Confounding variables (#35)

* Write confounding variables section

* Add confounding variables in the experiment section

* Add suggestions

Co-authored-by: Sven F. <[email protected]>

* change definition

Co-authored-by: Sven F. <[email protected]>

* remove tab specification

* apply suggestions

Co-authored-by: Sven F. <[email protected]>

* Make it UI Agnostic

Co-authored-by: Sven F. <[email protected]>

* improve information on confounding

* Smaller corrections

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Co-authored-by: KochTobi <[email protected]>
Co-authored-by: Sven F. <[email protected]>
Co-authored-by: Sven Fillinger <[email protected]>

Author: KochTobi

Diff for: docs/confounding-variables.md

@@ -0,0 +1,41 @@
+# Confounding Variables
+
+!!!info
+    _"Confounding, sometimes referred to as confounding bias, is mostly described as a ‘mixing’ or 
+    ‘blurring’ of effects. It occurs when an investigator tries to determine the effect of an 
+    exposure on the occurrence of a disease (or other outcome), but then actually measures the effect 
+    of another factor, a confounding variable."_
+    
+    Jager, K. J., Zoccali, C., MacLeod, A., & Dekker, F. W. (2008). Confounding: What it is and how to deal with it. Kidney International, 73(3), 256-260. [https://doi.org/10.1038/sj.ki.5002650](https://doi.org/10.1038/sj.ki.5002650)
+
+### Define confounding variables in your experiment
+
+In order to work with confounding variables, first you must define them.
+Confounding variables are experiment-specific. Currently, it is not possible to reuse the same 
+variable in other experiments metadata in Data Manager.
+
+Confounding variables are defined in your experiment, so navigate to your experiment first.
+There you can find the controls to add new confounding variables.
+
+### Assign levels of a confounding variable to your sample
+
+To get the full potential and account for effects of confounding variables in your experiment, you 
+can now annotate the samples with your observation of the variables' manifestation.
+In contrast to experimental variables, not all samples need to have a level in one confounding variable.
+
+After [defining the confounding variables in your experiment](#define-confounding-variables-in-your-experiment), 
+the confounding variables are added in the sample registration and sample editing process. 
+In the sample registration and sample editing processes, you have the possibility to annotate 
+samples with levels for the confounding variables.
+
+### Rename a confounding variable
+
+To remove a confounding variable, navigate to your experiment, locate the confounding variables editing and rename your confounding variable.
+After renaming a variable, the levels are preserved and only the name of the confounding variable are changed.
+
+### Delete a confounding variable
+
+To remove a confounding variable navigate to your experiment, locate the confounding variables editing and remove the variables you want to delete.
+
+!!!warning
+    Removing a confounding variable will delete all annotated levels of that variable on all samples in your experiment.

Diff for: mkdocs.yml

@@ -21,6 +21,7 @@ nav:
   - Experiment:
       - Introduction: experiment/experiment_introduction.md
       - Creation: experiment/experiment_creation.md
+      - Confounding Variables: confounding-variables.md
   - Measurement:
       - Introduction: measurement/measurement_introduction.md
       - Registration: measurement/measurement_registration.md