Installation instructions for R
1. Prerequisites
Assuming you have a version of R installed on your computer, as well as Python3 and pip. This is automatic in all recent Linux distributions. Otherwise instructions are available here: Python and pip.
2. Installation
The reticulate library is used to load the python package into R:
install.packages("reticulate")
Then the package needs to be installed. This can be done directly in R. If you do not have conda on your computer, you will be asked to install Miniconda. You should say yes and R will take care of everything. This will isolate this python environment from your system environment:
library(reticulate)
py_install("geoenrich", pip = TRUE)
If you already have conda installed, R should find it automatically. If it does not, you can try installing the packages this way:
conda_create("r-reticulate-geoenrich")
conda_install("r-reticulate-geoenrich", "geoenrich", pip = TRUE)
Finally, you can check that geoenrich submodules can be imported properly:
dataloader <- import("geoenrich.dataloader")
3. Configuration
3.1. First configuration
The first time you import the dataloader or enrichment module, it will display the location of the credentials_example.py configuration file. You will need to edit it and then remove _example from the file name so its name is just credentials.py.
In this file, you need to specify the root_path where all persistent data will be stored. You should pick a stable location with plenty of free space available (depending on your data download needs).
If you want to use services that require authentification, you need to specify your credentials there. You will see 3 variables that need to be filled with GBIF credentials if you want to download occurrence data from GBIF. If you don’t already have an account you can register on the GBIF website.
There is also a dictionary named dap_creds that is intended to store credentials to OpenDAP servers. The server domains are the keys, like the example provided for Copernicus. You can add as many credentials as you need into that dictionary.
Warning
If there are reserved characters in your username or password, you need to replace them with the %XX code as you would in an URL (eg. replace ‘@’ by ‘%40’). See the full list below.
␣ |
! |
“ |
# |
$ |
% |
& |
‘ |
( |
) |
, |
/ |
: |
; |
= |
? |
@ |
[ |
] |
||
%20 |
%21 |
%22 |
%23 |
%24 |
%25 |
%26 |
%27 |
%28 |
%29 |
%2A |
%2B |
%2C |
%2F |
%3A |
%3B |
%3D |
%3F |
%40 |
%5B |
%5D |
3.2. Adding other data sources
At the same location, there is a catalog.csv file that already contains a list of available variables. If you want to use a dataset from Copernicus, you first need to register on their website and write your credentials in the credentials.py file.
If you need additional variables, you can update add a personal_catalog.csv file to the same folder (template on GitHub). Three columns are compulsory:
variable: A unique name for that variable (user defined). It needs to be different from the variable names already in the built-in catalog.
url: OpenDAP URL.
varname: Name of the variable in the remote dataset.
4. Using the package
Congrats, you can now use the tutorial and start doing science!