conda-env | R Documentation |
These functions/variables are used to configure 'Miniconda' environment.
CONDAENV_NAME(env_name)
conda_path()
conda_bin()
env_path()
list_pkgs(...)
configure_matlab(matlab, python_ver = "auto")
configure_conda(
python_ver = "auto",
packages = NULL,
matlab = NULL,
update = FALSE,
force = FALSE,
standalone = FALSE
)
remove_conda(ask = TRUE)
add_packages(packages = NULL, python_ver = "auto", ...)
ensure_rpymat(verbose = TRUE, cache = TRUE)
matlab_engine()
call_matlab(
fun,
...,
.options = getOption("rpymat.matlab_opt", "-nodesktop -nojvm"),
.debug = getOption("rpymat.debug", FALSE)
)
env_name |
alternative environment name to use; default is
|
... |
for |
matlab |
'Matlab' path to add to the configuration path; see 'Details' |
python_ver |
|
packages |
additional |
update |
whether to update |
force |
whether to force install the 'Miniconda' even a previous
version exists; default is false. Setting |
standalone |
whether to install |
ask |
whether to ask for user's agreement to remove the repository.
This parameter should be true if your functions depend on
|
verbose |
whether to print messages |
cache |
whether to use cached configurations; default is true |
fun |
'Matlab' function name, character (experimental) |
.options |
'Matlab' compiler options |
.debug |
whether to enable debug mode |
None
Package reticulate
provides sophisticated tool-sets that
allow us to call python
functions within R
. However, the
installation of 'Miniconda' and python
can be tricky on many
platforms, for example, the 'M1' chip, or some other 'ARM' machines.
The package rpymat
provides easier approach to configure on these
machines with totally isolated environments. Any modifications to this
environment will not affect your other set ups.
Since 2014, 'Matlab' has introduced its official compiler for python
.
The package rpymat
provides a simple approach to link the
compiler, provided that you have proper versions of 'Matlab' installed.
Here is a list of
'Matlab' versions with official compilers and their corresponding
python
versions.
If 'Matlab' compiler is not to be installed, In most of the cases,
function configure_conda
with default arguments automatically
downloads the latest 'Miniconda' and configures the latest python
.
If any other versions of 'Miniconda' is ought to be installed,
please set options "reticulate.miniconda.url"
to change the
source location.
If 'Matlab' is to be installed, please specify the 'Matlab' path when
running configure_conda
. If the environment has been setup,
configure_matlab
can link the 'Matlab' compilers without
removing the existing environment. For 'ARM' users, unfortunately,
there will be no 'Matlab' support as the compilers are written for
the 'Intel' chips.
Once conda
and python
environment has been installed, make sure
you run ensure_rpymat()
before running any python
code. This
function will make sure correct compiler is linked to your current
R
session.
# The script will interactively install \code{conda} to `R_user_dir`
## Not run:
# Install conda and python 3.9
configure_conda(python_ver = '3.9')
# Add packages h5py, pandas, jupyter
add_packages(c('h5py', 'pandas', 'jupyter'))
# Add pip packages
add_packages("itk", pip = TRUE)
# Initialize the isolated environment
ensure_rpymat()
# Remove the environment
remove_conda()
## End(Not run)
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