Shape as a Measure of Weapon Standardisation: A Replication

Contributors

Corey Christopherson (), Thomas Winegarden (), Richard Todd (), Zack Garcia ()

Archival Copy

An archival copy of this project is stored on osf.io
DOI: https://doi.org/10.17605/OSF.IO/PGV9D

Contents

The purpose of this repo is to provide a complete workflow record of our attempt to replicate Figure 8 in the paper Shape as a measure of weapon standardisation: From metric to geometric morphometric analysis of the Iron Age ‘Havor’ lance from Southern Scandinavia by Birch and Martinon-Torres. This figure shows the pair-wise correlation of all lance dimensions across the three underlying datasets next to bivariate plots and distributions of each single dimension with kernel density approximation. We attempt to verify whether these calculations and smoothed distributions look similar upon replication, and also are interested how close we can get to the correct style without any of the actual original figure code.

This project is an assignment for the class DATA 598 'Reproducibility for Data Science', taken as part of the UW Master of Data Science program.

Citation of Original Study

Birch, T., & Martinon-Torres, M. (2018). Shape as a measure of weapon standardisation: From metric to geometric morphometric analysis of the Iron Age ‘Havor’ lance from Southern Scandinavia. Journal of Archaeological Science, 101, 34-51. doi: https://doi.org/10.1016/j.jas.2018.11.002

Data (Extended) Datasets

Data for this study was obtained from the ScienceDirect online version of this article (https://doi.org/10.1016/j.jas.2018.11.002)

Included Files: mmc2.csv: Contains dimensionality information about 123 different lances. These are the following fields:

• site: Where the lance was found. This can be Ejsbol, Nydam, or Illerup.
• ID: Unique ID for each lance
• point: Boolean, whether it has a point
• socket: Boolean, whether it has a socket
• total_length: Total lance length in cm
• blade_length: Blade's length in cm
• socket_length: Just the socket of the lance's length in cm
• sock_bdiam: Maximum socket diameter in cm
• sock_sdiam: Minimum socket diameter in cm
• width: Blade width in cm
• thickness: Blade thickness in cm
• rdist: Distance between rivets in cm

mmc3.csv: Contains normalized coordinates for the seven main "landmark" points defining the shape of 78 different lances,

• site_lance-id: site and ID from mmc2.csv for the lance, concatenated
• x1: x-coordinate of point 1
• y1: y-coordinate of point 1
• ...
• x7: x-coordinate of point 7
• y7: y-coordinate of point 7

yjasc_4911_Appendix_A.R: Source R script for analysis and figure generation done in the paper.

Dependencies

Session info:

• setting value
• version R version 3.6.2 (2019-12-12)
• os Windows >= 8 x64
• system x86_64, mingw32
• ui RStudio
• language (EN)
• collate English_United States.1252
• ctype English_United States.1252
• tz America/Los_Angeles
• date 2020-02-23

Packages:

• package * version date lib source
• ape * 5.3 2019-03-17 [1] CRAN (R 3.6.2)
• assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.2)
• backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
• callr 3.4.0 2019-12-09 [1] CRAN (R 3.6.2)
• cli 2.0.1 2020-01-08 [1] CRAN (R 3.6.2)
• coda 0.19-3 2019-07-05 [1] CRAN (R 3.6.2)
• colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
• crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.2)
• crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.6.2)
• desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.2)
• deSolve 1.27.1 2020-01-02 [1] CRAN (R 3.6.2)
• devtools * 2.2.1 2019-09-24 [1] CRAN (R 3.6.2)
• digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.2)
• dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.2)
• ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.2)
• fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.2)
• farver 2.0.1 2019-11-13 [1] CRAN (R 3.6.2)
• fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.2)
• fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.2)
• geiger 2.0.6.4 2020-01-25 [1] CRAN (R 3.6.2)
• geomorph * 3.0.6 2018-04-29 [1] CRAN (R 3.6.2)
• GGally * 1.4.0 2018-05-17 [1] CRAN (R 3.6.2)
• ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.2)
• glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.2)
• gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.2)
• here * 0.1 2017-05-28 [1] CRAN (R 3.6.2)
• hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.2)
• htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.2)
• htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.2)
• httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.2)
• jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 3.6.1)
• jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.2)
• knitr 1.26 2019-11-12 [1] CRAN (R 3.6.2)
• labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
• later 1.0.0 2019-10-04 [1] CRAN (R 3.6.2)
• lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.2)
• lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.2)
• lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.2)
• magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.2)
• manipulateWidget 0.10.0 2018-06-11 [1] CRAN (R 3.6.2)
• MASS 7.3-51.4 2019-03-31 [2] CRAN (R 3.6.2)
• Matrix 1.2-18 2019-11-27 [2] CRAN (R 3.6.2)
• memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.2)
• mime 0.9 2020-02-04 [1] CRAN (R 3.6.2)
• miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 3.6.2)
• munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.2)
• mvtnorm 1.0-12 2020-01-09 [1] CRAN (R 3.6.2)
• nlme 3.1-142 2019-11-07 [2] CRAN (R 3.6.2)
• pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.2)
• pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.2)
• pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.2)
• pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.2)
• plyr 1.8.5 2019-12-10 [1] CRAN (R 3.6.2)
• prettyunits 1.1.0 2020-01-09 [1] CRAN (R 3.6.2)
• processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.2)
• progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.2)
• promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.2)
• ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.2)
• purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.2)
• R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.2)
• RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
• Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.2)
• remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.2)
• reshape 0.8.8 2018-10-23 [1] CRAN (R 3.6.2)
• reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.2)
• rgl * 0.100.30 2019-08-19 [1] CRAN (R 3.6.2)
• rlang 0.4.4 2020-01-28 [1] CRAN (R 3.6.2)
• rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.2)
• RRPP * 0.5.2 2020-01-26 [1] CRAN (R 3.6.2)
• rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.2)
• scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.2)
• scatterplot3d 0.3-41 2018-03-14 [1] CRAN (R 3.6.2)
• sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.2)
• shapes * 1.2.3 2017-11-18 [1] CRAN (R 3.6.2)
• shiny 1.4.0 2019-10-10 [1] CRAN (R 3.6.2)
• stringi 1.4.4 2020-01-09 [1] CRAN (R 3.6.2)
• stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.2)
• subplex 1.5-4 2018-04-05 [1] CRAN (R 3.6.2)
• testthat 2.3.1 2019-12-01 [1] CRAN (R 3.6.2)
• tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.2)
• tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.2)
• usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.2)
• utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.2)
• vctrs 0.2.1 2019-12-17 [1] CRAN (R 3.6.2)
• viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.2)
• webshot 0.5.2 2019-11-22 [1] CRAN (R 3.6.2)
• withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.2)
• xfun 0.12 2020-01-13 [1] CRAN (R 3.6.2)
• xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.2)
• yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.2)
• zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.2)

Contributing

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.