Python in RStudio Using reticulate Package

# 參考資料

- [R Interface to Python](https://rstudio.github.io/reticulate/index.html)
- [Python setup in R with Reticulate](https://rpubs.com/dku850/603511)
- [keras, kerasR, reticulate & Tensorflow in R-Studio with Python from Anaconda](https://psychcns.freshdesk.com/support/solutions/articles/43000570525-keras-kerasr-reticulate-tensorflow-in-r-studio-with-python-from-anaconda)
- [How to Set Up Python's Scikit-Learn in R in 5 minutes](https://www.business-science.io/learn-r/2020/04/20/setup-python-in-r-with-rmarkdown.html)
 
# 安裝 Anaconda

- `brew install --cask anaconda3`

# 安裝 R 與 RStudio

- `brew install r` 或 `brew install --cask r` 或 `brew install -s r` (Apple Silicon M1)
- `brew install --cask rstudio`

# 執行 R 之後安裝 `reticulate` Package

```r
> install.packages("tidyverse")
> install.packages("reticulate")
> library("reticulate")

> options(reticulate.conda_binary = "/usr/local/anaconda3/bin/conda")
或
> options(reticulate.conda_binary = "/opt/homebrew/Caskroom/miniforge/base/envs/ai/bin/conda")
```

# 建立 Conda Environment

執行 `py_config()` 指令，預設會建立一個 `r-reticulate` Conda Environment：

```
> py_config()
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /usr/local/anaconda3/envs/r-reticulate

  added / updated specs:
    - numpy
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.12.5          |   py36h79c6626_1         143 KB  conda-forge
    libblas-3.9.0              |       8_openblas          11 KB  conda-forge
    libcblas-3.9.0             |       8_openblas          11 KB  conda-forge
    libcxx-11.1.0              |       habf9029_0         1.0 MB  conda-forge
    libffi-3.3                 |       h046ec9c_2          45 KB  conda-forge
    libgfortran-5.0.0          |9_3_0_h6c81a4c_20          19 KB  conda-forge
    libgfortran5-9.3.0         |      h6c81a4c_20         1.7 MB  conda-forge
    liblapack-3.9.0            |       8_openblas          11 KB  conda-forge
    libopenblas-0.3.12         |openmp_h54245bb_1         8.8 MB  conda-forge
    llvm-openmp-11.1.0         |       hda6cdc1_0         268 KB  conda-forge
    ncurses-6.2                |       h2e338ed_4         881 KB  conda-forge
    numpy-1.19.5               |   py36h08dc641_1         5.0 MB  conda-forge
    pip-21.0.1                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
    python-3.6.13              |h7728216_0_cpython        20.6 MB  conda-forge
    python_abi-3.6             |          1_cp36m           4 KB  conda-forge
    readline-8.1               |       h05e3726_0         266 KB  conda-forge
    setuptools-49.6.0          |   py36h79c6626_3         916 KB  conda-forge
    sqlite-3.35.2              |       h44b9ce1_0         1.7 MB  conda-forge
    tk-8.6.10                  |       h0419947_1         3.3 MB  conda-forge
    wheel-0.36.2               |     pyhd3deb0d_0          31 KB  conda-forge
    xz-5.2.5                   |       haf1e3a3_1         228 KB  conda-forge
    zlib-1.2.11                |    h7795811_1010         102 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        46.0 MB

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.12.5-h033912b_0
  certifi            conda-forge/osx-64::certifi-2020.12.5-py36h79c6626_1
  libblas            conda-forge/osx-64::libblas-3.9.0-8_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-8_openblas
  libcxx             conda-forge/osx-64::libcxx-11.1.0-habf9029_0
  libffi             conda-forge/osx-64::libffi-3.3-h046ec9c_2
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_20
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_20
  liblapack          conda-forge/osx-64::liblapack-3.9.0-8_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.12-openmp_h54245bb_1
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.1.0-hda6cdc1_0
  ncurses            conda-forge/osx-64::ncurses-6.2-h2e338ed_4
  numpy              conda-forge/osx-64::numpy-1.19.5-py36h08dc641_1
  openssl            conda-forge/osx-64::openssl-1.1.1j-hbcf498f_0
  pip                conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.6.13-h7728216_0_cpython
  python_abi         conda-forge/osx-64::python_abi-3.6-1_cp36m
  readline           conda-forge/osx-64::readline-8.1-h05e3726_0
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py36h79c6626_3
  sqlite             conda-forge/osx-64::sqlite-3.35.2-h44b9ce1_0
  tk                 conda-forge/osx-64::tk-8.6.10-h0419947_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010



Downloading and Extracting Packages
python_abi-3.6       | 4 KB      | ########## | 100% 
ncurses-6.2          | 881 KB    | ########## | 100% 
sqlite-3.35.2        | 1.7 MB    | ########## | 100% 
numpy-1.19.5         | 5.0 MB    | ########## | 100% 
libopenblas-0.3.12   | 8.8 MB    | ########## | 100% 
wheel-0.36.2         | 31 KB     | ########## | 100% 
python-3.6.13        | 20.6 MB   | ########## | 100% 
xz-5.2.5             | 228 KB    | ########## | 100% 
readline-8.1         | 266 KB    | ########## | 100% 
libcxx-11.1.0        | 1.0 MB    | ########## | 100% 
libblas-3.9.0        | 11 KB     | ########## | 100% 
certifi-2020.12.5    | 143 KB    | ########## | 100% 
zlib-1.2.11          | 102 KB    | ########## | 100% 
tk-8.6.10            | 3.3 MB    | ########## | 100% 
libcblas-3.9.0       | 11 KB     | ########## | 100% 
pip-21.0.1           | 1.1 MB    | ########## | 100% 
llvm-openmp-11.1.0   | 268 KB    | ########## | 100% 
libgfortran-5.0.0    | 19 KB     | ########## | 100% 
libffi-3.3           | 45 KB     | ########## | 100% 
liblapack-3.9.0      | 11 KB     | ########## | 100% 
libgfortran5-9.3.0   | 1.7 MB    | ########## | 100% 
setuptools-49.6.0    | 916 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate r-reticulate
#
# To deactivate an active environment, use
#
#     $ conda deactivate

python:         /usr/local/anaconda3/bin/python3
libpython:      /usr/local/anaconda3/lib/libpython3.8.dylib
pythonhome:     /usr/local/anaconda3:/usr/local/anaconda3
version:        3.8.8 (default, Feb 24 2021, 13:46:16)  [Clang 10.0.0 ]
numpy:          /usr/local/anaconda3/lib/python3.8/site-packages/numpy
numpy_version:  1.19.2

python versions found: 
 /usr/local/anaconda3/bin/python3
 /usr/bin/python3
 /usr/local/bin/python3
 /usr/bin/python

> conda_list()
          name                                            python
1 r-reticulate /usr/local/anaconda3/envs/r-reticulate/bin/python
```

