# Fits the Linear Mixed Model

## Documentation for package ‘asreml’ version 4.1.0.189

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I K L M N O P R S T U V W

## -- A --

aexp | Metric based models in two dimensions.
aexph | Metric based models in two dimensions.
aexpv | Metric based models in two dimensions.
agau | Metric based models in two dimensions.
agauh | Metric based models in two dimensions.
agauv | Metric based models in two dimensions.
ainverse | Calculate an inverse relationship matrix.
and | Model term constructor functions.
ante | General structure variance models.
ar1 | Time series type variance models.
ar1h | Time series type variance models.
ar1v | Time series type variance models.
ar2 | Time series type variance models.
ar2h | Time series type variance models.
ar2v | Time series type variance models.
ar3 | Time series type variance models.
ar3h | Time series type variance models.
ar3v | Time series type variance models.
arma | Time series type variance models.
armah | Time series type variance models.
armav | Time series type variance models.
asreml | Fit the linear mixed model.
asreml.license.activate | Activates an asreml license.
asreml.license.deactivate | Deactivates the current asreml license.
asreml.license.offline | Request an asreml license to be used offline.
asreml.license.online | Request an asreml license to be used online
asreml.license.status | Check the status of the asreml license.
asreml.object | ASReml object
asreml.options | Set asreml options.
asreml.read.table | Read in a data frame.
asr_aexp | Metric based models in two dimensions.
asr_aexph | Metric based models in two dimensions.
asr_aexpv | Metric based models in two dimensions.
asr_agau | Metric based models in two dimensions.
asr_agauh | Metric based models in two dimensions.
asr_agauv | Metric based models in two dimensions.
asr_and | Model term constructor functions.
asr_ante | General structure variance models.
asr_ar1 | Time series type variance models.
asr_ar1h | Time series type variance models.
asr_ar1v | Time series type variance models.
asr_ar2 | Time series type variance models.
asr_ar2h | Time series type variance models.
asr_ar2v | Time series type variance models.
asr_ar3 | Time series type variance models.
asr_ar3h | Time series type variance models.
asr_ar3v | Time series type variance models.
asr_arma | Time series type variance models.
asr_armah | Time series type variance models.
asr_armav | Time series type variance models.
asr_at | Model term constructor functions.
asr_binomial | GLM family objects for asreml.
asr_C | Model term constructor functions.
asr_chol | General structure variance models.
asr_cir | Metric based models in two dimensions.
asr_cirh | Metric based models in two dimensions.
asr_cirv | Metric based models in two dimensions.
asr_con | Model term constructor functions.
asr_cor | General structure variance models.
asr_corb | General structure variance models.
asr_corbh | General structure variance models.
asr_corbv | General structure variance models.
asr_corg | General structure variance models.
asr_corgh | General structure variance models.
asr_corgv | General structure variance models.
asr_corh | General structure variance models.
asr_corv | General structure variance models.
asr_dev | Model term constructor functions.
asr_diag | General structure variance models.
asr_dsum | Model term constructor functions.
asr_exp | Metric based models in one dimension.
asr_exph | Metric based models in one dimension.
asr_expv | Metric based models in one dimension.
asr_fa | General structure variance models.
asr_facv | General structure variance models.
asr_families | GLM family objects for asreml.
asr_Gamma | GLM family objects for asreml.
asr_gau | Metric based models in one dimension.
asr_gauh | Metric based models in one dimension.
asr_gaussian | GLM family objects for asreml.
asr_gauv | Metric based models in one dimension.
asr_grp | Model term constructor functions.
asr_id | Default identity variance models.
asr_ide | Known variance structures.
asr_idh | Default identity variance models.
asr_idv | Default identity variance models.
asr_ieuc | Metric based models in two dimensions.
asr_ieuch | Metric based models in two dimensions.
asr_ieucv | Metric based models in two dimensions.
asr_iexp | Metric based models in two dimensions.
asr_iexph | Metric based models in two dimensions.
asr_iexpv | Metric based models in two dimensions.
asr_igau | Metric based models in two dimensions.
asr_igauh | Metric based models in two dimensions.
asr_igauv | Metric based models in two dimensions.
asr_ilv | Metric based models in two dimensions.
asr_ilvh | Metric based models in two dimensions.
asr_ilvv | Metric based models in two dimensions.
asr_inverse.gaussian | GLM family objects for asreml.
asr_leg | Model term constructor functions.
asr_lin | Model term constructor functions.
asr_lvr | Metric based models in one dimension.
asr_lvrh | Metric based models in one dimension.
asr_lvrv | Metric based models in one dimension.
asr_ma | Model term constructor functions.
asr_ma1 | Time series type variance models.
asr_ma1h | Time series type variance models.
asr_ma1v | Time series type variance models.
asr_ma2 | Time series type variance models.
asr_ma2h | Time series type variance models.
asr_ma2v | Time series type variance models.
asr_mbf | Model term constructor functions.
asr_mtrn | Matern variance structure.
asr_mtrnh | Matern variance structure.
asr_mtrnv | Matern variance structure.
asr_multinomial | GLM family objects for asreml.
asr_negative.binomial | GLM family objects for asreml.
asr_own | User-defined variance models.
asr_poisson | GLM family objects for asreml.
asr_pol | Model term constructor functions.
asr_pow | Model term constructor functions.
asr_rr | General structure variance models.
asr_sar | Time series type variance models.
asr_sar2 | Time series type variance models.
asr_sar2h | Time series type variance models.
asr_sar2v | Time series type variance models.
asr_sarh | Time series type variance models.
asr_sarv | Time series type variance models.
asr_sfa | General structure variance models.
asr_sph | Metric based models in two dimensions.
asr_sphh | Metric based models in two dimensions.
asr_sphv | Metric based models in two dimensions.
asr_spl | Model term constructor functions.
asr_str | General variance structures.
asr_us | General structure variance models.
asr_varioGram | Empirical variogram.
asr_vm | Known variance structures.
asuv | Univariate data frame.
asv | Approximate stratum variances method.
asv.asreml | Approximate stratum variances.
at | Model term constructor functions.

