Supplementary materials for a study of rocks associated with Holocene human burials at Madjedbebe, Northern Territory, Australia
Author of this repository:
Ben Marwick (email@example.com)
Lowe, Kelsey M., Lynley A. Wallis, Colin Pardoe, Ben Marwick5, Chris Clarkson, Tiina Manne, Mike A. Smith and Richard Fullagar 2014. Ground-penetrating radar and burial practices in western Arnhem Land, Australia. Archaeology in Oceania https://doi.org/10.1002/arco.5039
One rmarkdown file (Rocks-and-burials-at-MJB.Rmd) that can be executed in R. This file contains the narrative found in the published paper and R code used to analyse the data and generate the figures. To execute this file, ensure all the files are together in a directory in the same structure as they are in this repository, then open R and run
knitr::knit2html("Rocks-and-burials-at-MJB.Rmd"). There are many dependencies on non-core R packages and other software (see the dependencies list below), so you'll need to download and install all of those before attempting to run the rmarkdown file.
Two r files containing code that the rmarkdown file uses to load libraries and load data.
One html file (Rocks-and-burials-at-MJB.html). This is the output produced when the Rmd file is executed. It includes the text and figures.
Five shapefiles containing the raw data.
Text: CC-BY (http://creativecommons.org/licenses/by/4.0/)
Code: MIT (http://opensource.org/licenses/MIT year: 2014, copyright holder: Ben Marwick)
Data: CC0 (http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse
I used RStudio (version 0.98.682) for convenience, but it's not strictly necessary, unlike the following items which are:
R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252
 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252  LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:  splines grid stats graphics grDevices utils datasets  methods base
other attached packages:
 dependencies_0.0-1 Momocs_0.2-6 pander_0.3.8
 coin_1.0-23 survival_2.37-7 BEST_0.2.1
 rjags_3-13 coda_0.16-1 lattice_0.20-27
 plyr_1.8.1 reshape2_18.104.22.168 ggplot2_1.0.0
 gridExtra_0.9.1 splancs_2.01-34 rgeos_0.3-4
 PBSmapping_2.67.60 mapdata_2.2-2 maps_2.3-6
 maptools_0.8-29 sp_1.0-14
loaded via a namespace (and not attached):
 ade4_1.6-2 ape_3.1-1 boot_1.3-11
 colorspace_1.2-4 deldir_0.1-5 digest_0.6.4
 evaluate_0.5.3 foreign_0.8-61 formatR_0.10
 gtable_0.1.2 jpeg_0.1-8 jsonlite_0.9.7
 knitr_1.5 labeling_0.2 LearnBayes_2.12
 MASS_7.3-31 Matrix_1.1-3 modeltools_0.2-21
 munsell_0.4.2 mvtnorm_0.9-9999 nlme_3.1-117
 proto_0.3-10 Rcpp_0.11.1 rgl_0.93.996
 rmarkdown_0.1.4 scales_0.2.4 scatterplot3d_0.3-35  shapes_1.1-9 spdep_0.5-71 stats4_3.0.3
 stringr_0.6.2 tools_3.0.3 yaml_2.1.11
Other system dependencies identified using
- "Pandoc (>= 1.12.3, http://johnmacfarlane.net/pandoc) for exporting markdown files to other formats."
- "jags (>= 3.0.0)"
- "GEOS (>= 3.2.0); for building from source: GEOS from http://trac.osgeo.org/geos/; GEOS OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX."
- "OpenGL, GLU Library, zlib (optional), libpng (>=1.2.9, optional), FreeType(optional)"