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Text, data and code to accompany the analysis of rocks and burials reported in Lowe et al. 2014
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readme.md

Supplementary materials for a study of rocks associated with Holocene human burials at Madjedbebe, Northern Territory, Australia

Compendium DOI:

http://dx.doi.org/10.5281/zenodo.10616

Author of this repository:

Ben Marwick (benmarwick@gmail.com)

Published in:

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

Contents:

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.

Licences:

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

Dependencies:

I used RStudio (version 0.98.682) for convenience, but it's not strictly necessary, unlike the following items which are:

Identified using sessionInfo():

R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit)

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] dependencies_0.0-1 Momocs_0.2-6 pander_0.3.8
[4] coin_1.0-23 survival_2.37-7 BEST_0.2.1
[7] rjags_3-13 coda_0.16-1 lattice_0.20-27
[10] plyr_1.8.1 reshape2_1.4.0.99 ggplot2_1.0.0
[13] gridExtra_0.9.1 splancs_2.01-34 rgeos_0.3-4
[16] PBSmapping_2.67.60 mapdata_2.2-2 maps_2.3-6
[19] maptools_0.8-29 sp_1.0-14

loaded via a namespace (and not attached): [1] ade4_1.6-2 ape_3.1-1 boot_1.3-11
[4] colorspace_1.2-4 deldir_0.1-5 digest_0.6.4
[7] evaluate_0.5.3 foreign_0.8-61 formatR_0.10
[10] gtable_0.1.2 jpeg_0.1-8 jsonlite_0.9.7
[13] knitr_1.5 labeling_0.2 LearnBayes_2.12
[16] MASS_7.3-31 Matrix_1.1-3 modeltools_0.2-21
[19] munsell_0.4.2 mvtnorm_0.9-9999 nlme_3.1-117
[22] proto_0.3-10 Rcpp_0.11.1 rgl_0.93.996
[25] rmarkdown_0.1.4 scales_0.2.4 scatterplot3d_0.3-35 [28] shapes_1.1-9 spdep_0.5-71 stats4_3.0.3
[31] stringr_0.6.2 tools_3.0.3 yaml_2.1.11

Other system dependencies identified using dependencies::needs() (https://github.com/ropensci/dependencies):

  • "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."
  • "libjpeg"
  • "OpenGL, GLU Library, zlib (optional), libpng (>=1.2.9, optional), FreeType(optional)"
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