sjSDM: Help with the installation of dependencies

PyTorch Installation - Before you start:

A few notes before you start with the installation (skip this point if you do not know conda):

• existing ‘conda’ installations: make sure you have the latest ‘conda’ or ‘miniconda’ version and remove unnecessary ‘conda’ installations.
• existing ‘conda’ or ‘virtualenv’ environments (skip this point if you do not know ‘conda’): we currently enforce the usage of a specific environment called ‘r-sjsdm’,so if you want use a custom environment it should be named ‘r-sjsdm’

Windows - automatic installation:

Sometimes the automatic ‘miniconda’ installation (via r sjSDM::install_sjSDM() ).doesn’t work because of white spaces in the user’s name. But you can easily download and install ‘conda’ on your own:

Download and install the latest ‘conda’ version

Afterwards run:

install_sjSDM(version = c("gpu")) # or "cpu" if you do not have a proper gpu device

Reload the package and run the example, if this doesn’t work:

• Restart RStudio
• Install manually pytorch, see the following section

Windows - manual installation:

Download and install the latest ‘conda’ version

Open the command window (cmd.exe - hit windows key + r and write cmd)

Run in cmd.exe:

conda create --name r-sjsdm python=3.7
conda activate r-sjsdm
conda install pytorch torchvision cpuonly -c pytorch # cpu
conda install pytorch torchvision cudatoolkit=11.3 -c pytorch #gpu
python -m pip install pyro-ppl torch_optimizer madgrad

Restart R, try to run the example, and if this doesn’t work:

• Restart RStudio
• See the ‘Help and bugs’ section

Linux - automatic installation:

Run in R:

install_sjSDM(version = c("gpu")) # or "cpu" if you do not have a proper gpu device

Restart R try to run the example, if this doesn’t work:

• Restart RStudio
• Install manually ‘PyTorch’, see the following section

Linux - manual installation:

We strongly advise to use a ‘conda’ environment but a virtual environment should also work. The only requirement is that it is named ‘r-sjsdm’

Download and install the latest ‘conda’ version

Open your terminal and run:

conda create --name r-sjsdm python=3.7
conda activate r-sjsdm
conda install pytorch torchvision cpuonly -c pytorch # cpu
conda install pytorch torchvision cudatoolkit=11.3 -c pytorch #gpu
python -m pip install pyro-ppl torch_optimizer madgrad

Restart R try to run the example, if this doesn’t work:

• Restart RStudio
• See the ‘Help and bugs’ section

MacOS - automatic installation:

Run in R:

install_sjSDM()

Restart R try to run the example, if this doesn’t work:

• Restart RStudio
• Install manually ‘PyTorch’, see the following section

MacOS - manual installation:

We strongly advise to use a ‘conda’ environment but a virtual environment should also work. The only requirement is that it is named ‘r-sjsdm’

Download and install the latest conda conda version

Open your terminal and run:

conda create --name r-sjsdm python=3.7
conda activate r-sjsdm
python -m pip install torch torchvision torchaudio 
python -m pip install pyro-ppl torch_optimizer madgrad

Restart R try to run the example, if this doesn’t work:

• Restart RStudio
• See the ‘Help and bugs’ section

Help and bugs

• ask for help via the issue tracker. Please post the output of r sjSDM::install_diagnostic()as a quote.
• report bugs with a reproducible example via the issue tracker

Example

library(sjSDM)
community <- simulate_SDM(sites = 100, species = 10, env = 5)
Env <- community$env_weights
Occ <- community$response

model <- sjSDM(Y = Occ, env = linear(Env, ~0+X1*X2 + X3 + X4))
summary(model)