In weecology/MATSS: Macroecological Analyses of Time Series Structure

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", 
  eval = FALSE
)

1. If you need a HiPerGator account, follow the instructions on the lab-wiki: https://github.com/weecology/lab-wiki/wiki/Programming:-HiPerGator-Intro-Guide

2. Log onto HiPerGator (substituting your username for ).

    ssh <USERNAME>@hpg2.rc.ufl.edu

1. Follow the installation instructions for Python on HiPerGator. No need to actually install packages yet.

2. Create a file named .Rprofile to allow for local installs (substituting your username for ):

    echo '.libPaths(c("/home/<USERNAME>/R_libs", .libPaths()))' >> .Rprofile

1. Make sure that you have the specified folder for storing R packages (substituting your username for ):

   mkdir /home/<USERNAME>/R_libs

1. Load the R module (which makes R available in your HiPerGator session), and then open R:

    ml R
    R

1. In R, install the core Python retriever (yes, this happens in R, which is kind of magical).

    install.packages('reticulate')
    library(reticulate)
    conda_install('r-reticulate', 'retriever')

If you get an error that the conda environment 'r-reticulate' does not exist, you may need to create it first. Run the following lines and then retry the conda_install('r-reticulate', 'retriever') command:

    conda_create('r-reticulate')

1. Restart R

2. Install the rdataretriever

    remotes::install_github('ropensci/rdataretriever')
    library(rdataretriever)

If you get an error about "HTTP error 404" and "Rate limit remaing", you may need to setup a GITHUB_PAT key on HiPerGator - https://happygitwithr.com/github-pat.html

1. Install MATSS

    remotes::install_github("weecology/MATSS")

1. Try installing a dataset from retriever:

    MATSS::install_retriever_data("veg-plots-sdl", force_install = TRUE)

If you receive an error about the number of arguments, e.g.

    Error in py_call_impl(callable, dots$args, dots$keywords) : 
      TypeError: install_csv() takes from 1 to 4 positional arguments but 5 were given

then you will need a newer version of retriever than was previously installed.

Exit R to return to the command line, and then use the following commands to install retriever from github:

    conda activate r-reticulate
    conda install git pip
    pip install git+git://github.com/weecology/retriever@master

Then, retry the command at the beginning of this step in R.

1. To run a MATSS pipeline on HiPerGator you will need to setup drake to use slurm for parallel scheduling. See https://github.com/weecology/MATSS-LDATS/ for an example of how to do this.

weecology/MATSS documentation built on May 15, 2020, 7:03 p.m.