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ElaineYChu committed Apr 24, 2022
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49 changes: 47 additions & 2 deletions README.md
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# subadult_size_variable_2022
This repository houses the research compendium to accompany the article: "An alternative size variable for allometric investigations in subadults"
# Contents
This repository contains full documentation for the paper:
> Chu, E.Y., Stull, K.E., & Sylvester, A.D. (2022). An alternative size variable for allometric investigations in subadults. *In review.*
To run the code for this paper locally, please ensure that [R](https://cran.r-project.org/), and optionally [RStudio](https://www.rstudio.com/), are installed on the local system.

### How to cite
Please cite this compendium as:
> Chu, E.Y., Stull, K.E., & Sylvester, A.D. (2022). Compendium of R code and data for *An alternative size variable for allometric investigations in subadults.* Accessed *Current Date*.
## The data
All data are from the [Subadult Virtual Anthropology Database](https://zenodo.org/communities/svad) (SVAD). Specifically, this project uses portions of data from the [United States](10.5281/zenodo.5193208) and [South Africa](https://zenodo.org/record/3950301#.YmRaW9rMIdU), which are also directly provided in the [data folder](data).

## How to use this repository
There are two ways to add this repository to a local system:

1. If you are using a Mac operating system or have another shell terminal system (such as [Git for Windows](https://gitforwindows.org/)), open your terminal and enter the following commands:

```console
cd "file/path/to/desired/repository/location" # set file location
git clone https://github.com/ElaineYChu/subadult_sv_2022 # clone the repository
cd subadult_sv_2022 # enter the new directory
ls # check that there are files in the new directory
```

2. If you do not have or are unfamiliar with terminal command systems, you may also locate and click on the green button in this repository labeled "Code" with a downward arrow and select "Download ZIP." This will download a zipped file to your local system (probably found in your *Downloads* folder). Extract the embedded folder ("subadult_sv_2022-main") and relocate it to your desired folder location.

**Next, rename the folder to "subadult_sv_2022" before proceeding further.**

Inside the **subadult_sv_2022** folder, you should find the following folders and files:

* [data](data) - A folder containing the original subsetted data from SVAD and subsequent files after data manipulation
* [results](results) - A folder housing the resulting files from all analyses
* [documentation](documentation.html) - An HTML file containing all code and analyses to replicate publication results
* [elaine_theme](elaine_theme.R) - A personalized theme for plots using `ggplot2`












9 changes: 9 additions & 0 deletions data/Auerbach&Sylvester_2011.csv
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"long_bone","method","slope","study"
"Humerus","Stature",1.03,"Auerbach & Sylvester (2011)"
"Radius","Stature",1.23,"Auerbach & Sylvester (2011)"
"Femur","Stature",1.145,"Auerbach & Sylvester (2011)"
"Tibia","Stature",1.315,"Auerbach & Sylvester (2011)"
"Humerus","GM_Length",0.89,"Auerbach & Sylvester (2011)"
"Radius","GM_Length",1.085,"Auerbach & Sylvester (2011)"
"Femur","GM_Length",0.92,"Auerbach & Sylvester (2011)"
"Tibia","GM_Length",1.095,"Auerbach & Sylvester (2011)"
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818 changes: 818 additions & 0 deletions documentation.html

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21 changes: 21 additions & 0 deletions results/rma_coefficients.csv
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"size_var","slope","intercept","diff"
"FMSB",1.01127702088615,-4.24584978852087,0.0112770208861523
"FDB",1.18068415861875,-4.27257831947747,0.180684158618754
"TPB",1.26169932136514,-5.0564654403095,0.26169932136514
"TMSB",1.02805415432923,-4.483873861947,0.0280541543292308
"TDB",1.21438988563494,-5.0999732489568,0.214389885634943
"HPB",1.04598359325182,-3.93123666418961,0.0459835932518207
"HMSB",1.08111475327605,-4.83025264208261,0.0811147532760506
"HDB",0.982618700198854,-3.26082209115267,0.0173812998011459
"RPB",0.974579508391367,-4.22334972021013,0.0254204916086326
"RMSB",0.989084086902178,-4.51855003880929,0.0109159130978225
"RDB",0.93427882346334,-3.53629735199861,0.0657211765366601
"GM_all",1.04578442685343,-4.19447232772462,0.0457844268534262
"GM_pb",1.08018981827519,-4.31201850741521,0.0801898182751863
"GM_msb",1.01252206779919,-4.42161443397964,0.0125220677991915
"GM_db",1.06665307476847,-3.96762243649149,0.0666530747684728
"GM_fem",1.08971974762679,-4.2179187099202,0.0897197476267897
"GM_tib",1.1554895906841,-4.79727402659138,0.1554895906841
"GM_hum",1.02697255534676,-3.94411897211456,0.0269725553467637
"GM_rad",0.949709497540908,-3.98540751274892,0.0502905024590922
"GM_len",1.35516393217667,-4.30583487846494,0.355163932176669
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21 changes: 21 additions & 0 deletions results/us_allometry_coefs.csv
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"long_bone","method","slope"
"Humerus","Stature",1.28077081673659
"Humerus","RMSB",1.29509106164325
"Humerus","FMSB",1.26659128450226
"Humerus","GM_Midshaft",1.26505085182427
"Humerus","GM_Length",0.945110495559198
"Radius","Stature",1.20300557498712
"Radius","RMSB",1.21645632997996
"Radius","FMSB",1.18968698894058
"Radius","GM_Midshaft",1.18824008753145
"Radius","GM_Length",0.887725719761143
"Femur","Stature",1.49869926728039
"Femur","RMSB",1.51545616107312
"Femur","FMSB",1.48210702900304
"Femur","GM_Midshaft",1.4803044853351
"Femur","GM_Length",1.10592495447597
"Tibia","Stature",1.44446148435753
"Tibia","RMSB",1.46061194776905
"Tibia","FMSB",1.42846971759408
"Tibia","GM_Midshaft",1.42673240780881
"Tibia","GM_Length",1.06590163630976
21 changes: 21 additions & 0 deletions results/za_allometry_coefs.csv
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"long_bone","method","slope"
"Humerus","Stature",1.32432107660931
"Humerus","RMSB",0.94797646389312
"Humerus","FMSB",1.15755145630686
"Humerus","GM_Midshaft",1.18138193217464
"Humerus","GM_Length",0.989735827430445
"Radius","Stature",1.23653492277547
"Radius","RMSB",0.88513731622717
"Radius","FMSB",1.08082007144201
"Radius","GM_Midshaft",1.1030708806735
"Radius","GM_Length",0.924128549002069
"Femur","Stature",1.40776258150413
"Femur","RMSB",1.00770562183618
"Femur","FMSB",1.23048530687634
"Femur","GM_Midshaft",1.25581726965986
"Femur","GM_Length",1.05209611780698
"Tibia","Stature",1.42215403125051
"Tibia","RMSB",1.01800731972639
"Tibia","FMSB",1.2430644645342
"Tibia","GM_Midshaft",1.26865539404561
"Tibia","GM_Length",1.06285161635958

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