Package: lmDiallel 1.0.1

lmDiallel: Linear Fixed/Mixed Effects Models for Diallel Crosses

Several service functions to be used to analyse datasets obtained from diallel experiments within the frame of linear models in R, as described in Onofri et al (2020) <doi:10.1007/s00122-020-03716-8>.

Authors:Andrea Onofri [aut, cre], Niccolo Terzaroli [aut]

lmDiallel_1.0.1.tar.gz
lmDiallel_1.0.1.zip(r-4.5)lmDiallel_1.0.1.zip(r-4.4)lmDiallel_1.0.1.zip(r-4.3)
lmDiallel_1.0.1.tgz(r-4.4-any)lmDiallel_1.0.1.tgz(r-4.3-any)
lmDiallel_1.0.1.tar.gz(r-4.5-noble)lmDiallel_1.0.1.tar.gz(r-4.4-noble)
lmDiallel_1.0.1.tgz(r-4.4-emscripten)lmDiallel_1.0.1.tgz(r-4.3-emscripten)
lmDiallel.pdf |lmDiallel.html✨
lmDiallel/json (API)

# Install 'lmDiallel' in R:

install.packages('lmDiallel', repos = c('https://onofriandreapg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/onofriandreapg/lmdiallel/issues

Datasets:

diallelMET - Factitious dataset for Diallel analysis
griffing56 - Griffing's dataset for diallel analysis
hayman54 - Hayman dataset for diallel analysis
lonnquist61 - Half diallel of maize dataset
zhang05 - Data for diallel analysis from Zhang

On CRAN:

3.74 score 5 stars 22 scripts 186 downloads 1 mentions 48 exports 16 dependencies

Last updated 2 years agofrom:b1d5b85940. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 24 2024
R-4.5-win	WARNING	Oct 24 2024
R-4.5-linux	WARNING	Oct 24 2024
R-4.4-win	WARNING	Oct 24 2024
R-4.4-mac	WARNING	Oct 24 2024
R-4.3-win	WARNING	Oct 24 2024
R-4.3-mac	WARNING	Oct 24 2024

Exports:anova.diallel blockMatrixDiagonal checkScheme DD diallel.eff emm.diallel expand.diallel G1.eff G2.eff G3.eff G4.eff GCA GCAC GCAmis GE2.eff GE2r.eff GE3.eff GE3r.eff glht.diallelMod H.BAR hayman1.eff hayman2.eff Hi int.matrix lm.diallel matBlock MDD MET1.eff MET2.eff MET3.eff mmer.diallel model.matrix.diallel model.matrixDiallel model.matrixDiallel.MET predict.diallel REC REC.G3 RGCA RSCA SCA SCA.G3 SCA.GE SCAmis SP summary.diallel tSCA vcov.diallel VEi

Dependencies:codetools crayon lattice MASS Matrix multcomp mvtnorm plyr Rcpp RcppArmadillo RcppProgress sandwich sommer survival TH.data zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Creates block diagonal matrix. It is used internally.	blockMatrixDiagonal
Dominant Deviation effect	DD
Factitious dataset for Diallel analysis	diallelMET
Functions to retreive full list of genetical effects	diallel.eff G1.eff G2.eff G3.eff G4.eff GE2.eff GE2r.eff GE3.eff GE3r.eff glht.diallelMod hayman1.eff hayman2.eff MET1.eff MET2.eff MET3.eff
Create a Data Frame from All Combinations of Parentals	expand.diallel
General Combining Ability effect	GCA GCAmis
General Combining Ability without considering the selfed parents	GCAC
Griffing's dataset for diallel analysis	griffing56
Average heterosis effect	H.BAR
Hayman dataset for diallel analysis	hayman54
Average heterosis effect	Hi
Utilities for fitting diallel models.	checkScheme int.matrix
Fitting diallel linear models	lm.diallel
Methods for diallel model fitting	anova.diallel glht.diallel model.matrix.diallel predict.diallel summary.diallel vcov.diallel
Half diallel of maize dataset	lonnquist61
Design matrix for blocks	matBlock
Mean Dominance Deviation effect	MDD
Fitting random diallel linear models	mmer.diallel
Incidence matrices for Diallel model parametrisation	model.matrixDiallel model.matrixDiallel.MET
Reciprocal Effect not parted into RGCA and RSCA	REC REC.G3
Reciprocal General Combining Ability	RGCA
Reciprocal Specific Combining Ability	RSCA
Specific Combining Ability	SCA SCA.G3 SCA.GE SCAmis
Selfed Parents effect	SP
Total Specific Combining Ability	tSCA
Variety Effect	VEi
Data for diallel analysis from Zhang (2005)	zhang05