This GitHub repository is a template repo for the PFTC courses. For more information about PFTC see here.
This repo is aimed at data sciences in ecology, but can also be used in other fields.
To use the template click on the green button "use this template" and follow the instructions on GitHub.
This repo has a specific folder structure that we recommend as best practice. The data are kept in separate folders named raw_data and clean_data, while the code is stored in the folder code. The raw data are the original and untouched files usually .csv or .txt formatted files. The clean data is often produced from the raw data using code and stored automatically.
In addition, there is a .gitignore text file, which tells git all the files that should be ignored. This file can be edited and adapted to the users needs.
We also recommend to use a user licence.
We strongly recommend to document the data, which is best practice. The code folder contains a subfolder data_dic with files scripts to produce a data dictionary.
The data_description.xlsx file contains basic information about each variable: description, unit and how it was collected. This file has to be done manually (until we find a solution to automate it).
The R file make_data_dictionary.R contains a function that makes the data dictionary from the data file and the description file.
The data_dic.R file contains example code to make the data dictionary for each data set and to compile it to one file in the end. Here each dataset needs to be entered.
The download_clean_data.R shows and example for how to download the clean data if it is stored externally on a data repository, for example on OSF.