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@LubomirBednar: add the "infection isolate" for each mouse in the experiment! Either by having it directly in the table (probably better) or by merging with another table.

I made comments to guide you in this new script. It looks like we'll have a very nice and clean data pipeline once the raw data is sanitized!

So do it ;-) ...

This script is broken:
https://github.com/derele/Eimeria_Lab/blob/master/R/Exp008.R

source("functions4InfectionExperiments.R")

The sourced script does not exist anywhere.

Please fix it @LubomirBednar ? Are these functions still used? What is the script used for?

This can be deleted, right @alicebalard ?

@LubomirBednar This has now it's own repository!!!

Please figures and analysis scripts/code unless they can be linked to an example in the documentation of access or addition of data.

Either include the mouse id in the shedding tables (preferably) or use another table to associate faeces/flotation labels with mouse ids (EH_ID in the weight datasets, I guess).

A main guidance table with all the experiments described. Could also be very helpful... Consider this when writing more documentation!

This data storage should be used for two purposes. Accessing data (Access/retrieval) and storage (adding of new data). Access to data is likely more frequent and should be explained first!

I could imagine a structure.

1. Accessing data
   1.1. General description
   1.2. Examples
   1.2.1. Example 1
   1.2.1. Example 2

This should give the user (myself and you) the most important info on how to get something out of the data. Examples (1, 2) can be: how to tabulate the number of mice per experiment, how to tabulate the samples taken in an experimetn etc.. Examples in the documentation should use code in an appropriately named folder.

2. Adding data
   1.1. General description
   1.2. Examples
   1.2.1. Adding genotype data
   1.2.2. Adding qPCR data.

Again if code (concise would be goo!) is needed to add the data put it in an appropriate folder (structure). E.g. Examples/addingData/addqPCRfromRaw.R (or similar). Point in the documentation to the example scripts (if needed).

I think the readme is a nice place for the documentation if you can keep it concise!

You can move stuff to a new repository without losing history (if you are keen on that).

@LubomirBednar please remove outdated parts of the documentation. There is even a paragraph in the readme that is called "historic"! That's quite ridiculous!