There is more than one way to approach a data analysis and some of the ways lead to easier modifications and updates and help make your work more reproducible. This paper talks about steps that they recommend based on years of teaching software carpentry and data carpentry classes.
Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK (2017) Good enough practices in scientific computing. PLoS Comput Biol 13(6): e1005510. Available at https://doi.org/10.1371/journal.pcbi.1005510.