## -- B --

binnor | Footrot scores on lambs.

## -- C --

C | Model term constructor functions.
captions | Axis captions
cheese | Cheese tasting.
cheese.cat | Cheese tasting incidence.
chkPed | Check a pedigree
chol | General structure variance models.
cir | Metric based models in two dimensions.
cirh | Metric based models in two dimensions.
cirv | Metric based models in two dimensions.
coef | Extract model coefficients
coef.asreml | Extract model coefficients
con | Model term constructor functions.
cor | General structure variance models.
corb | General structure variance models.
corbh | General structure variance models.
corbv | General structure variance models.
corg | General structure variance models.
corgh | General structure variance models.
corgv | General structure variance models.
corh | General structure variance models.
corv | General structure variance models.

## -- D --

dev | Model term constructor functions.
diag | General structure variance models.
dsum | Model term constructor functions.

## -- E --

ebay | Nested correlated observations.
exp | Metric based models in one dimension.
exph | Metric based models in one dimension.
expv | Metric based models in one dimension.

## -- F --

fa | General structure variance models.
fa.init | Factor analytic initial values
facv | General structure variance models.
fitted.asreml | Extract fitted values.

## -- G --

gau | Metric based models in one dimension.
gauh | Metric based models in one dimension.
gauv | Metric based models in one dimension.
grass | Plant height
grassUV | Plant height (univariate form)
grp | Model term constructor functions.

## -- H --

harvey | Weights of cattle.
harvey.ped | Pedigree of cattle.
harveyg.ped | Pedigree of cattle.

## -- I --

id | Default identity variance models.
ide | Known variance structures.
idh | Default identity variance models.
idv | Default identity variance models.
ieuc | Metric based models in two dimensions.
ieuch | Metric based models in two dimensions.
ieucv | Metric based models in two dimensions.
iexp | Metric based models in two dimensions.
iexph | Metric based models in two dimensions.
iexpv | Metric based models in two dimensions.
igau | Metric based models in two dimensions.
igauh | Metric based models in two dimensions.
igauv | Metric based models in two dimensions.
ilv | Metric based models in two dimensions.
ilvh | Metric based models in two dimensions.
ilvv | Metric based models in two dimensions.

