Motivation
+Motivation
- There is a replication crisis in science today
- There are plenty of incentives to publish more papers @@ -34,7 +34,7 @@
+
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Our institutions are implicated
+Our institutions are implicated
- Publishers charge outrageous fees for essentially running a web / archive service
- Universities continue to promote staff based on questionable metrics @@ -56,8 +56,8 @@
The public are starting not to trust academics
+The public are starting not to trust academics
- Surprisingly, academics are still respected
- Public trust is not a given and should not be taken for granted @@ -72,8 +72,8 @@
Ideas for improving replicability
+Ideas for improving replicability
These ideas are focused on the analysis rather than the experimental work itself.
@@ -81,8 +81,8 @@ These ideas are focused on the analysis rather than the experimental workPlease stop using Word and Excel
+Please stop using Word and Excel
- An old version of Excel caused a statistical analysis error during the Covid pandemic
-
@@ -97,8 +97,8 @@ These ideas are focused on the analysis rather than the experimental work
Use the command line and GNU Make
+Use the command line and GNU Make
- Analysis ends up having several steps
-
@@ -115,8 +115,8 @@ These ideas are focused on the analysis rather than the experimental work
Method for using Make
+Method for using Make
- Each step should be performed with a command or script (e.g., gnuplot)
- Form multiple steps into a pipeline with GNU Make @@ -129,8 +129,8 @@ These ideas are focused on the analysis rather than the experimental work
Example—generating data
+Example—generating data
For example, say we have a script to generate some data a.csv, b.csv, c.csv called gen.py
Example—combine data
+Example—combine data
We might then have another script comb.py to combine them.
Example—table
+Example—table
We can produce a table using python tabulate in a script called maketable.py
maketable.
Example—graph
+Example—graph
Finally, we might use graph.py to plot a versus b (ok, this is not a very meaningful graph!)
+
@@ -227,8 +227,8 @@ plt.savefig("graph.png")
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diff --git a/2022-03-replication/replication.org b/2022-03-replication/replication.org
index f288d73..5535f7a 100644
--- a/2022-03-replication/replication.org
+++ b/2022-03-replication/replication.org
@@ -204,13 +204,16 @@ a.csv: gen.py
* Further reading
-1. I thoroughly recommend Science Fictions [[cite:&ritchieScienceFictionsExposing2020]]
-2. John Kitchin has a nice article on embedding data into PDFs. [[cite:&kitchinExamplesEffectiveData2015]]
+1. I thoroughly recommend Science Fictions [cite:@ritchieScienceFictionsExposing2020]
+2. John Kitchin has a nice article on embedding data into PDFs. [cite:@kitchinExamplesEffectiveData2015]
3. He also has a youtube describing org mode for research https://youtu.be/1-dUkyn_fZA
-
-
+** References
+#+print_bibliography:
+#+bibliography: ~/Documents/zotero-export.bib
+#+CITE_EXPORT: csl ~/Zotero/styles/harvard-cite-them-right.csl
* build :noexport:
[[elisp:(org-beamer-export-to-pdf)]]
bibliographystyle:plainnat
bibliography:~/Documents/zotero-export.bib
+
diff --git a/index.org b/index.org
index 734ba97..e4bf92d 100644
--- a/index.org
+++ b/index.org
@@ -11,4 +11,4 @@
* 2022
-[[https://github.coventry.ac.uk/pages/aa3172/presentations/2022-03-replication/replication.pdf][Making your work replicable (2022-03)]]
+[[https://github.coventry.ac.uk/pages/aa3172/presentations/2022-03-replication/replication.html][Making your work replicable (2022-03)]]
Example—LaTeX doc
+Example—LaTeX doc
Naturally, we need a LaTeX document:
@@ -256,8 +256,8 @@ Blah blah blah.Example—Makefile
+Example—Makefile
Finally, we tie everything together with a Makefile
Makefile
Using RStudio
+Using RStudio
- RStudio allows you to put all the steps into a notebook form
- The result can be exported to a LaTeX document @@ -297,8 +297,8 @@ Finally, we tie everything together with a
Makefile
RStudio example
+RStudio example
---
@@ -360,8 +360,8 @@ that generated the plot.
-
-Use Jupyter Notebook
+
+Use Jupyter Notebook
- Jupyter notebook supports Python and several other languages
- As with Rstudio, can produce LaTeX by combining code, graphs, and markdown
@@ -372,8 +372,8 @@ that generated the plot.
-
-Use Emacs org-mode
+
+Use Emacs org-mode
- Org mode is a powerful editing environment that comes with Emacs
- Org mode documents are similar to Rmarkdown (or pandoc) with easy formatting instructions
@@ -385,8 +385,8 @@ that generated the plot.
-
-Using a different latex class
+
+Using a different latex class
- Your org mode document will need
#+latex_class: IEEEtran
- You'll need to configure Emacs using something like:
@@ -409,15 +409,22 @@ that generated the plot.
-
-Further reading
+
+Further reading
-- I thoroughly recommend Science Fictions &ritchieScienceFictionsExposing2020
-- John Kitchin has a nice article on embedding data into PDFs. &kitchinExamplesEffectiveData2015
+- I thoroughly recommend Science Fictions (Ritchie, 2020)
+- John Kitchin has a nice article on embedding data into PDFs. (Kitchin, 2015)
- He also has a youtube describing org mode for research https://youtu.be/1-dUkyn_fZA
+
+References
+
+ Kitchin, J.R. (2015) “Examples of Effective Data Sharing in Scientific Publishing,” Acs catalysis, 5(6), pp. 3894–3899. Available at: https://doi.org/10.1021/acscatal.5b00538.
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