This repository contains data files and R scripts for the book Compositional Data Analysis in Practice (Michael Greenacre, Chapman & Hall / CRC Press, 2018):
https://www.crcpress.com/Compositional-Data-Analysis-in-Practice/Greenacre/p/book/9781138316430
as well as some other files related to articles on compositional data analysis.
The easyCODA R package accompanies the book and is available on CRAN, presently version 0.40.2.
This latest update includes two new functions STEPR() and FINDALR(), which are also listed below.
The package is still under development and the latest version can always be found on R-Forge, installing as follows from R:
install.packages("easyCODA", repos="http://R-Forge.R-project.org")
The package does include the data sets, but the data files are given here as well in Excel or character format.
ERRATA in "Compositional Data Analysis in Practice":
CDAiP_typos.pdf: For the readers of my book, there is a provisional list of errors that I and others have found since its publication.
CDAiP_typos.rtf: rich text format of the above
DATA SETS for Compositional Data Analysis in Practice:
Vegetables.txt: Vegetables data set, data object 'veg' in easyCODA
TimeBudget.txt: Time budget data set, data object 'time' in easyCODA
RomanCups.xls: Archaeometric data on Roman glass cups, data object 'cups' in easyCODA
FishMorphology.txt: Fish morphometric data, with three additional variables, data object 'fish' in easyCODA
R SCRIPTS for Compositional Data Analysis in Practice:
easyCODA_script.R: file of all the R commands in Appendix C, also with some slight corrections.
PLEASE REPORT ANY BUGS OR DIFFICULTIES WITH THE PACKAGE TO Michael Greenacre at [email protected]
ARTICLE: "A comparison of amalgamation logratio balances and isometric logratio balances in compositional data analysis", by Michael Greenacre, Eric Grunsky and John Bacon-Shone, Computers and Geosciences (2020)
CAGEOscript.R: script related Greenacre, Grunsky & Bacon-Shone (2020)
ARTICLE: "Amalgamations are valid in compositional data analysis, can be used in agglomerative clustering, and their logratios have an inverse transformation", by Michael Greenacre, Applied Computing and Geosciences (2020)
SLRscript.R: script related to article
ARTICLE: "The selection and analysis of fatty acid ratios: A new approach for the univariate and multivariate analysis of fatty acid trophic markers in marine pelagic organisms", by Martin Graeve and Michael Greenacre, Limnology & Oceanography Methods (2020)
amphipod_ratios.R: script related to the article by Graeve & Greenacre (2020)
amphipods.csv: data set for R script above
copepod_ratios.R: script related to the article "The selection and analysis of fatty acid ratios: A new approach for the univariate and multivariate analysis of fatty acid trophic markers in marine pelagic organisms", by Martin Graeve and Michael Greenacre, Limnology & Oceanography Methods (2020)
copepods.csv: data set for R script above
ARTICLE: "Compositional Data Analysis", by Michael Greenacre, Annual Reviews in Statistics and its Application (2021)
ANNUALREVIEWSscript.R: R script for article by Greenacre (2021)
copepods_TL.csv: data set for R script above (same data set as for Graeve & Greenacre (2020), with added variable Total Lipids (TL))
Baxter_OTU_table.txt: microbiome data set for R script above. From Baxter et al. (2016)
Baxter_metadata.txt: metadata that goes with the OTU table. From Baxter et al. (2016)
ARTICLE: "Making the most of expert knowledge to analyse archaeologicaldata: a case study on Parthian and Sasanian glazed pottery", by Jonathan Wood and Michael Greenacre, Archaeological and Anthropological Sciences (2021)
Supplementary material for the article by Wood & Greenacre (2021). Two zip files:
Wood&Greenacre_CSV: data files
Wood&Greenacre_CODE&FUNCTIONS: R code and additional R functions
ARTICLE: "Compositional data analysis of microbiome and any-omics datasets: a validation of the additive logratio transformation", by Michael Greenacre, Marina Martinez-Alvaro and Agustin Blasco, Frontiers in Microbiology (2021)
Frontiers_ALR.R: script for Greenacre et al. (2021)
Frontiers_ALR_supplementary.R: script for supplementary material of Greenacre et al. (2021)
FINDALR.R: function FINDALR to identify optimal ALR reference, without or with weights
Rabbits.xlsx: Rabbits data set (89 rows, 3937 columns), rabbits x microbial genes. The different case ID label style refers to the two laboratories that did the testing
Baxter_OTU_table.txt: microbiome data set (Baxter et al., 2016), used in supplementary material of Greenacre et al. (2021)
Baxter_metadata.txt: metadata of above data set (Baxter et al., 2016), used in supplementary material of Greenacre et al. (2021)
Deng_vaginal_microbiome.txt: Vaginal microbiome data (Deng et al., 2018), cited by Wu et al. (2021)
ARTICLE: "Three approaches to supervised learning for compositional data with pairwise logratios", by Germà Coenders and Michael Greenacre (2022)
Coenders&Greenacre_CODE.R: R code for analysis of Crohn data (Crohn data available in R package selbal, as shown in code)
STEPR.R: function for stepwise selection of logratios for GLM models
ARTICLE: "Aitchison's Compositional Data Analysis 40 Years On: A Reappraisal", by Michael Greenacre, Eric Grunsky, John Bacon-Shone, Ionas Erb and Thomas Quinn (2022). There are two versions: the original Version 1, and the new revised Version 2
tellus_Appendix.R: script for reproducing the analysis of the Tellus geochemical data set in Appendix of Version 1
tellus_CoDA_script.R: script for reproducing the analysis of the Tellus geochemical data set in Version 2 (essentially the same as before)
tellus.xrf.a.cation.txt: Tellus cation data set
singlecell_CoDA_script.R: script for reproducing the analysis of the single cell genetic data set in Version 2
SingleCell.RData: R workspace containing all the data files for the single cell application in Section 6 of Version 2
ARTICLE: "GeoCoDA: Recognizing and Validating Structural Processes in Geochemical Data. A Workflow on Compositional Data Analysis in Lithogeochemistry", by Eric Grunsky, Michael Greenacre, and Bruce Kjarsgaard (2023).
kimberlite.cation.closed.txt: kimberlite cation data (Grunsky and Kjarsgaard, 2008), samples closed to sum to 100%
GeoCoDA_script.R: script for reproducing the GeoCoDA workflow
ARTICLE: "A Comprehensive Workflow for Compositional Data Analysis in Archaeometry, with code in R", by Michael Greenacre and Jonathan Wood (2024).
Bronze.csv: dataset of Chinese ritual bronzes
Bronze_script.R: script for reproducing the workflow