## -- K --

knownStruc | Known variance structures.

## -- L --

lamb | Footrot counts on lambs.
leg | Model term constructor functions.
Levels | Combine factor levels.
lin | Model term constructor functions.
lrt | Likelihood ratio tests.
lrt.asreml | REML Likelihood ratio tests
lsasr | Asreml object size.
lvr | Metric based models in one dimension.
lvrh | Metric based models in one dimension.
lvrv | Metric based models in one dimension.

## -- M --

ma | Model term constructor functions.
ma1 | Time series type variance models.
ma1h | Time series type variance models.
ma1v | Time series type variance models.
ma2 | Time series type variance models.
ma2h | Time series type variance models.
ma2v | Time series type variance models.
matern | Matern variance structure.
mbf | Model term constructor functions.
meff | Marker effects.
meff.asreml | Marker effects.
metric-1d | Metric based models in one dimension.
metric-2d | Metric based models in two dimensions.
modelFunctions | Model term constructor functions.
mtrn | Matern variance structure.
mtrnh | Matern variance structure.
mtrnv | Matern variance structure.

## -- N --

na.method | Missing value action for asreml dataframes.
naf | MBF example
naf31H | naf marker scores
naf32H | naf marker scores
nassau | Clone data.
nassau.grm | Genetic relationship matrix.
nassau.snp | Genetic marker scores.
nin89 | Advanced breeding trial.

## -- O --

oats | Split plot design.
orange | Tree circumference.
own | User-defined variance models.
owt | Orange whether trial

## -- P --

plot | Plot diagnostics for an asreml object.
plot.asreml | Plot diagnostics for an asreml object.
plot.varioGram | Plot a variogram.
plot_coef | Plot method for model coefficients.
plot_coef.asreml | Plot constructor for 'plot_coef'
pol | Model term constructor functions.
pow | Model term constructor functions.
predict.asreml | Predict linear functions of effects.
print.asreml.predict | Print predictions.
print.wald | Print a wald object.

## -- R --

rats | Reproductive study on rats
resid | Extract model residuals.
residuals.asreml | Extract model residuals.
rice | Rice bloodworms.
riceMV | Rice bloodworms (multivariate form).
rr | General structure variance models.

## -- S --

sar | Time series type variance models.
sar2 | Time series type variance models.
sar2h | Time series type variance models.
sar2v | Time series type variance models.
sarh | Time series type variance models.
sarv | Time series type variance models.
sfa | General structure variance models.
shf | Slate Hall farm wheat variety trial.
sp2mat | Convert sparse matrix.
sp2Matrix | Convert sparse matrix.
sph | Metric based models in two dimensions.
sphh | Metric based models in two dimensions.
sphv | Metric based models in two dimensions.
spl | Model term constructor functions.
splinek | Spline knot points.
str | General variance structures.
Subset | Subset a factor.
summary | Summarize an asreml object
summary.asreml | Summarize an asreml object

## -- T --

timeSeries | Time series type variance models.
tr | Trace convergence.
tr.asreml | Convergence trace for asreml objects.

## -- U --

Units | Unit level numbers.
unstructured | General structure variance models.
update | Update an asreml model.
update.asreml | Update an asreml model.
us | General structure variance models.

## -- V --

varioGram | Empirical variogram method.
varioGram.asreml | Empirical variogram constructor.
vcm.lm | Specify constraints among variance parameters.
vm | Known variance structures.
voltage | Voltage regulators
vpc.char | Variance parameter constraint codes
vpredict | Functions of variance parameters.
vpt.char | Variance parameter type codes

## -- W --

wald | Wald statistics method.
wald.asreml | Wald test constructor for asreml objects.
wheat | Wheat variety trial
wolfinger | Growth curve study on rats