enhancer is a collection of functions useful in the fitting of linear mixed effect models and general data manipulation. As more of my packages use the same special functions I decided to have the special functions as its own package to facilitate the maintenance.
Giovanny Covarrubias-Pazaran
The package provides kernels to the estimate additive (A.matr)
relationship matrix for diploid and polyploid organisms. A good converter from
letter code to numeric format is implemented in the function atcg1234
and atcg1234BackTransform,
which supports higher ploidy levels than diploid. Additional functions for genetic
analysis have been included such as build a genotypic hybrid marker matrix
(build.HMM). If you need to use pedigree you need to convert your
pedigree into a relationship matrix (use the `getA` function from the pedigreemm package).
Also the LD.decay and the neMarker functions can be used
to calculate linkage disequilibrium and effective population size.
Recently, spatial modeling has been added added to enhancer using the two-dimensional
spline tps function. Based on bbasis
Available are add.diallel.vars, leg,
overlay, rrm, redmm,
simGECorMat function.
Available are adiag1, imputev, propMissing
replaceValues, stan, logspace
function.
Simple coloring functions available are jet.colors, bathy.colors,
transp
The enhancer package is updated on CRAN every 4-months due to CRAN policies but you can find the latest source at https://github.com/covaruber/enhancer. This can be easily installed typing the following in the R console:
library(devtools)
install_github("covaruber/enhancer")
This is recommended if you reported a bug, was fixed and was immediately pushed to GitHub but not in CRAN until the next update.
If you have any questions or suggestions please post it in https://stackoverflow.com or https://stats.stackexchange.com
I'll be glad to help or answer any question. I have spent a valuable amount of time developing this package. Please cite this package in your publication. Type 'citation("enhancer")' to know how to cite it.