# 重新執行 R 並且載入 `reticulate` Package

之後每次都要執行的步驟：

```
> library("reticulate")

> options(reticulate.conda_binary = "/usr/local/anaconda3/bin/conda")

> conda_list()
          name                                            python
1 r-reticulate /usr/local/anaconda3/envs/r-reticulate/bin/python

> use_condaenv("r-reticulate")

> py_config()
python:         /usr/local/anaconda3/envs/r-reticulate/bin/python
libpython:      /usr/local/anaconda3/envs/r-reticulate/lib/libpython3.6m.dylib
pythonhome:     /usr/local/anaconda3/envs/r-reticulate:/usr/local/anaconda3/envs/r-reticulate
version:        3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:16)  [GCC Clang 11.0.1]
numpy:          /usr/local/anaconda3/envs/r-reticulate/lib/python3.6/site-packages/numpy
numpy_version:  1.19.5

python versions found: 
 /usr/local/anaconda3/envs/r-reticulate/bin/python
 /usr/bin/python3
 /usr/local/bin/python3
 /usr/bin/python

> Sys.which("python")
                                             python 
"/usr/local/anaconda3/envs/r-reticulate/bin/python" 
```

# 直接執行 Python 指令

```
> repl_python()
Python 3.6.13 (/usr/local/anaconda3/envs/r-reticulate/bin/python)
Reticulate 1.18 REPL -- A Python interpreter in R.
>>> print("Hello, Python!")
Hello, Python!
>>> exit
>
```

# 安裝 Python Package

安裝到預設的 `r-reticulate` Conda Environment：

```
> py_install("pandas")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /usr/local/anaconda3/envs/r-reticulate

  added / updated specs:
    - pandas
    - python


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pandas-1.1.5               |   py36h2be6da3_0        10.0 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    pytz-2021.1                |     pyhd8ed1ab_0         239 KB  conda-forge
    six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        10.5 MB

The following NEW packages will be INSTALLED:

  pandas             conda-forge/osx-64::pandas-1.1.5-py36h2be6da3_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0



Downloading and Extracting Packages
python-dateutil-2.8. | 220 KB    | ########## | 100% 
pytz-2021.1          | 239 KB    | ########## | 100% 
six-1.15.0           | 14 KB     | ########## | 100% 
pandas-1.1.5         | 10.0 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
```

