Package: enhancer 1.1.1

enhancer: Mixed-Effects Models Enhancing Functions

Special functions that enhance other mixed effect model packages by creating overlayed, reduced rank, and reduced model matrices together with multiple data sets to practice the use of these models. For more details see Covarrubias-Pazaran (2016) <doi:10.1371/journal.pone.0156744>.

Authors:Giovanny Covarrubias-Pazaran [aut, cre]

enhancer_1.1.1.tar.gz
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enhancer_1.1.1.tgz(r-4.6-any)enhancer_1.1.1.tgz(r-4.5-any)
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enhancer_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION
card.svg |card.png
enhancer/json (API)

# Install 'enhancer' in R:
install.packages('enhancer', repos = c('https://covaruber.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/covaruber/enhancer/issues

Datasets:
  • A_example - Broad sense heritability calculation.
  • A_gryphon - Gryphon data from the Journal of Animal Ecology
  • A_ige - Data to fit indirect genetic effects.
  • A_wheat - Wheat lines dataset
  • DT_augment - DT_augment design example.
  • DT_big - Big GxE Quantitative Genetic Simulation
  • DT_btdata - Blue Tit Data for a Quantitative Genetic Experiment
  • DT_cornhybrids - Corn crosses and markers
  • DT_cpdata - Genotypic and Phenotypic data for a CP population
  • DT_example - Broad sense heritability calculation.
  • DT_expdesigns - Data for different experimental designs
  • DT_fulldiallel - Full diallel data for corn hybrids
  • DT_gryphon - Gryphon data from the Journal of Animal Ecology
  • DT_h2 - Broad sense heritability calculation.
  • DT_halfdiallel - Half diallel data for corn hybrids
  • DT_ige - Data to fit indirect genetic effects.
  • DT_legendre - Simulated data for random regression
  • DT_mohring - Full diallel data for corn hybrids
  • DT_polyploid - Genotypic and Phenotypic data for a potato polyploid population
  • DT_rice - Rice lines dataset
  • DT_sleepstudy - Reaction times in a sleep deprivation study
  • DT_technow - Genotypic and Phenotypic data from single cross hybrids
  • DT_wheat - Wheat lines dataset
  • DT_yatesoats - Yield of oats in a split-block experiment
  • DTi_cornhybrids - Corn crosses and markers
  • GT_cornhybrids - Corn crosses and markers
  • GT_cpdata - Genotypic and Phenotypic data for a CP population
  • GT_polyploid - Genotypic and Phenotypic data for a potato polyploid population
  • GT_rice - Rice lines dataset
  • GT_wheat - Wheat lines dataset
  • GTn_rice - Rice lines dataset
  • M - Simulated phenotypic records for a set of 100 environments and 200 entries.
  • M_big - Big GxE Quantitative Genetic Simulation
  • Md_technow - Genotypic and Phenotypic data from single cross hybrids
  • Mf_technow - Genotypic and Phenotypic data from single cross hybrids
  • MP_cpdata - Genotypic and Phenotypic data for a CP population
  • MP_polyploid - Genotypic and Phenotypic data for a potato polyploid population
  • P_gryphon - Gryphon data from the Journal of Animal Ecology
  • W - Simulated phenotypic records for a set of 100 environments and 200 entries.

On CRAN:

Conda:

5.46 score 12 packages 5.4k downloads 29 exports 4 dependencies

Last updated from:74031a36c7. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING183
source / vignettesOK167
linux-release-x86_64WARNING151
macos-release-arm64WARNING145
macos-oldrel-arm64WARNING108
windows-develWARNING167
windows-releaseWARNING144
windows-oldrelWARNING146
wasm-releaseOK124

Exports:A.matradd.diallel.varsadiag1atcg1234atcg1234BackTransformbathy.colorsbbasisbuild.HMMI.matrimputevjet.colorsLD.decayleglogspacemanhattanmap.plotneMarkeroverlaypropMissingredmmreplaceValuesrrmsimagesimage2simGECorMatstantpstranspwald.test

Dependencies:crayonlatticeMASSMatrix

Readme and manuals

Help Manual

Help pageTopics
Mixed Effect Model Enhancing Functionsenhancer
Additive relationship matrixA.matr
add.diallel.varsadd.diallel.vars
Binds arrays corner-to-corneradiag1
Letter to number converteratcg1234
Letter to number converteratcg1234BackTransform
Generate a sequence of colors for plotting bathymetric data.bathy.colors
Function for creating B-spline basis functions (Eilers & Marx, 2010)bbasis
Build a hybrid marker matrix using parental genotypes from inbred individualsbuild.HMM
DT_augment design example.DT_augment
Big GxE Quantitative Genetic SimulationDT_big M_big
Blue Tit Data for a Quantitative Genetic ExperimentDT_btdata
Corn crosses and markersDTi_cornhybrids DT_cornhybrids GT_cornhybrids
Genotypic and Phenotypic data for a CP populationDT_cpdata GT_cpdata MP_cpdata
Simulated phenotypic records for a set of 100 environments and 200 entries.DT_envs M W
Broad sense heritability calculation.A_example DT_example
Data for different experimental designsDT_expdesigns
Full diallel data for corn hybridsDT_fulldiallel
Gryphon data from the Journal of Animal EcologyA_gryphon DT_gryphon P_gryphon
Broad sense heritability calculation.DT_h2
half diallel data for corn hybridsDT_halfdiallel
Data to fit indirect genetic effects.A_ige DT_ige
Simulated data for random regressionDT_legendre
Full diallel data for corn hybridsDT_mohring
Genotypic and Phenotypic data for a potato polyploid populationDT_polyploid GT_polyploid MP_polyploid
Rice lines datasetDT_rice GTn_rice GT_rice
Reaction times in a sleep deprivation studyDT_sleepstudy
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)Ad_technow Af_technow DT_technow Md_technow Mf_technow
wheat lines datasetA_wheat DT_wheat GT_wheat
Yield of oats in a split-block experimentDT_yatesoats
Identity relationship matrixI.matr
Imputing a numeric or character vectorimputev
Generate a sequence of colors alog the jet colormap.jet.colors
Calculation of linkage disequilibrium decayLD.decay
Legendre polynomial matrixleg
Decreasing logarithmic trendlogspace
Creating a manhattan plotmanhattan
Creating a genetic map plotmap.plot
Effective population size based on marker matrixneMarker
Overlay Matrixoverlay
Proportion of missing datapropMissing
Reduced Model Matrixredmm
Replace the values of a vectorreplaceValues
reduced rank matrixrrm
Image of sparsity between two variablessimage
Shortcut to sparse matrix imagesimage2
Create a GE correlation matrix for simulation purposes.simGECorMat
Standardize a vector of values in range 0 to 1stan
Get Tensor Product Spline Mixed Model Incidence Matricestps
Creating color with transparencytransp
Wald Test for Model Coefficientsprint.wald.test wald.test