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Code for analysing logitudinal microbiome data

Output of sessionInfo():

R version 3.2.2 (2015-08-14)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C

attached base packages: splines, parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: pander(v.0.6.0), lme4(v.1.1-10), refund(v.0.1-14), DT(v.0.1), R.utils(v.2.3.0), R.oo(v.1.20.0), R.methodsS3(v.1.7.1), tidyr(v.0.4.1), readr(v.0.2.2), reshape2(v.1.4.1), dplyr(v.0.4.3), lazyeval(v.0.1.10), lpSolve(v.5.6.13), cplm(v.0.7-4), Matrix(v.1.2-2), coda(v.0.18-1), stringr(v.1.0.0), doParallel(v.1.0.10), iterators(v.1.0.8) and foreach(v.1.4.3)

loaded via a namespace (and not attached): biglm(v.0.9-1), statmod(v.1.4.24), lattice(v.0.20-33), colorspace(v.1.2-6), gamm4(v.0.2-3), htmltools(v.0.3.5), stats4(v.3.2.2), yaml(v.2.1.13), mgcv(v.1.8-9), MCMCpack(v.1.3-6), nloptr(v.1.0.4), DBI(v.0.3.1), tweedie(v.2.2.1), plyr(v.1.8.3), MatrixModels(v.0.4-1), munsell(v.0.4.3), gtable(v.0.2.0), htmlwidgets(v.0.6), codetools(v.0.2-14), evaluate(v.0.8.3), magic(v.1.5-6), knitr(v.1.12.3), SparseM(v.1.7), RLRsim(v.3.1-2), quantreg(v.5.21), Rcpp(v.0.12.10), pbs(v.1.1), scales(v.0.4.0), formatR(v.1.3), jsonlite(v.0.9.19), grpreg(v.2.8-1), mcmc(v.0.9-4), ggplot2(v.2.1.0), digest(v.0.6.9), stringi(v.1.0-1), grid(v.3.2.2), tools(v.3.2.2), magrittr(v.1.5), fda(v.2.4.4), MASS(v.7.3-45), assertthat(v.0.1), minqa(v.1.2.4), rmarkdown(v.0.9.5), R6(v.2.1.2), boot(v.1.3-17), compiler(v.3.2.2) and nlme(v.3.1-122)>

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