Shir Dekel's PhD Thesis

This repository contains the code that was used to compile the thesis document. The thesis itself can be found at https://thesis.shirdekel.com/. The {targets} package was used to run everything as a reproducible pipeline. _targets.R contains each step of the pipeline.

The thesis is made up of fourteen experiments. Seven of these are reported in the main text, and the other seven are reported in the appendices. Each experiment's data is stored as a separate R package. The table below shows the name of the relevant data package, where it is primarily reported, and the relevant experiment number that it corresponds to in the thesis text.

Data R package	Location in thesis text	Thesis experiment number
aggregation1	Chapter 2	Experiment 1
aggregation2	Chapter 2	Experiment 2
aggregation3	Appendix A	Experiment 3
aggregation4	Appendix A	Experiment 4
alignment2	Chapter 4	Experiment 1
alignment3	Chapter 4	Experiment 2
alignment8	Chapter 4	Experiment 3
alignment1	Appendix B	Experiment 4
alignment4	Appendix B	Experiment 5
alignment5	Appendix B	Experiment 6
alignment6	Appendix B	Experiment 7
alignment7	Appendix B	Experiment 8
anecdotes1	Chapter 6	Experiment 1
anecdotes2	Chapter 6	Experiment 2

Data for any given experiment can be accessed by installing the relevant package from GitHub. Simply use the Data R package name from the table above. For instance, the data from Chapter 2 Experiment 1 can be installed by running:

## First install the `{remotes}` pacakge if it is not already installed by using:
## install.packages("remotes")
remotes::install_github("shirdekel/aggregation1")

Once installed, you can simply call the data using:

aggregation1::data

To reproduce any of the analyses or plots in the thesis, use targets::tar_read(). For instance, if you want to see the R object of all the results used in Chapter 2 Experiment 1, you can run:

targets::tar_read(results_aggregation_1)

The plots are accessed through:

targets::tar_read(plot_aggregation_1)

Similarly, the directory that contains the materials is accessed through:

targets::tar_read(materials_aggregation_1)

Alternatively, the code can be accessed manually by visiting the R/ directory. For instance, you can produce the results reported in Chapter 2 Experiment 1 by loading and then calling the relevant function and data:

source("get_results_aggregation_1.R")
get_results_aggregation_1(aggregation1::data)

shirdekel/phd_thesis

Shir Dekel's PhD Thesis