R: Fits Linear Mixed Models using REML

# Fits Linear Mixed Models using REML

## Documentation for package ‘asreml’ version 4.2.0.480

- 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 variance models in two dimensions
aexph | Metric-based variance models in two dimensions
aexpv | Metric-based variance models in two dimensions
agau | Metric-based variance models in two dimensions
agauh | Metric-based variance models in two dimensions
agauv | Metric-based variance models in two dimensions
ainverse | Calculate an inverse relationship matrix
and | Model term constructor functions
ante | General structure variance models
ar1 | Time series type correlation and variance structures.
ar1h | Time series type correlation and variance structures.
ar1v | Time series type correlation and variance structures.
ar2 | Time series type correlation and variance structures.
ar2h | Time series type correlation and variance structures.
ar2v | Time series type correlation and variance structures.
ar3 | Time series type correlation and variance structures.
ar3h | Time series type correlation and variance structures.
ar3v | Time series type correlation and variance structures.
arma | Time series type correlation and variance structures.
armah | Time series type correlation and variance structures.
armav | Time series type correlation and variance structures.
asreml | Mixed effects linear models
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 | This (S3) class object contains a fitted linear mixed model from the 'asreml()' function
asreml.options | Set less frequently used 'asreml()' options
asreml.read.table | Read in a data frame
asr_aexp | Metric-based variance models in two dimensions
asr_aexph | Metric-based variance models in two dimensions
asr_aexpv | Metric-based variance models in two dimensions
asr_agau | Metric-based variance models in two dimensions
asr_agauh | Metric-based variance models in two dimensions
asr_agauv | Metric-based variance models in two dimensions
asr_and | Model term constructor functions
asr_ante | General structure variance models
asr_ar1 | Time series type correlation and variance structures.
asr_ar1h | Time series type correlation and variance structures.
asr_ar1v | Time series type correlation and variance structures.
asr_ar2 | Time series type correlation and variance structures.
asr_ar2h | Time series type correlation and variance structures.
asr_ar2v | Time series type correlation and variance structures.
asr_ar3 | Time series type correlation and variance structures.
asr_ar3h | Time series type correlation and variance structures.
asr_ar3v | Time series type correlation and variance structures.
asr_arma | Time series type correlation and variance structures.
asr_armah | Time series type correlation and variance structures.
asr_armav | Time series type correlation and variance structures.
asr_at | Model term constructor functions
asr_C | Model term constructor functions
asr_chol | General structure variance models
asr_cholc | General structure variance models
asr_cir | Metric-based variance models in two dimensions
asr_cirh | Metric-based variance models in two dimensions
asr_cirv | Metric-based variance 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 variance models in one dimension.
asr_exph | Metric-based variance models in one dimension.
asr_expv | Metric-based variance models in one dimension.
asr_fa | General structure variance models
asr_facv | General structure variance models
asr_gau | Metric-based variance models in one dimension.
asr_gauh | Metric-based variance models in one dimension.
asr_gauv | Metric-based variance 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 variance models in two dimensions
asr_ieuch | Metric-based variance models in two dimensions
asr_ieucv | Metric-based variance models in two dimensions
asr_iexp | Metric-based variance models in two dimensions
asr_iexph | Metric-based variance models in two dimensions
asr_iexpv | Metric-based variance models in two dimensions
asr_igau | Metric-based variance models in two dimensions
asr_igauh | Metric-based variance models in two dimensions
asr_igauv | Metric-based variance models in two dimensions
asr_ilv | Metric-based variance models in two dimensions
asr_ilvh | Metric-based variance models in two dimensions
asr_ilvv | Metric-based variance models in two dimensions
asr_leg | Model term constructor functions
asr_lin | Model term constructor functions
asr_lvr | Metric-based variance models in one dimension.
asr_lvrh | Metric-based variance models in one dimension.
asr_lvrv | Metric-based variance models in one dimension.
asr_ma | Model term constructor functions
asr_ma1 | Time series type correlation and variance structures.
asr_ma1h | Time series type correlation and variance structures.
asr_ma1v | Time series type correlation and variance structures.
asr_ma2 | Time series type correlation and variance structures.
asr_ma2h | Time series type correlation and variance structures.
asr_ma2v | Time series type correlation and variance structures.
asr_mbf | Model term constructor functions
asr_mtrn | Matern variance structure
asr_mtrnh | Matern variance structure
asr_mtrnv | Matern variance structure
asr_own | User-defined variance models or structures
asr_pol | Model term constructor functions
asr_pow | Model term constructor functions
asr_ric | Known variance structures
asr_rr | General structure variance models
asr_sar | Time series type correlation and variance structures.
asr_sar2 | Time series type correlation and variance structures.
asr_sar2h | Time series type correlation and variance structures.
asr_sar2v | Time series type correlation and variance structures.
asr_sarh | Time series type correlation and variance structures.
asr_sarv | Time series type correlation and variance structures.
asr_sfa | General structure variance models
asr_sph | Metric-based variance models in two dimensions
asr_sphh | Metric-based variance models in two dimensions
asr_sphv | Metric-based variance models in two dimensions
asr_spl | Model term constructor functions
asr_str | Variance structure spanning several model terms
asr_us | General structure variance models
asr_varioGram | Empirical variogram
asr_vm | Known variance structures
asuv | Univariate data frame
asv.asreml | Approximate stratum variances
at | Model term constructor functions

