Python interface, it is possible to use reticulate's in-built Python configuration tools. Since these commands are outside of rMIDAS, you must also manually call midas_setup() after configuring your Python install, e.g.:


reticulate::use_condaenv(condaenv = "myenv", conda = "some_conda_executable", required = FALSE)

# Then proceed as normal...

As with option 2, reticulate only allows you to set a Python binary once per R session. If you wish to switch to a different Python binary, or have already run train() or convert(), you will need to restart R prior to changing Python version and then call midas_setup().

Troubleshooting errors

Sometimes the above three options may fail due to system configuration issues. Here we note a few common issues and fixes.

Mac defaults to Python 2.7

If you are using a Mac, reticulate may be defaulting to Python 2.7 which is not supported by rMIDAS. If this is the case you will have to configure the R session to use a Python 3 binary, as in option 2 above, by running:


# Then proceed as normal...

If this returns an error, it's likely reticulate cannot find a Python environment related to the binary. In which case we recommend restarting the R session and creating a virtualenv that points to your desired Python 3 binary, as follows:

reticulate::virtualenv_create(envname = "myenv", python = "/path/to/your/python3/bin")
set_python_env("myenv", type = "virtualenv")

# Then proceed as normal...

Shared library access

If, after setting a Python binary/virtualenv/conda environment using either rMIDAS or reticulate, you still get an error, it is worth calling reticulate::py_discover_config to check whether the required python binary is visible.

If the python path is correct, but libpython is listed as [NOT FOUND] this suggests your Python binary does not have a shared library. In which case, either point to an alternative Python binary or reinstall your Python version with shared library enabled. On a Unix/Linux system, and using pyenv, this can be done as follows (replacing the version number as required):

{bash, eval = FALSE} env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.8.6

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rMIDAS documentation built on Jan. 30, 2021, 9:05 a.m.