clean MMM_process_Data

[topohl]

• clean code for readability
• look for redundancies
• are calculations correct?
• formatting and rearranging of code so that it makes more sense

[anja7777]

I cleaned some tiny things in three files:

"MMM_BatchMerge":

• excluded functions from file and put them into extra file "MMM_functions.R" which is mentioned as a source at the beginning
• in this fil we work with the function "process_and_save_xlsx" and I modified the function (in the new function file) by adding an if case who checks first if xlsx-files of the input csv already exist before processing them again and do unnecessary overwriting
• already started to generalize the csv-file reading process for male and female batches together, still has to be differed by a column"sex" that has written male/female, depending on the batch number

"MMM_processData":

• Created a csv file for the list of SUS animals ("sus_animals.csv"), it can be used with readline instead of hardcoding each SUS animal number into each file (SUS animals are used in multiple files, so you only need to make changes in one place).

"MMM_sleepAnalysis":

• Created a csv file for the list of SUS animals ("sus_animals.csv"), it can be used with readline instead of hardcoding each SUS animal number into each file (SUS animals are used in multiple files, so you only need to make changes in one place).
• excluded functions from file and put them into extra file "MMM_functions.R" which is mentioned as a source at the beginning
• added request which checks if all column names(esp."Phase" and "Sex") exist in data_filtered(and summarized_data) before using group_by
  • added include_sex=False for more possibilities(does not work as true at the moment) and put include_phase and include_sex to the top of the file
• defined variables for long paths that are used more than once and declared them at the beginning of the file
  • changed the directory for saving the plots to a new fdolder"graphs" ("S:/Lab_Member/Tobi/Experiments/Exp9_Social- Stress/Analysis/SIS_Analysis/statistics/sleep/graphs")

in all three files I used "S:/Lab_Member/Anja" as working directory, has to be adjusted

[anja7777]

new column "Sex" is now added in ProcessData(depending on batch)