## -- B --

binnor | Footrot scores on lambs

## -- C --

C | Model term constructor functions
chkPed | Check a pedigree
chol | General structure variance models
cir | Metric-based variance models in two dimensions
cirh | Metric-based variance models in two dimensions
cirv | Metric-based variance models in two dimensions
coef | Extract model coefficients
coef.asreml | Extract model coefficients
complex_vs | Variance structure spanning several model terms
con | Model term constructor functions
coop | Coopworth lamb data
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 | Ebay bids
exp | Metric-based variance models in one dimension.
exph | Metric-based variance models in one dimension.
expv | Metric-based variance 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 variance models in one dimension.
gauh | Metric-based variance models in one dimension.
gauv | Metric-based variance models in one dimension.
general_vs | General structure variance models
grass | Plant height disease study (multivariate form)
grassUV | Plant height disease study (univariate form)
grp | Model term constructor functions

## -- H --

harvey | Weights of Hereford cattle
harvey.ped | Pedigree of Hereford cattle
harveyg.ped | Pedigree of Hereford cattle (with genetic groups)

## -- I --

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

## -- K --

known_vs | Known variance structures

## -- L --

lamb | Footrot counts on lambs
leg | Model term constructor functions
Levels | Combine factor levels
lin | Model term constructor functions
lrt.asreml | REML likelihood ratio test (REMLRT)
lvr | Metric-based variance models in one dimension.
lvrh | Metric-based variance models in one dimension.
lvrv | Metric-based variance models in one dimension.

## -- M --

ma | Model term constructor functions
ma1 | Time series type correlation and variance structures.
ma1h | Time series type correlation and variance structures.
ma1v | Time series type correlation and variance structures.
ma2 | Time series type correlation and variance structures.
ma2h | Time series type correlation and variance structures.
ma2v | Time series type correlation and variance structures.
matern_vs | Matern variance structure
mbf | Model term constructor functions
meff.asreml | Calculate marker effects
met | Multi-environmental wheat data from 8 locations with spatial coordinates
metric-1D_vs | Metric-based variance models in one dimension.
metric-2D_vs | Metric-based variance models in two dimensions
model_functions | Model term constructor functions
mtrn | Matern variance structure
mtrnh | Matern variance structure
mtrnv | Matern variance structure

## -- N --

na.method | Missing value action for 'asreml' data frames
naf | Barley study (naf)
naf31H | Marker scores barley study (naf)
naf32H | Marker scores barley study (naf)
nassau | Loblolly pine clone trial
nassau.grm | Loblolly genetic relationship matrix (GRM)
nassau.snp | Loblolly genetic marker scores
nin89 | Wheat advanced breeding trial

## -- O --

oats | Oats variety-nitrogen factorial study
orange | Orange tree circumference
own | User-defined variance models or structures
owt | Orange wether wool trial

## -- P --

pixel | Repeated CT scans on dogs
plot | Plot diagnostics for an 'asreml' object
plot.asreml | Plot diagnostics for an 'asreml' object
plot.varioGram | Plot an empirical variogram
plot_coef.asreml | Plot model coefficients
pol | Model term constructor functions
pow | Model term constructor functions
predict.asreml | Predict linear functions of model effects

## -- R --

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

## -- S --

sar | Time series type correlation and variance structures.
sar2 | Time series type correlation and variance structures.
sar2h | Time series type correlation and variance structures.
sar2v | Time series type correlation and variance structures.
sarh | Time series type correlation and variance structures.
sarv | Time series type correlation and variance structures.
sfa | General structure variance models
shf | Slate Hall farm wheat variety trial
sph | Metric-based variance models in two dimensions
sphh | Metric-based variance models in two dimensions
sphv | Metric-based variance models in two dimensions
spl | Model term constructor functions
splinek | Spline knot points
str | Variance structure spanning several model terms
Subset | Subset a factor
summary | Summarize an 'asreml' object
summary.asreml | Summarize an 'asreml' object

## -- T --

time_series_vs | Time series type correlation and variance structures.
tr.asreml | REML convergence trace for 'asreml' objects.

## -- U --

Units | Unit level numbers
update | Update an 'asreml' model fit
update.asreml | Update an 'asreml' model fit
us | General structure variance models
user_vs | User-defined variance models or structures

## -- V --

varioGram.asreml | Empirical variogram constructor method
vcm.lm | Specify constraints among variance components
vm | Known variance structures
voltage | Voltage regulators
vpredict | Functions of variance components

## -- W --

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