sje30/eglen2015

Eglen 2015 review article

Introduction

This is the home page for the following review:

Eglen SJ (2016) Bivariate spatial point patterns in the retina: a reproducible review. Journal de la Société Française de Statistique 157:33–48. PDF

This package contains all the material needed to regenerate the article for itself. Some key parts of the package are:

• vignettes/eglen2015.Rnw: the source file for the article in LaTeX format.
• inst/extdata: a folder containing all the data files studied in this article.

Recompiling the paper

This R package depends on a few other packages, from CRAN and my personal library. The following sequence should install everything you need:

Rscript -e 'install.packages(c("splancs", "spatstat", "devtools", "knitr", "xtable", "tinytex"))'
Rscript -e 'install.packages(c("sjedmin", "sjedrp", "sjevor","sjedist"), type="source", contriburl="http://damtp.cam.ac.uk/user/eglen/r/")'
Rscript -e 'devtools::install_github("sje30/eglen2015",build_vignettes=TRUE)'

The last line should load this package. Once it is installed, you can then view the paper, or view the knitr document that created the paper:

vignette("eglen2015")
eglen2015:::edit()

This does of course assume that your system already has R, latex, and various unix tools. That may not be the case; however, you can still use the package through the Docker system, see next.

Docker

Once you have docker installed on your system, you can download and run this package using:

docker run -d -p 8787:8787 sje30/eglen2015

(View sje30/eglen2015 to check the status of this Docker package.)

Then visit the web page to start R (username and password are "rstudio"):

http://localhost:8787/        ## linux
http://192.168.99.100:8787/   ## mac, windows users

The IP address for mac/windows may vary; you can check it by running the command:

docker-machine ip default

Once you have logged in, you can then do the following commands to recompile the document:

setwd("eglen2015/vignettes/")
source("run.R")

Then examine the vignettes folder and you should see eglen2015.pdf.

Thanks to the Rocker team for the R-based docker images, on which this work is based.

eglen2015's Issues

knitr has limited support for latin1

When I tried including the French abstract, and encoded the file with latin1, I got many warnings from knitr. It seems that knitr is optimised for UTF8, so I have kept things simple here and kept my latex in ASCII.

kitemarking

Hi Stephen,

I was interested to see that part two of this paper deals with some of the topics discussed in the INCF meeting in Dec, I look forward to reading it!

On the topic of kitemarking, it might also be relevant to note the badging system that has been adopted by a few journals, as a signal for code and data sharing (I've been peppering journals in my field to adopt it also). Here are a few relevant links, etc.:

http://pss.sagepub.com/content/25/8.toc.pdf
Table of Contents from August's issue of Psych Science (showing badges)

http://pss.sagepub.com/content/25/8/1571.full
a manuscript from the same issue (badges at the top of the first page, and then again at the end of the article along with the URLs to the evidence for the badges).

Additionally, all of the articles in this special issue of Social Psychology (with the exception of the editorial) have been awarded badges. In Social Psychology, the badges appear only at the end of the articles.

An example of Psychological Science badged article:
http://pss.sagepub.com/content/25/12/2199.full

Psychological Science's Explanation of Open Practices
http://www.psychologicalscience.org/index.php/publications/journals/psychological_science/ps-submissions#OPEN
And about the badges
http://www.psychologicalscience.org/index.php/publications/journals/psychological_science/badges

Cognition data policy:
http://www.sciencedirect.com.offcampus.lib.washington.edu/science/article/pii/S0010027714002248

And you've probably seen the recent editorial from 'Scientific Data" that says they're going to demand code availability where it seems necessary, and recommend github plus a DOI-issuing repository: http://blogs.nature.com/scientificdata/2015/02/19/code-sharing-tips/

best,

Ben

link to PDF version of paper is broken

the link to the PDF file at the of the citation is broken.

Compiling with jsfds.sty

When compiling with jsfds.sty, I get errors in the first run of pdflatex. This is a problem, as I need pdflatex to run without errors (e.g. for Docker images, reproducible research). I found that the problem was due to jsfds.sty using the microtype package. This seems to be a recent problem reported elsewhere:

https://bitbucket.org/kleberj/pdfcomment/issues/16/exampletex-does-not-build

So, in jsfds.sty, I have commented out the use of microtype package as a workaround, and my program now compiles without errors.

buildVignettes fails with layers_csn3.pdf not found.

Not quite sure why this is happening, since I can see the pdf file in the directory with the Rnw file... I'm doing this in the RStudio I get from docker run -d -p 8787:8787 sje30/eglen2015 I've never had any problem like this with my own work, though I use a 'figures' directory within the vignette directory to hold this kind of thing. What do you think? Can you build the vignette in the docker container?

> tools::buildVignettes("eglen2015")
Read 4 items
Read 222 items
Read 116 items
Read 10 items
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'eglen2015.tex' failed.
LaTeX errors:
! Package pdftex.def Error: File `layers_csn3.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.