LEEF CA planning

Description

This document contains information on

1. How the pipeline as it s implemented by the LEEF-UZH project ( by using the LEEF package) can be used and managed, and
2. How the pipeline can be setup and internals of the LEEF package.

Reading this documentation

The easiest to read the documentation is to go to the package website to see all documentation of the functions under the menu item Reference and to access further documentation in the “Articles” menu. The articles are also available as vignettes in the R package LEEF.

Measurements in the Pipeline

The actual measurement protocols are located on the Teams server of pour group. If you have access to it, the links below will point you tho the documents.

• sampling see link for manual
• bemovi see link for manual
• flowcam see link for manual
• flowcytometer see link for manual
• manual count see link for manual
• O₂ meter see link for manual

Installation of the LEEF R package

This R package contains the functionality used for processing the data in the LEEF project.

The R package is in a drat repository, i.e. an R repository with the same functionality as CRAN, only managed by the maintainer of the LEEF-UZH organisation on github.

To install it, you need to install the drat package if it is not installed yet

install.packages("drat")

To install the LEEF package, you simply have to run

drat::addRepo("LEEF-UZH")
install.packages("LEEF")

This installs the LEEF package and all additional LEEF.xxx packages needed for processing, archiving and adding the research ready data to an SQLite database.

Funding

The project is funded by the SNF Project 310030_188431.