my PhD thesis

How to store ...

Archive file name

Format:	PhD_thesis_<lastname>_<year>.zip
Example:	PhD_thesis_Molleman_2014.zip MSc_thesis_vanderPlas_2013.zip

To ensure general accessibility of the archives, all file names, metadata and other description files and comment lines in code must be in English. File names should not contain special characters other than dashes (-) or underscores (_); use underscores instead of spaces.

Contents of the .zip archive

The final version of the PhD thesis, both as a text file (rtf, doc, docx) and a as a pdf file.
Relevent metadata: a text file read_me_first.txt containing the description of the thesis and any relevant general information.

In a separate folder for each chapter of the thesis:

All primary (raw) data underlying the chapter. Primary data include a scanned pdf of original data sheets, field books etc. by preference; if this is not possible raw data should be at least included in some electronic way, i.e., in a table, spreadsheet or text file.
All secondary (processed) data used in the preparation of the chapter.
All program code and scripts used to produce the final results such as figures, tables, statistical analyses etc.
Relevent metadata: a text file read_me_first.txt describing the data sources in relation to (corresponding sections of) the chapter. If many data files are present, additional metadata can be included in a spreasheet or database that is referred to in the read_me_first.txt file.

Example: PhD_thesis_Molleman_2013.zip

Main file:
Chapter_2 [file folder] Chapter_3 [file folder] Chapter_4 [file folder] Chapter_5 [file folder] Chapter_6 [file folder] Chapter_7 [file folder] Social_learning_and_human_cooperation_final.pdf read_me_first.txt zleaf.exe ztree.exe Folder Chapter_2:
Cult_Evo_Coop_maintext_resub_final.docx Cult_Evo_Coop_maintext_resub_final.pdf CulturalGroupSelection.cpp CulturalGroupSelectionMutation.cpp Figure_1.pptx Figure_2_take_one_plot_out.r Figure_2.pptx Figure_3_gamma_for_alpha_is-0.8_and_beta_is_0.5.r ... Load_model_results_MUTATION.r Load_model_results.r Plot_alpha_vs_beta_for_gammas_of_choice_MUTATION.r Plot_alpha_vs_beta_for_gammas_of_choice.r read_me_first.txt

Contents of the metadata file

The following metadata fields:
- Author name
- P-number
- Title of the PhD thesis
- Year of publication
- Research group
- Promotor(s) & co-promotor(s)
- Contact information of the author
A short description of all chapters/folders in the archive.
For each chapter:
- If published: a complete reference to the published paper
- A short description of all data files in the chapter/folder.
- If relevant: A short description of external data sets used for the study, including a reference to their home institute & the principal scientist responsible for their quality.
- A short description of the purpose of program code and script files in the folder, and their associated parameter files.
- If relevant: references to any on-line programs that were used to produce (parts of) the folder contents.

Download metadata template file

Example: read_me_first.txt in .zip archive

Name: Molleman L.S.
P-number: p123456
Title: Social learning and human cooperation
Year: 2014
Research group: Theoretical Biology
Promotor: Prof. F.J. Weissing
For any additional questions: l.s.molleman[at]rug.nl, or lucasmolleman[at]hotmail.com

                              

Program z-Tree: version 3.3.11, University of Zurich, http://www.iew.uzh.ch/ztree , ztree@iew.uzh.ch

Example: read_me_first.txt in folder Chapter_2

This chapter was published as: Molleman L, Quinones AE, Weissing FJ (2013). Cultural evolution of cooperation: The interplay between forms of social learning and group selection. Evolution and Human Behavior 34:342-349, doi:10.1016/j.evolhumbehav.2013.06.001

                              

Figures are produced by first generating the datafiles.
For this, extensive computer simulations were run using the "CulturalGroupSelection.cpp" file in this folder.
To reproduce the figures of the paper, please use the R scripts.
Figure 1 is not based on data (it presents the model structure)
Figure 2 and 3 are the 'no mutation' scenarios. First, load the data ('Load_no_mut.r'). Second, plot figure 2 ("Plot_fig2.r"), then figure 3 ("Plot_fig3.r") n.b. you HAVE to plot figure 2 first to make figure 3)
For figure 4, do the same: first, load the data ('load_mut.r'). Second, plot the Figure ("Plot_fig4.r")

                              

For any additional questions: l.s.molleman[at]rug.nl, or lucasmolleman[at]hotmail.com

Which PhD theses to archive

Required:	All PhD theses done within GELIFES, with a GELIFES professor as first promotor All external PhD theses (e.g. done at a KNAW or NWO institute) with a GELIFES professor as first promotor
Voluntary:	PhD theses with a non-GELIFES professor as first promotor

NOTE: Chapters in a PhD thesis that have been previously published in a journal/book and have been archived as a publication, must be archived (again) as part of the PhD thesis archive. Similarly, chapters of a PhD thesis that have been archived as part of the PhD thesis archive and are published in a journal/book at a later moment, must be archived again as a publication.

When to deposit the archive

The documented data archive of the study should be deposited with the promotor upon handing in the final manuscript for the manuscript committee. The promotor will only sign the approval form of the PhD thesis when the data archive of the study has been handed in. The promotor deposits the data archive of the thesis in the repositorye within 1 month after the thesis has been handed in.

How to deposit the archive

The data are deposited by sending an email with the full reference of the publication, and the zip file of the data archive to gelifes-data rug.nl. For sending larger files (>5 MB) the service SURF File Sender can be used, or other file transfer services such as Unishare, Dropbox, Google Drive, WeTransfer.

For questions or problems, contact the data manager.

Last modified:

11 December 2020 4.08 p.m.