#### sound project organization your closest collaborator is you six months ago, but you do not reply to emails *K. Broman* .pull-left[ <img src="assets/figures/projectOrganizationCropped.png" width="95%"> ] .pull-right[ .small[ * segregate all materials for a project in one directory * organize according to prevailing conventions (e.g., R package structure) * maintain a clear separation of data, method, and output while unambiguously expressing the relationship among them * specify the computational environment used for the original analysis * organize such that another person can know what to expect from the plain meaning of the file and directory names * include README files ]] .footnote[K. Broman [Steps toward reproducible research](https://kbroman.org/steps2rr/pages/organize.html)] --- #### sound project organization the project determines the structure .pull-left[ 📂 project_folder `\(~~~\)`📂 src `\(~~~\)`📂 output `\(~~~\)`📂 data `\(~~~~~\)`📂 raw `\(~~~~~\)`📂 processed `\(~~~~~\)`📂 temp `\(~~~\)`📄 README.md `\(~~~\)`📄 run_analyses.R `\(~~~\)`📄 .gitignore ] .pull-right[ 📂 project_folder `\(~~~\)`📂 src `\(~~~\)`📂 output `\(~~~~~\)`📂 figures `\(~~~\)`📂 data `\(~~~~~\)`📄 README.md `\(~~~\)`📂 docs `\(~~~~~\)`📄 README.md `\(~~~\)`📄 README.md `\(~~~\)`📄 run_analyses.R `\(~~~\)`📄 .gitignore ] .footnote[C. Csefalvay [Structuring R Projects](https://chrisvoncsefalvay.com/2018/08/09/structuring-r-projects)] --- .center[ <img src="assets/figures/git_file_sizes.png" width="100%"> ] --- #### hybrid approach: data in the cloud .center[ <img src="assets/figures/data_in_the_cloud.png" width="100%"> ] --- #### keep the raw data raw <br> <br> .center[ <img src="assets/figures/Fleetwood-Mac-Cant-Go-Back-Love.jpg" width="70%"> ] .footnote[Wilson et al. 2017 [Good enough practices in scientific computing](https://doi.org/10.1371/journal.pcbi.1005510)] --- class: inverse <br> <br> “There are only two hard things in Computer Science: cache invalidation and naming things.” Phil Karlton ??? #### Phil Karlton quote --- #### naming things: principles for file and object names * machine readable - regular expression and globbing friendly + avoid spaces, punctuation, accented characters, case sensivity - easy to compute on with deliberate use of delimiters + example: *2017-11-17_berneilwash_oxygen_day_1.csv* .footnote[J. Bryan [Naming things](https://speakerdeck.com/jennybc/how-to-name-files)] -- * human readable - names contain info about the content - easy to figure out what what something is based on the name + *2016_salmon_counts.csv* conveys a lot of information about the object, and has far more meaning than *fishData.csv* -- * play well with default ordering .pull-left[ - 1_file_name.csv - 11_file_name.csv - 2_file_name.csv ] .pull-right[ - 01_file_name.csv - 02_file_name.csv - 11_file_name.csv ] --- class: inverse #### names matter in times of stress which set of file(names)s would you prefer at 3 a.m. before a dealine? .center[ <img src="assets/figures/good_bad_names.png" width="85%"> ] .footnote[J. Bryan [Naming things](https://speakerdeck.com/jennybc/how-to-name-files)]