Call a bash variable within a R using conda environement

Question

I need to run PBS Job Arrays. In these scripts, I need to run R in a conda environment.

To run my jobs as arrays, I need to be able to call up variables previously defined by my pbs script (typically, the working directory, the names of individuals...).

I have a R script launched by a pbs job exactly like this :

########################################
##      Load environment              ##
########################################

. /appli/anaconda/latest/etc/profile.d/conda.sh

########################################
##      Execute script                ##
########################################

conda activate r4-base

Rscript $HOME/Documents/script/fm_fit_model.r

conda deactivate

Is there a way I can modify my variables in my Rscript by defining variables in my PBS jobs. For example, I would like to define the variable species=fish in my pbs script and that it would modify the corresponding variable in my R script, so that I can make everything run in arrays.