Man pages for digiYozhik/msc_thesis
Functions to support master thesis
| boxplots_with_checks | Boxplots with checks alongside the boxes |
| calculateH2 | Compute the broad-sense heritability from a mixed model... |
| crossValidate | Cross-validation function |
| CVcommit | Function to make a CV scheme based on a commited test set. |
| CVincompleteTrial | Function to make a CV scheme based on random sampling of... |
| CVrandomAccrossFactor | Function to make a CV scheme based on random sampling of... |
| CVrandomByID | Function to make a CV scheme based on random sampling of... |
| CVrandomWithinFactor | Function to make a CV scheme based on random sampling of... |
| data-exampleCV | Example data for CV functionalities used in thesis |
| dataframe.to.list | Convert data frame to list |
| data-G | Realization of the G-matrix used in thesis |
| data-genotypes | Raw SNP marker data used in thesis |
| data-M | Cleaned numeric SNP marker data used in thesis |
| data-Mraw | Numeric SNP marker data used in thesis |
| data-P | Modeled cleaned phenotypic data used in thesis |
| data-phenotypes | Raw phenotype data used in thesis |
| data-Praw | Modeled phenotypic data used in thesis |
| inferenceBGLR | Function to make inference on a cross validation analysis and... |
| list.to.dataframe | Transform a list of data frames to one data frame |
| LR.test.asreml | Likelihood ratio test for two asreml-models. |
| make_design_rectangular | Add observations to a data frame so that the design is... |
| makeG | Make genomic relationship matrix using Van Raden (2008) |
| makeZ | Make a centered (scaled) genetic marker matrix |
| MaStatThesisRuud | MaStatThesisRuud |
| permute | Function to generate a table of combinations when applying... |
| plotCV | Plot a CV scheme based on crossValidate function |
| plotCVThesisData | Plot a CV scheme for the data used in the thesis |
| plotFields | Create a field-layout plot from a data frame. |
| plotResiduals | Plot a series of residual plots obtained from a linear mixed... |
| plotVariogram | Plot variogram from residuals |
| summarizeInference | Summarize the inference results from from inferenceBGLR |
