Rubric

1. (0 p) Set up your bibliography manager.

• Alternatively, ONLY if you are an experienced PubMed user, you may use TeXMed to get the bibtex format.
3. (3 p) Find three references that relate to your dataset and variables, copy BibTeX reference into your bibliography manager or text file.

4. (2 p) Add your bibliography .bib file to the YAML (top of Rmd file).

5. (3 p) Write a couple short sentences that cite the reference keys following the example below.

6. (2 p) Ensure that the references automatically appear at the bottom of the document.

7. (0 p) Remove anything in this document that does not pertain to your references.

The only references from your ADA1_Stat_145.bib file that will appear at the end of a document are those that have been cited in the text. You can use nocite to get a full bibliography but we will not discuss that further here. When you create your *.Rmd file, you will need to add the line bibliography: ADA1_Stat_145.bib to the YAML metadata section. If you have more than one *.bib file, place each file indented on a separate line, preceeded with a dash, and make sure to leave a space after the dash.

bibliography:
- First.bib
- Second.bib
- Third.bib

Set up bibliography manager

Edit text file directly in RStudio

To create an ADA1_Stat_145.bib,

1. Menu: File / New File / Text File
2. Menu: File / Save As… Save the file as “ADA1_Stat_145.bib”, or something similar (without spaces).
3. You now have an empty file that you can paste bibtex entries into.
4. Each time you need to add a bib item, open this file, paste the bibtex text to the bottom of the file, and save it.
5. If this gets large, you may want to install a program like JabRef to browse the entries.

Mendeley users (preferred)

To create an ADA1_Stat_145.bib by creating an automatic syncing .bib file,

1. Menu: Tools / Options / BibTeX
2. Check “Enable BibTeX syncing” with “Create one BibTeX file per group” and select the Path to your ADA1 folder, click OK.
3. Under “My Library” create a group called “ADA1_Stat_145”, or something similar (without spaces).
4. Check the Path you specified and see whether there are new *.bib files in that folder.
5. Note, this ADA1_Stat_145.bib file will always be up to date with your Mendeley library.

Zotero users

To create an ADA1_Stat_145.bib,

1. Highlight the titles you want to select in Zotero.
2. For Windows users, right click on the highlighted items; for Mac users, Control-click on the highlighted items.
3. Select Export Items. Use the drop down menu to select Bib$$\TeX$$ (not Bib$$\LaTeX$$) as the format.
4. Click OK. Change the name of the file to ADA1_Stat_145.bib in the Save As: box.
5. Click Save.

Citation example

• Beckschäfer et al. (2014) said an interesting thing about X and Y and I will try that relationship with my variables A and B.
• There were other citations that are related and I want to read them more carefully (Murphy 2012; Dean and ebrary, Inc 2014; Beckschäfer et al. 2014)

For more documentation on bibliographies and citations with R Markdown, see http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html. For general help with R Markdown, see https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf.

Citations to appear in parentheses are cited in brackets like this (Beckschäfer et al. 2014; Richert 2013; Murphy 2012; Dean and ebrary, Inc 2014). A citation you want to refer to in text, such as Beckschäfer et al. (2014), doesn’t have the brackets.

References

Beckschäfer, P, L Fehrmann, Rd Harrison, J Xu, and C Kleinn. 2014. “Mapping Leaf Area Index in Subtropical Upland Ecosystems Using RapidEye Imagery and the randomForest Algorithm.” iForest - Biogeosciences and Forestry 7 (1): 1–11. doi:10.3832/ifor0968-006.

Dean, Jared, and ebrary, Inc. 2014. Big Data, Data Mining, and Machine Learning Value Creation for Business Leaders and Practitioners. Wiley & SAS Business Series. Hoboken, NJ: Wiley.

Murphy, Kevin P. 2012. Machine Learning a Probabilistic Perspective. Adaptive Computation and Machine Learning Series. Cambridge, Mass: MIT Press.

Richert, Willi. 2013. Building Machine Learning Systems with Python. Birmingham, UK: Packt Publishing.