安裝到指定的 Conda Environment：

```
> conda_install(envname = "r-reticulate", packages = "plotnine")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /usr/local/anaconda3/envs/r-reticulate

  added / updated specs:
    - plotnine
    - python


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cycler-0.10.0              |             py_2           9 KB  conda-forge
    descartes-1.1.0            |             py_4           7 KB  conda-forge
    freetype-2.10.4            |       h4cff582_1         890 KB  conda-forge
    jpeg-9d                    |       hbcb3906_0         250 KB  conda-forge
    kiwisolver-1.3.1           |   py36h615c93b_1          59 KB  conda-forge
    lcms2-2.12                 |       h577c468_0         404 KB  conda-forge
    libpng-1.6.37              |       h7cec526_2         313 KB  conda-forge
    libtiff-4.2.0              |       h355d032_0         639 KB  conda-forge
    libwebp-base-1.2.0         |       h0d85af4_2         700 KB  conda-forge
    lz4-c-1.9.3                |       h046ec9c_0         155 KB  conda-forge
    matplotlib-base-3.3.4      |   py36h4ea959b_0         6.8 MB  conda-forge
    mizani-0.7.2               |     pyhd8ed1ab_0          53 KB  conda-forge
    olefile-0.46               |     pyh9f0ad1d_1          32 KB  conda-forge
    palettable-3.3.0           |             py_0          86 KB  conda-forge
    patsy-0.5.1                |             py_0         187 KB  conda-forge
    pillow-8.1.2               |   py36h154fef6_0         642 KB  conda-forge
    plotnine-0.7.1             |             py_0         3.6 MB  conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    scipy-1.5.3                |   py36h04de62b_0        17.1 MB  conda-forge
    statsmodels-0.12.2         |   py36hf14bfbd_0        10.6 MB  conda-forge
    tornado-6.1                |   py36h20b66c6_1         643 KB  conda-forge
    zstd-1.4.9                 |       h582d3a0_0         460 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        43.5 MB

The following NEW packages will be INSTALLED:

  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  descartes          conda-forge/noarch::descartes-1.1.0-py_4
  freetype           conda-forge/osx-64::freetype-2.10.4-h4cff582_1
  jpeg               conda-forge/osx-64::jpeg-9d-hbcb3906_0
  kiwisolver         conda-forge/osx-64::kiwisolver-1.3.1-py36h615c93b_1
  lcms2              conda-forge/osx-64::lcms2-2.12-h577c468_0
  libpng             conda-forge/osx-64::libpng-1.6.37-h7cec526_2
  libtiff            conda-forge/osx-64::libtiff-4.2.0-h355d032_0
  libwebp-base       conda-forge/osx-64::libwebp-base-1.2.0-h0d85af4_2
  lz4-c              conda-forge/osx-64::lz4-c-1.9.3-h046ec9c_0
  matplotlib-base    conda-forge/osx-64::matplotlib-base-3.3.4-py36h4ea959b_0
  mizani             conda-forge/noarch::mizani-0.7.2-pyhd8ed1ab_0
  olefile            conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  palettable         conda-forge/noarch::palettable-3.3.0-py_0
  patsy              conda-forge/noarch::patsy-0.5.1-py_0
  pillow             conda-forge/osx-64::pillow-8.1.2-py36h154fef6_0
  plotnine           conda-forge/noarch::plotnine-0.7.1-py_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  scipy              conda-forge/osx-64::scipy-1.5.3-py36h04de62b_0
  statsmodels        conda-forge/osx-64::statsmodels-0.12.2-py36hf14bfbd_0
  tornado            conda-forge/osx-64::tornado-6.1-py36h20b66c6_1
  zstd               conda-forge/osx-64::zstd-1.4.9-h582d3a0_0



Downloading and Extracting Packages
plotnine-0.7.1       | 3.6 MB    | ########## | 100% 
pillow-8.1.2         | 642 KB    | ########## | 100% 
patsy-0.5.1          | 187 KB    | ########## | 100% 
libpng-1.6.37        | 313 KB    | ########## | 100% 
freetype-2.10.4      | 890 KB    | ########## | 100% 
cycler-0.10.0        | 9 KB      | ########## | 100% 
libwebp-base-1.2.0   | 700 KB    | ########## | 100% 
kiwisolver-1.3.1     | 59 KB     | ########## | 100% 
pyparsing-2.4.7      | 60 KB     | ########## | 100% 
lcms2-2.12           | 404 KB    | ########## | 100% 
palettable-3.3.0     | 86 KB     | ########## | 100% 
scipy-1.5.3          | 17.1 MB   | ########## | 100% 
lz4-c-1.9.3          | 155 KB    | ########## | 100% 
mizani-0.7.2         | 53 KB     | ########## | 100% 
olefile-0.46         | 32 KB     | ########## | 100% 
libtiff-4.2.0        | 639 KB    | ########## | 100% 
tornado-6.1          | 643 KB    | ########## | 100% 
matplotlib-base-3.3. | 6.8 MB    | ########## | 100% 
statsmodels-0.12.2   | 10.6 MB   | ########## | 100% 
zstd-1.4.9           | 460 KB    | ########## | 100% 
descartes-1.1.0      | 7 KB      | ########## | 100% 
jpeg-9d              | 250 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
```

