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leef

Core of Data Processing Pipeline for the LEEF Experiment - See https://leef-uzh.github.io/LEEF/ for documentation - WORK IN PROGRESS

https://github.com/leef-uzh/leef

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.5%) to scientific vocabulary

Keywords

data-analysis data-processing leef r
Last synced: 4 months ago · JSON representation

Repository

Core of Data Processing Pipeline for the LEEF Experiment - See https://leef-uzh.github.io/LEEF/ for documentation - WORK IN PROGRESS

Basic Info
  • Host: GitHub
  • Owner: LEEF-UZH
  • License: mit
  • Language: R
  • Default Branch: LEEF-2
  • Homepage:
  • Size: 35.8 MB
Statistics
  • Stars: 0
  • Watchers: 1
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  • Open Issues: 1
  • Releases: 5
Topics
data-analysis data-processing leef r
Created over 7 years ago · Last pushed 11 months ago
Metadata Files
Readme License Codemeta

README.Rmd 

---
title: "LEEF CA planning"
output:
  github_document:
    toc: yes
  html_document:
    toc: yes
---


```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# 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](https://leef-uzh.github.io/LEEF/) to see all documentation of the functions under the menu item [Reference](https://leef-uzh.github.io/LEEF/reference/index.html) 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
- **O~2~ 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](https://dirk.eddelbuettel.com/code/drat.html) 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

```{r eval = FALSE}
install.packages("drat")
```

To install the `LEEF` package, you simply have to run
```{r eval=FALSE}
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.

Owner

  • Name: LEEF-UZH
  • Login: LEEF-UZH
  • Kind: organization

CodeMeta (codemeta.json) 

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