Well, at least most of the functions are. There are some other things here, too, including a password generator. For several years I collected functions I wrote and used often into a package I called MyRutils. But I really can't post a package with that name, can I? It just doesn't make sense if you are going to use it. So I changed the name to QsRutils. After all, it fits because decades ago a student gave me the nickname Q. Knowing she was a Trekkie, I let it slide.
The functions here are a bit of a mish-mash. Several are related to phyloseq and vegan, packages I use extensively. veganotu extracts a phyloseq otu_table as a matrix with samples as rows and taxa as columns, the format used by vegan functions. vegansam extracts a phyloseq sample_data object as a data frame while preserving all data types, again ready to use in vegan. vegan_stand applies any vegan decostand transformation to the otu_table in a phyloseq object.
Several other functions are related to making tables comparing taxa abundances among treatments, as in the supplementary tables in Zhang, et.al., 2017. A vignette for creating such table is included in this package.
Not all functions from MyRutils have made it here yet, so you can expect that more will be added as time goes by, especially any I use in my workshops, tutorials and blogs at john-quensen.com.
Version 0.1.3 adds a function to root trees in phyloseq objects by their longest terminal branch.
Version 0.1.4 adds a function to get ggplot2 plot limits.
Version 0.1.5 adds function srs_p to normalize the OTU table in a phyloseq object. This is an alternative to "rarefying" to the same number of counts per sample.
You can install QsRutils from github with:
install.packages("devtools")
devtools::install_github("jfq3/QsRutils", build_vignettes = TRUE)Zhang, B., Penton, C.R., Xue, C., Quensen, J.F., Roley, S.S., Guo, J., Garoutte, A., Zheng, T., Tiedje, J.M., 2017. Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems. Soil Biology & Biochemistry 112, 140-152.