# 重建 `r-reticulate` Conda Environment

因為 `reticulate` Package 預設建立的 Conda Environment 使用的是 3.6 版本的 Python，所以可以考慮砍掉重建，但是記得要有 `NumPy` Package，不然 `reticulate` Package：

```
% conda env remove --name r-reticulate

Remove all packages in environment /usr/local/anaconda3/envs/r-reticulate:

% conda create --name r-reticulate python=3.8 conda pip numpy
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /usr/local/anaconda3/envs/r-reticulate

  added / updated specs:
    - conda
    - pip
    - python=3.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ruamel_yaml-0.15.100       |   py38h9ed2024_0         247 KB
    sqlite-3.35.2              |       hce871da_0         1.1 MB
    ------------------------------------------------------------
                                           Total:         1.4 MB

The following NEW packages will be INSTALLED:

  brotlipy           pkgs/main/osx-64::brotlipy-0.7.0-py38h9ed2024_1003
  ca-certificates    pkgs/main/osx-64::ca-certificates-2021.1.19-hecd8cb5_1
  certifi            pkgs/main/osx-64::certifi-2020.12.5-py38hecd8cb5_0
  cffi               pkgs/main/osx-64::cffi-1.14.5-py38h2125817_0
  chardet            pkgs/main/osx-64::chardet-4.0.0-py38hecd8cb5_1003
  conda              pkgs/main/osx-64::conda-4.9.2-py38hecd8cb5_0
  conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.7.2-py38h22f3db7_0
  cryptography       pkgs/main/osx-64::cryptography-3.4.6-py38h2fd3fbb_0
  idna               pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0
  libcxx             pkgs/main/osx-64::libcxx-10.0.0-1
  libffi             pkgs/main/osx-64::libffi-3.3-hb1e8313_2
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1j-h9ed2024_0
  pip                pkgs/main/osx-64::pip-21.0.1-py38hecd8cb5_0
  pycosat            pkgs/main/osx-64::pycosat-0.6.3-py38h1de35cc_1
  pycparser          pkgs/main/noarch::pycparser-2.20-py_2
  pyopenssl          pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1
  pysocks            pkgs/main/osx-64::pysocks-1.7.1-py38_1
  python             pkgs/main/osx-64::python-3.8.8-h88f2d9e_4
  readline           pkgs/main/osx-64::readline-8.1-h9ed2024_0
  requests           pkgs/main/noarch::requests-2.25.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/osx-64::ruamel_yaml-0.15.100-py38h9ed2024_0
  setuptools         pkgs/main/osx-64::setuptools-52.0.0-py38hecd8cb5_0
  six                pkgs/main/osx-64::six-1.15.0-py38hecd8cb5_0
  sqlite             pkgs/main/osx-64::sqlite-3.35.2-hce871da_0
  tk                 pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0
  tqdm               pkgs/main/noarch::tqdm-4.59.0-pyhd3eb1b0_1
  urllib3            pkgs/main/noarch::urllib3-1.26.4-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  yaml               pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)?


Downloading and Extracting Packages
sqlite-3.35.2        | 1.1 MB    | ################################################################################################################## | 100%
ruamel_yaml-0.15.100 | 247 KB    | ################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate r-reticulate
#
# To deactivate an active environment, use
#
#     $ conda deactivate
```


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Python in RStudio Using reticulate Package #5

參考資料

安裝 Anaconda

安裝 R 與 RStudio

執行 R 之後安裝 `reticulate` Package

建立 Conda Environment

重新執行 R 並且載入 `reticulate` Package

直接執行 Python 指令

安裝 Python Package

重建 `r-reticulate` Conda Environment

Metadata

Assignees

Labels

Projects

Milestone

Relationships

Development

Python in RStudio Using reticulate Package #5

Description

參考資料

安裝 Anaconda

安裝 R 與 RStudio

執行 R 之後安裝 reticulate Package

建立 Conda Environment

重新執行 R 並且載入 reticulate Package

直接執行 Python 指令

安裝 Python Package

重建 r-reticulate Conda Environment

Metadata

Metadata

Assignees

Labels

Projects

Milestone

Relationships

Development

Issue actions

執行 R 之後安裝 `reticulate` Package

重新執行 R 並且載入 `reticulate` Package

重建 `r-reticulate` Conda Environment