BLAB_DATA

A set of GitHub repositories with data from SEEDLingS and VIHI that are cloned to ~/BLAB_DATA allowing the code to access specific versions of that data.

Get access to the data

With the exception of seedlings-nouns, all repositories are private to the members of the BergelsonLab github organization. Every new lab member should be added to it. If you haven't been added yet, ask someone on staff to add you.

Clone data to your computer

In Terminal:

$ cd ~
$ mkdir BLAB_DATA
$ cd BLAB_DATA

Download the current version of the repositories you need:

git clone https://github.com/BergelsonLab/all_basiclevel.git
git clone https://github.com/BergelsonLab/cdi_spreadsheet.git
git clone https://github.com/BergelsonLab/motor_spreadsheet.git
git clone https://github.com/BergelsonLab/reliability.git
git clone https://github.com/BergelsonLab/seedlings-nouns_private.git
git clone https://github.com/BergelsonLab/seedlings-nouns.git
git clone https://github.com/BergelsonLab/vihi_annotations.git

Load data from R code

Use blabr's get_* functions to load data into memory. Always default to specifying a version when doing that so that your script is reproducible. If you want to use the latest version at the moment you are writing the code, run these functions once without specifying the version - you will receive a warning saying that you shouldn't do that. That warning will also include the version - copy it into the function call.

Updating data

Because of how blabr and blabpyaccess data in ~/BLAB_DATA, avoid editing data directly in that folder. Instead, make a dedicated clone to work in.

What can happen is that your script that updates the data calls a `blabr` function that checks out a different version of a repo while you are updating leading to unpredictable results.