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README.Rmd
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---
title: "LEEF CA planning"
output:
github_document:
toc: yes
html_document:
toc: yes
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{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 <a href="https://teams.microsoft.com/l/file/7E868619-064E-4C6B-BC89-935C190130D4?tenantId=c7e438db-e462-4c22-a90a-c358b16980b3&fileType=docx&objectUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF%2FShared%20Documents%2FGeneral%2F05_protocols%2FSampling_manual.docx&baseUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF&serviceName=teams&threadId=19:[email protected]&groupId=13ba9e9a-1d5d-42b1-9a95-08fd956973cc" target="_blank">link</a> for manual
- **bemovi** see <a href="https://teams.microsoft.com/_#/school/files/General?threadId=19%3Ad14a98eb700e4721b35583265c27e8a3%40thread.tacv2&ctx=channel&context=1_Videoing_documents&rootfolder=%252Fsites%252FLEEF%252FShared%2520Documents%252FGeneral%252F05_protocols%252F1_Videoing_documents" target="_blank">link</a> for manual
- **flowcam** see <a href="https://teams.microsoft.com/l/file/2381A032-18A4-4649-B072-871BFF45B788?tenantId=c7e438db-e462-4c22-a90a-c358b16980b3&fileType=docx&objectUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF%2FShared%20Documents%2FGeneral%2F05_protocols%2FFlowcam_manual.docx&baseUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF&serviceName=teams&threadId=19:[email protected]&groupId=13ba9e9a-1d5d-42b1-9a95-08fd956973cc" target="_blank">link</a> for manual
- **flowcytometer** see <a href="https://teams.microsoft.com/l/file/D0C66850-57BD-49D1-8ED9-528C57B7FC36?tenantId=c7e438db-e462-4c22-a90a-c358b16980b3&fileType=docx&objectUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF%2FShared%20Documents%2FGeneral%2F05_protocols%2FFlowcytometer_manual.docx&baseUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF&serviceName=teams&threadId=19:[email protected]&groupId=13ba9e9a-1d5d-42b1-9a95-08fd956973cc" target="_blank">link</a> for manual
- **manual** count see <a href="https://teams.microsoft.com/l/file/336D64DD-53FC-4ED1-9E2D-DDE653C357BF?tenantId=c7e438db-e462-4c22-a90a-c358b16980b3&fileType=docx&objectUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF%2FShared%20Documents%2FGeneral%2F05_protocols%2FManual_count_manual.docx&baseUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF&serviceName=teams&threadId=19:[email protected]&groupId=13ba9e9a-1d5d-42b1-9a95-08fd956973cc" target="_blank">link</a> for manual
- **O~2~ meter** see <a href="https://teams.microsoft.com/l/file/A486E46E-A2F1-44F6-89A2-6A05E5B44F27?tenantId=c7e438db-e462-4c22-a90a-c358b16980b3&fileType=docx&objectUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF%2FShared%20Documents%2FGeneral%2F05_protocols%2FO2_manual.docx&baseUrl=https%3A%2F%2Fuzh.sharepoint.com%2Fsites%2FLEEF&serviceName=teams&threadId=19:[email protected]&groupId=13ba9e9a-1d5d-42b1-9a95-08fd956973cc" target="_blank">link</a> 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.